ALBERT

Description: The endocannabinoid system is the target of the main psychoactive component of the plant Cannabis sativa , the Δ 9 -tetrahydrocannabinol (THC). This system is composed by the cannabinoid receptors, the endogenous ligands, and the enzymes involved in their metabolic processes, which works both centrally and peripherally to regulate a plethora of physiological functions. This review aims at explaining how the site-specific actions of the endocannabinoid system impact on memory and feeding behavior through the cannabinoid receptors 1 (CB 1 R). Centrally, CB 1 R is widely distributed in many brain regions, different cell types (e.g. neuronal or glial cells) and intracellular compartments (e.g. mitochondria). Interestingly, cellular and molecular effects are differentially mediated by CB 1 R according to their cell-type localization (e.g. glutamatergic or GABAergic neurons). Thus, understanding the cellular and subcellular function of CB 1 R will provide new insights and aid the design of new compounds in cannabinoid-based medicine. The widespread localization of CB1 receptors in different brain regions (e.g. hippocampus, hypothalamus, and cortex), cell types (e.g. GABAergic and glutamatergic neurons), and subcellular domains (e.g. plasma membrane and mitochondria) allows the endocannabinoid system to control different behaviors (e.g. memory and food intake) in a multimodal and versatile fashion. Also watch the Video Abstract .

Description: Here, we review genomic target site selection during retroviral integration as a multistep process in which specific biases are introduced at each level. The first asymmetries are introduced when the virus takes a specific route into the nucleus. Next, by co-opting distinct host cofactors, the integration machinery is guided to particular chromatin contexts. As the viral integrase captures a local target nucleosome, specific contacts introduce fine-grained biases in the integration site distribution. In vivo, the established population of proviruses is subject to both positive and negative selection, thereby continuously reshaping the integration site distribution. By affecting stochastic proviral expression as well as the mutagenic potential of the virus, integration site choice may be an inherent part of the evolutionary strategies used by different retroviruses to maximise reproductive success. Retroviral integration is a multistep process moulded by nuclear entry, host cofactors and target recognition by the viral integrase. At each level, biases are introduced and the resulting distribution is reshaped by host selection processes. By affecting gene expression, site selection represents a selectable part of the retroviral evolutionary strategy.

Description: N 6 -methyladenine (6mA) is one of the most abundant types of DNA methylation, and plays an important role in bacteria; however, its roles in higher eukaryotes, such as plants, insects, and mammals, have been considered less important. Recent studies highlight that 6mA does indeed occur, and that it plays an important role in eukaryotes, such as worm, fly, and green algae, and thus the regulation of 6mA has emerged as a novel epigenetic mechanism in higher eukaryotes. Despite this intriguing development, a number of important issues regarding its biological roles are yet to be addressed. In this review, we focus on the 5mC and 6mA modifications in terms of their production, distribution, and the erasure of 6mA in higher eukaryotes including mammals. We perform an analysis of the potential functions of 6mA, hence widening understanding of this new epigenetic mark in higher eukaryotes, and suggesting future studies in this field. Like 5mC, 6mA functions as a potential epigenetic mark in higher eukaryotes. The expression of target genes can be modulated via dynamic and reversible pattern of DNA methylation in a variety of biological processes.

Description: Rotate and activate . On pages 959–967 , Ichiro Maruyama proposes a “rotation model” for the activation of transmembrane cell-surface receptors. Following this model, receptors exist in a dimeric form prior to ligand binding. The extracellular domain (ECD) has a rotationally flexible structure while the intracellular domain (ICD) is relatively stable. Ligand binding stabilizes the flexible ECD and induces conformational changes of the domains. This in turn induces or allows a rotation of the transmembrane domains leading to a rearrangement of the ICD, hence making the ICD flexible for activation of/interaction with cytoplasmic proteins.

Description: It has long been thought that transmembrane cell-surface receptors, such as receptor tyrosine kinases and cytokine receptors, among others, are activated by ligand binding through ligand-induced dimerization of the receptors. However, there is growing evidence that prior to ligand binding, various transmembrane receptors have a preformed, yet inactive, dimeric structure on the cell surface. Various studies also demonstrate that during transmembrane signaling, ligand binding to the extracellular domain of receptor dimers induces a rotation of transmembrane domains, followed by rearrangement and/or activation of intracellular domains. The paper here describes transmembrane cell-surface receptors that are known or proposed to exist in dimeric form prior to ligand binding, and discusses how these preformed dimers are activated by ligand binding. “Rotation model” for a molecular mechanism underlying ligand-induced activation of preformed, cell-surface receptor dimers. Ligand binding induces conformational changes of the extracellular domains that cause rotations of the transmembrane domains. The transmembrane domain rotations dissociate and rearrange the intracellular domain dimers for activation and/or interaction with other cytoplasmic proteins.

Description: A vast network of cellular circadian clocks regulates 24-hour rhythms of behavior and physiology in mammals. Complex environments are characterized by multiple, and often conflicting time signals demanding flexible mechanisms of adaptation of endogenous rhythms to external time. Traditionally this process of circadian entrainment has been conceptualized in a hierarchical scheme with a light-reset master pacemaker residing in the hypothalamus that subsequently aligns subordinate peripheral clocks with each other and with external time. Here we review new experiments using conditional mouse genetics suggesting that resetting of the circadian system occurs in a more “federated” and tissue-specific fashion, which allows for increased noise resistance and plasticity of circadian timekeeping under natural conditions. A network of cellular circadian clocks adapts physiology to the 24-hour day cycle. Traditionally clock entrainment has been conceptualized in a hierarchical scheme with a light-reset SCN pacemaker that subsequently aligns subordinate peripheral clocks. New experiments suggest that resetting of the circadian system occurs in a more “federated” fashion allowing for increased noise resistance and plasticity of circadian timekeeping under complex natural conditions.

Description: hiCLIP (RNA hybrid and individual-nucleotide resolution ultraviolet cross-linking and immunoprecipitation), is a novel technique developed by Sugimoto et al. (2015). Here, the use of different adaptors permits a controlled ligation of the two strands of a RNA duplex allowing the identification of each arm in the duplex upon sequencing. The authors chose a notoriously difficult to study double-stranded RNA-binding protein (dsRBP) termed Staufen1, a mammalian homolog of Drosophila Staufen involved in mRNA localization and translational control. Using hiCLIP, they discovered a dominance of intramolecular RNA duplexes compared to the total RNA duplexes identified. Importantly, the authors discovered two different types of intramolecular duplexes in the cell: highly translated mRNAs with long-range duplexes in their 3′-UTRs and poorly translated mRNAs with duplexes in their coding region. In conclusion, the authors establish hiCLIP as an important novel technique for the identification of RNA secondary structures that serve as in vivo binding sites for dsRBPs. The hiCLIP technique has allowed Sugimoto et al. (2015) to unravel Staufen 1 (Stau1) function in mRNA translational regulation, showing that transcript translation is dependent on the location of intramolecular double-stranded duplexes recognized by Stau1.

Description: Alzheimer's disease (AD) is the most common cause of dementia, and there is currently no cure. The “β-amyloid cascade hypothesis” of AD is the basis of current understanding of AD pathogenesis and drug discovery. However, no AD models have fully validated this hypothesis. We recently developed a human stem cell culture model of AD by cultivating genetically modified human neural stem cells in a three-dimensional (3D) cell culture system. These cells were able to recapitulate key events of AD pathology including β-amyloid plaques and neurofibrillary tangles. In this review, we will discuss the progress and current limitations of AD mouse models and human stem cell models as well as explore the breakthroughs of 3D cell culture systems. We will also share our perspective on the potential of dish models of neurodegenerative diseases for studying pathogenic cascades and therapeutic drug discovery. Recently, we recapitulated key events of Alzheimer's disease pathogenesis in a 3D human stem cells culture system. This model enhances beta-amyloid accumulation and neurofibrillary tau tangles (NFT), providing a powerful cellular model for Alzheimer's disease. In this review, we discuss the current progress of modeling neurodegenerative diseases in 3D cultures.

Description: RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence-specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross-linking immuno-precipitation (CLIP) and other recently developed high-throughput methods provide comprehensive, genome-wide maps of protein-RNA interactions in the cell. Structural biology gives detailed insights into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high-throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein-RNA recognition in gene regulation, as we review in this article. Multi-protein-RNA networks play important roles in post-transcriptional regulation of gene expression. Deciphering the underlying protein-RNA recognition code will greatly benefit from combining large-scale quantitative methods with integrated structural biology.

Description: Chromosomes are not only carriers of the genetic material, but also actively regulate the assembly of complex intracellular architectures. During mitosis, chromosome-induced microtubule polymerisation ensures spindle assembly in cells without centrosomes and plays a supportive role in centrosome-containing cells. Chromosomal signals also mediate post-mitotic nuclear envelope (NE) re-formation. Recent studies using novel approaches to manipulate histones in oocytes, where functions can be analysed in the absence of transcription, have established that nucleosomes, but not DNA alone, mediate the chromosomal regulation of spindle assembly and NE formation. Both processes require the generation of RanGTP by RCC1 recruited to nucleosomes but nucleosomes also acquire cell cycle stage specific regulators, Aurora B in mitosis and ELYS, the initiator of nuclear pore complex assembly, at mitotic exit. Here, we review the mechanisms by which nucleosomes control assembly and functions of the spindle and the NE, and discuss their implications for genome maintenance. Chromosomes act as reaction platforms for spindle assembly and nuclear envelope formation. Both processes depend on nucleosomes, which induce spindles by recruiting RCC1 and Aurora B in mitosis, and nuclear envelopes by recruiting RCC1 and ELYS in interphase. Here, we review these mechanisms, and discuss their implications for genome maintenance.

Description: In the organelles of plants and mammals, recent evidence suggests that genomic instability stems in large part from template switching events taking place during DNA replication. Although more than one mechanism may be responsible for this, some similarities exist between the different proposed models. These can be separated into two main categories, depending on whether they involve a single-strand-switching or a reciprocal-strand-switching event. Single-strand-switching events lead to intermediates containing Y junctions, whereas reciprocal-strand-switching creates Holliday junctions. Common features in all the described models include replication stress, fork stalling and the presence of inverted repeats, but no single element appears to be required in all cases. We review the field, and examine the ideas that several mechanisms may take place in any given genome, and that the presence of palindromes or inverted repeats in certain regions may favor specific rearrangements. Short-range inversions are a major component of genomic instability in the organelles of Arabidopsis thaliana and humans. Here, we review proposed replication-based mechanisms for the formation of these rearrangements. We identify common characteristics of the mechanisms and examine their impact on organelle genomes.

Description: Inflammatory responses are essential for the clearance of pathogens and the repair of injured tissues; however, if these responses are not properly controlled chronic inflammation can occur. Chronic inflammation is now recognized as a contributing factor to many age-associated diseases including metabolic disorders, arthritis, neurodegeneration, and cardiovascular disease. Due to the connection between chronic inflammation and these diseases, it is essential to understand underlying mechanisms behind this process. In this review, factors that contribute to chronic inflammation are discussed. Further, we emphasize the emerging roles of microRNAs (miRNAs) and other noncoding RNAs (ncRNA) in regulating chronic inflammatory states, making them important future diagnostic markers and therapeutic targets. Copyright Line: © 2015 The Authors BioEssays Published by Wiley-VCH Verlag GmbH & Co. KGaA. Although immune responses are necessary for proper clearance of pathogens and tissue repair, these responses can become dysregulated resulting in a chronic inflammatory state. Chronic inflammation is a contributing factor to many age-associated diseases. Recently, noncoding RNAs have been shown to regulate chronic inflammation and are emerging as potential therapeutic targets.

Description: The small ubiquitin-like modifier SUMO regulates many aspects of cellular physiology to maintain cell homeostasis, both under normal conditions and during cell stress. Components of the transcriptional apparatus and chromatin are among the most prominent SUMO substrates. The prevailing view is that SUMO serves to repress transcription. However, as we will discuss in this review, this model needs to be refined, because recent studies have revealed that SUMO can also have profound positive effects on transcription. SUMO targets a number of transcription factors, and the current dogma is that sumoylation of transcription factors generally inhibits the transcription process. In this review, we nuance this dogma by discussing recent findings that reveal SUMO as an activator of transcription of pro-growth genes in yeast and mammalian cells.

Description: The nuclear pore complex (NPC) is emerging as a center for recruitment of a class of “difficult to repair” lesions such as double-strand breaks without a repair template and eroded telomeres in telomerase-deficient cells. In addition to such pathological situations, a recent study by Su and colleagues shows that also physiological threats to genome integrity such as DNA secondary structure-forming triplet repeat sequences relocalize to the NPC during DNA replication. Mutants that fail to reposition the triplet repeat locus to the NPC cause repeat instability. Here, we review the types of DNA lesions that relocalize to the NPC, the putative mechanisms of relocalization, and the types of recombinational repair that are stimulated by the NPC, and present a model for NPC-facilitated repair. Triplet repeat sequences occurring in physiological DNA are able to form secondary structures. During S phase, these structures relocalize to the nuclear pore complex (NPC) to facilitate their stable replication. Such relocalization to the NPC is emerging as a general strategy to facilitate recombinational repair of “difficult-to-repair” DNA lesions.

Description: In metazoans, the extracellular matrix (ECM) provides a dynamic, heterogeneous microenvironment that has important supportive and instructive roles. Although the primary site of action of ECM proteins is extracellular, evidence is emerging for non-canonical intracellular roles. Examples include osteopontin, thrombospondins, IGF-binding protein 3 and biglycan, and relate to roles in transcription, cell-stress responses, autophagy and cancer. These findings pose conceptual problems on how proteins signalled for secretion can be routed to the cytosol or nucleus, or can function in environments with diverse redox, pH and ionic conditions. We review evidence for intracellular locations and functions of ECM proteins, and current knowledge of the mechanisms by which they may enter intracellular compartments. We evaluate the experimental methods that are appropriate to obtain rigorous evidence for intracellular localisation and function. Better insight into this under-researched topic is needed to decipher the complete spectrum of physiological and pathological roles of ECM proteins. It is a given that ECM proteins function outside cells. We evaluate emerging data that implicate non-canonical roles in the cytoplasm or nucleus. We discuss the conceptual and experimental challenges that will need to be met to investigate this under-studied area of ECM biology more rigorously.

Description: We recently used genome sequencing to study the evolutionary history of the Darwin's finches. A prominent feature of our data was that different polymorphic sites in the genome tended to indicate different genetic relationships among these closely related species. Such patterns are expected in recently diverged genomes as a result of incomplete lineage sorting. However, we uncovered conclusive evidence that these patterns have also been influenced by interspecies hybridisation, a process that has likely played an important role in the radiation of Darwin's finches. A major discovery was that segregation of two haplotypes at the ALX1 locus underlies variation in beak shape among the Darwin's finches, and that differences between the two haplotypes in a 240 kb region in blunt and pointed beaked birds involve both coding and regulatory changes. As we review herein, the evolution of such adaptive haplotypes comprising multiple causal changes appears to be an important mechanism contributing to the evolution of biodiversity. Whole genome studies, when combined with field data, provide a powerful method of investigating evolution. We review an example with two discoveries in Darwin's finches. Interspecific hybridisation has occurred throughout the radiation, and involved a locus encoding the ALX1 transcription factor that controls variation in beak shape and hence diets.

Description: Mitochondrial function is key for maintaining cellular health, while mitochondrial failure is associated with various pathologies, including inherited metabolic disorders and age-related diseases. In order to maintain mitochondrial quality, several pathways of mitochondrial quality control have evolved. These systems monitor mitochondrial integrity through antioxidants, DNA repair systems, and chaperones and proteases involved in the mitochondrial unfolded protein response. Additional regulation of mitochondrial function involves dynamic exchange of components through mitochondrial fusion and fission. Sustained stress induces a selective autophagy – termed mitophagy – and ultimately leads to apoptosis. Together, these systems form a network that acts on the molecular, organellar, and cellular level. In this review, we highlight how these systems are regulated in an integrated context- and time-dependent network of mitochondrial quality control that is implicated in healthy aging. Mitochondrial stress is an important hallmark of metabolic diseases and aging. Various mitochondrial stress response pathways are in place to counter this imposed stress. In this review, we discuss the existing mitochondrial quality control pathways, and focus on the recent insight that these pathways are highly context- and time-dependent.

Description: The study of cellular senescence and proliferative lifespan is becoming increasingly important because of the promises of autologous cell therapy, the need for model systems for tissue disease and the implication of senescent cell phenotypes in organismal disease states such as sarcopenia, diabetes and various cancers, among others. Here, we explain the concepts of proliferative cellular lifespan and cellular senescence, and we present factors that have been shown to mediate cellular lifespan positively or negatively. We review much recent literature and present potential molecular mechanisms by which lifespan mediation occurs, drawing from the fields of telomere biology, metabolism, NAD + and sirtuin biology, growth factor signaling and oxygen and antioxidants. We conclude that cellular lifespan and senescence are complex concepts that are governed by multiple independent and interdependent pathways, and that greater understanding of these pathways, their interactions and their convergence upon specific cellular phenotypes may lead to viable therapies for tissue regeneration and treatment of age-related pathologies, which are caused by or exacerbated by senescent cells in vivo. Replicative cellular lifespan is regulated by myriad cellular factors and processes, including telomeres, oxygen, DNA damage signaling, growth factors and metabolism. In this review, we will explain some of the molecular means by which these and other factors mediate cellular lifespan.

Description: Uncoupling proteins (UCPs) regulate mitochondrial function, and thus cellular metabolism. Angiotensin-converting enzyme (ACE) is the central component of endocrine and local tissue renin–angiotensin systems (RAS), which also regulate diverse aspects of whole-body metabolism and mitochondrial function (partly through altering mitochondrial UCP expression). We show that ACE expression also appears to be regulated by mitochondrial UCPs. In genetic analysis of two unrelated populations ( healthy young UK men and Scandinavian diabetic patients ) serum ACE (sACE) activity was significantly higher amongst UCP3-55C (rather than T) and UCP2 I (rather than D) allele carriers. RNA interference against UCP2 in human umbilical vein endothelial cells reduced UCP2 mRNA sixfold ( P  〈 0·01) whilst increasing ACE expression within a physiological range (〈1·8-fold at 48 h; P  〈 0·01). Our findings suggest novel hypotheses. Firstly, cellular feedback regulation may occur between UCPs and ACE. Secondly, cellular UCP regulation of sACE suggests a novel means of crosstalk between (and mutual regulation of) cellular and endocrine metabolism. This might partly explain the reduced risk of developing diabetes and metabolic syndrome with RAS antagonists and offer insight into the origins of cardiovascular disease in which UCPs and ACE both play a role. Uncoupling proteins (UCPs) regulate mitochondrial function, and thus cellular metabolism. Angiotensin-converting enzyme (ACE) is the central component of endocrine and local tissue renin–angiotensin systems, which also regulate diverse aspects of whole-body metabolism and mitochondrial function. We demonstrate that ACE expression appears to be regulated by mitochondrial UCPs.

Description: Positive transcription elongation factor (P-TEFb) plays an important role in host cell and viral gene expression. Many viruses, including Herpes Simplex Virus 1, have evolved strategies to hijack this key factor via their own regulatory proteins. The central role of P-TEFb in viral life cycles raises the possibility that Cdk9 inhibitors might be useful antiviral agents. See article “P-TEFb goes viral” by Justyna Zaborowska, Nur F. Isa and Shona Murphy in this issue.

Description: Tumors are often viewed as unique entities with specific behaviors. However, tumors are a mixture of differentially evolved subpopulations of cells in constant Darwinian evolution, selecting the fittest clone and allowing it to outgrow the rest. As in the natural environment, the niche defines the properties the fittest clones must possess. Therefore, there can be multiple fit clones because of the various microenvironments inside a single tumor. Hypoxia is considered to be a major feature of the tumor microenvironment and is a potential contributor to the cancer stem cell (CSC) phenotype and its enhanced tumorigenicity. The acidic microenvironment around hypoxic cells is accompanied by the activation of a subset of proteases that contribute to metastasis. Because of aberrant angiogenesis and the inaccessibility of their locations, hypoxic cells are less likely to accumulate therapeutic concentrations of chemotherapeutics that can lead to therapeutic resistance. Therefore, the targeting of the hypoxic CSC niche in combination with chemotherapy may provide a promising strategy for eradicating CSCs. In this review, we examine the cancer stem cell hypothesis and its relationship to the microenvironment, specifically to hypoxia and the subsequent metabolic switch and how they shape tumor behavior. Tumors are a mixture of differentially evolved subpopulations of cells in constant evolution. As in the natural environment, the niche defines the properties the fittest clones must possess. Therefore, there can be multiple fit clones because of the various microenvironments inside a single tumor. Hypoxia is considered to be a major feature of the tumor microenvironment and is a potential contributor to the cancer stem cell phenotype and its enhanced tumorigenicity.

Description: Eukaryotic gene expression is extensively controlled at the level of mRNA stability and the mechanisms underlying this regulation are markedly different from their archaeal and bacterial counterparts. We propose that two such mechanisms, nonsense-mediated decay (NMD) and motif-specific transcript destabilization by CCCH-type zinc finger RNA-binding proteins, originated as a part of cellular defense against RNA pathogens. These branches of the mRNA turnover pathway might have been used by primeval eukaryotes alongside RNA interference to distinguish their own messages from those of RNA viruses and retrotransposable elements. We further hypothesize that the subsequent advent of “professional” innate and adaptive immunity systems allowed NMD and the motif-triggered mechanisms to be efficiently repurposed for regulation of endogenous cellular transcripts. This scenario explains the rapid emergence of archetypical mRNA destabilization pathways in eukaryotes and argues that other aspects of post-transcriptional gene regulation in this lineage might have been derived through a similar exaptation route. mRNA turnover in eukaryotes is remarkably different from its prokaryotic counterparts and possible reasons underlying this divergence remain unclear. Here we propose that eukaryotic mRNA destabilization pathways evolved as a part of host defense against RNA pathogens and were subsequently repurposed for post-transcriptional regulation of cell-encoded genes.

Description: Soma to germline inheritance of extrachromosomal genetic information. Non-Mendelian transgenerational inheritance is a growingly recognized phenomenon, yet still elusive in its molecular nature . On pages 726–733 of this issue, Corrado Spadafora proposes a model, whereby extrachromosomal genetic information released form somatic cells can cross the Weismann barrier and become internalized in epididymal spermatozoa, which thereafter mediate the acquisition of new traits in the offspring at fertilization. The sperm endogenous reverse transcriptase (RT) plays a key role in developmental control. Sperm cells therefore act as recipients, and at the same time transgenerational vectors, of somatically derived genetic information, which they pass to the next generation in a non chromosomally-integrated form, yet with the potential to modify the fate of the developing embryos.

Description: The conventional approach to developing disease-modifying treatments for neurodegenerative conditions has been to identify drivers of pathology and inhibit such pathways. Here we discuss the possibility that the efficacy of such approaches may be increasingly attenuated as disease progresses. This is based on experiments using mouse models of spinocerebellar ataxia type 1 and Huntington's disease (HD), where expression of the dominantly acting mutations could be switched off, as well as studies in human HD, which suggest that the primary genetic driver of age-of-onset of disease is a much weaker determinant of disease progression in affected individuals. The idea that one may approach a point in the disease course where such rational therapeutic strategies based on targets which determine onset of disease have minimal efficacy, suggests that one needs to consider other approaches to therapies and clinical trial design, including initiation of therapies in presymptomatic individuals. Different factors may determine the onset of a neurodegenerative disease versus its progression. Thus, treatments aiming to slow progression based on targets which determine onset may have less efficacy with increased disease duration.

Description: Coiled-coils are found in proteins throughout all three kingdoms of life. Coiled-coil domains of some proteins are almost invariant in sequence and length, betraying a structural and functional role for amino acids along the entire length of the coiled-coil. Other coiled-coils are divergent in sequence, but conserved in length, thereby functioning as molecular spacers. In this capacity, coiled-coil proteins influence the architecture of organelles such as centrioles and the Golgi, as well as permit the tethering of transport vesicles. Specialized coiled-coils, such as those found in motor proteins, are capable of propagating conformational changes along their length that regulate cargo binding and motor processivity. Coiled-coil domains have also been identified in enzymes, where they function as molecular rulers, positioning catalytic activities at fixed distances. Finally, while coiled-coils have been extensively discussed for their potential to nucleate and scaffold large macromolecular complexes, structural evidence to substantiate this claim is relatively scarce. Supercoiling of α-helices gives rise to coiled-coil structures of theoretically infinite length. The tunable length and mechanical properties of coiled-coils make them suitable for a wide variety of functions in the cell including molecular rulers or spacers, molecular tethers, and for communicating information along their length.

Description: Observing adaptive evolution is difficult. In the fossil record, phenotypic evolution happens much more slowly than in artificial selection experiments or in experimental evolution. Yet measures of selection on phenotypic traits, with high heritabilities, suggest that phenotypic evolution should also be rapid in the wild, and this discrepancy often remains even after accounting for correlations between different traits (i.e. making predictions using the multivariate version of the breeder's equation). Are fitness correlations with quantitative traits adequate measures of selection in the wild? We should instead view fitnesses as average properties of genotypes, while acknowledging that they can be environment-dependent. Populations will tend to remain at fitness equilibria, once these are attained, and phenotypes will then be stable. Thus, studying the causes of adaptive change at a genotypic rather than phenotypic level may reveal that, typically, it is occurring too slowly to be easily observed. Measured phenotypic evolutionary rates are high under artificial selection and in changed environments, but are low when environments are constant and are very low over paleontological time. Additive genetic variance (heritability) and apparent selection predict high rates of phenotypic evolution, which is not seen. Why?

Description: One of the main questions in the use of genome editing tools is their specificity and the degree of possible off-target events. The cover shows two of the protein scaffolds commonly used for this purpose, TALE and Cas9, targeting a DNA site for the generation of specific cleavage. As discussed by Stella and Montoya in this issue, a key element in this genome modification strategy is whether DNA binding has been achieved accurately to generate the desired modification in the right genomic site.

Description: Cancer is an evolutionary and ecological process in which complex interactions between tumour cells and their environment share many similarities with organismal evolution. Tumour cells with highest adaptive potential have a selective advantage over less fit cells. Naturally occurring transmissible cancers provide an ideal model system for investigating the evolutionary arms race between cancer cells and their surrounding micro-environment and macro-environment. However, the evolutionary landscapes in which contagious cancers reside have not been subjected to comprehensive investigation. Here, we provide a multifocal analysis of transmissible tumour progression and discuss the selection forces that shape it. We demonstrate that transmissible cancers adapt to both their micro-environment and macro-environment, and evolutionary theories applied to organisms are also relevant to these unique diseases. The three naturally occurring transmissible cancers, canine transmissible venereal tumour (CTVT) and Tasmanian devil facial tumour disease (DFTD) and the recently discovered clam leukaemia, exhibit different evolutionary phases: (i) CTVT, the oldest naturally occurring cell line is remarkably stable; (ii) DFTD exhibits the signs of stepwise cancer evolution; and (iii) clam leukaemia shows genetic instability. While all three contagious cancers carry the signature of ongoing and fairly recent adaptations to selective forces, CTVT appears to have reached an evolutionary stalemate with its host, while DFTD and the clam leukaemia appear to be still at a more dynamic phase of their evolution. Parallel investigation of contagious cancer genomes and transcriptomes and of their micro-environment and macro-environment could shed light on the selective forces shaping tumour development at different time points: during the progressive phase and at the endpoint. A greater understanding of transmissible cancers from an evolutionary ecology perspective will provide novel avenues for the prevention and treatment of both contagious and non-communicable cancers. Transmissible cancers are ideal to investigate the evolutionary arms race between cancer cells and their surrounding environment. While all three contagious cancers show ongoing adaptations to selective forces, canine transmissible venereal tumour has reached an evolutionary stalemate with its host, while devil facial tumor disease and clam leukaemia are still in a more dynamic phase of their evolution.

Description: Entry into mitosis is driven by the activity of kinases, which phosphorylate over 7000 proteins on multiple sites. For cells to exit mitosis and segregate their genome correctly, these phosphorylations must be removed in a specific temporal order. This raises a critical and important question: how are specific phosphorylation sites on an individual protein removed? Traditionally, the temporal order of dephosphorylation was attributed to decreasing kinase activity. However, recent evidence in human cells has identified unique patterns of dephosphorylation during mammalian mitotic exit that cannot be fully explained by the loss of kinase activity. This suggests that specificity is determined in part by phosphatases. In this review, we explore how the physicochemical properties of an individual phosphosite and its surrounding amino acids can affect interactions with a phosphatase. These positive and negative interactions in turn help determine the specific pattern of dephosphorylation required for correct mitotic exit. During mitotic exit, phosphatases reverse thousands of phosphorylation events in a specific temporal order to ensure that cell division occurs correctly. This review explores how the physicochemical properties of the phosphosite and surrounding amino acids affect interactions with phosphatase/s and help determine the dephosphorylation of individual phosphorylation sites during mitotic exit.

Description: Cellular senescence is an anti-proliferative program that restricts the propagation of cells subjected to different kinds of stress. Cellular senescence was initially described as a cell-autonomous tumor suppressor mechanism that triggers an irreversible cell cycle arrest that prevents the proliferation of damaged cells at risk of neoplastic transformation. However, discoveries during the last decade have established that senescent cells can also impact the surrounding tissue microenvironment and the neighboring cells in a non-cell-autonomous manner. These non-cell-autonomous activities are, in part, mediated by the selective secretion of extracellular matrix degrading enzymes, cytokines, chemokines and immune modulators, which collectively constitute the senescence-associated secretory phenotype. One of the key functions of the senescence-associated secretory phenotype is to attract immune cells, which in turn can orchestrate the elimination of senescent cells. Interestingly, the clearance of senescent cells seems to be critical to dictate the net effects of cellular senescence. As a general rule, the successful elimination of senescent cells takes place in processes that are considered beneficial, such as tumor suppression, tissue remodeling and embryonic development, while the chronic accumulation of senescent cells leads to more detrimental consequences, namely, cancer and aging. Nevertheless, exceptions to this rule may exist. Now that cellular senescence is in the spotlight for both anti-cancer and anti-aging therapies, understanding the precise underpinnings of senescent cell removal will be essential to exploit cellular senescence to its full potential. Senescent cells secrete a variety of cytokines, immune modulators and extracellular matrix degrading enzymes, which constitute the senescence-associated secretory phenotype (SASP). The SASP can direct immune cells for senescent cell clearance, promoting tissue homeostasis, tumor suppression and rejuvenation. In the absence of clearance, SASP can promote tumorigenesis, fibrosis and aging.

Description: In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than the previously available DNA binding templates, zinc fingers and meganucleases. Recently, the area experimented a quantum leap because of the introduction of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system (clustered regularly interspaced short palindromic sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR-Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human pathways or to improve key organisms for biotechnological applications, such as plants, livestock genome as well as yeasts and bacterial strains. The area of genome editing using engineered nucleases is growing extremely fast because of platforms such as Transcription Activator-Like Effector (TALE) and CRIPSR-Cas9. However, a reliable method to assess the off-target effect of these engineered nucleases is still missing. This review comments the existing techniques to measure off-target effects.

Description: Polo-like kinase 1 (PLK1) is a serine/threonine kinase that plays multiple and essential roles during the cell division cycle. Its inhibition in cultured cells leads to severe mitotic aberrancies and cell death. Whereas previous reports suggested that Plk1 depletion in mice leads to a non-mitotic arrest in early embryos, we show here that the bi-allelic Plk1 depletion in mice certainly results in embryonic lethality due to extensive mitotic aberrations at the morula stage, including multi- and mono-polar spindles, impaired chromosome segregation and cytokinesis failure. In addition, the conditional depletion of Plk1 during mid-gestation leads also to severe mitotic aberrancies. Our data also confirms that Plk1 is completely dispensable for mitotic entry in vivo. On the other hand, Plk1 haploinsufficient mice are viable, and Plk1-heterozygous fibroblasts do not harbor any cell cycle alterations. Plk1 is overexpressed in many human tumors, suggesting a therapeutic benefit of inhibiting Plk1, and specific small-molecule inhibitors for this kinase are now being evaluated in clinical trials. Therefore, the different Plk1 mouse models here presented are a valuable tool to reexamine the relevance of the mitotic kinase Plk1 during mammalian development and animal physiology. Two different mouse strains, a classical gene-trapping KO and a conditional KO by Cre recombinase excision, demonstrate that the mitotic kinase Plk1 is essential at any stage of the embryonic development, and its depletion leads to mitotic aberrancies and embryonic death. Instead, Plk1 haploinsufficient mice do not show any alteration.

Description: Human pluripotent stem cells (hPSCs) have the potential to fundamentally change the way that we go about treating and understanding human disease. Despite this extraordinary potential, these cells also have an innate capability to form tumors in immunocompromised individuals when they are introduced in their pluripotent state. Although current therapeutic strategies involve transplantation of only differentiated hPSC derivatives, there is still a concern that transplanted cell populations could contain a small percentage of cells that are not fully differentiated. In addition, these cells have been frequently reported to acquire genetic alterations that, in some cases, are associated with certain types of human cancers. Here, we try to separate the panic from reality and rationally evaluate the true tumorigenic potential of these cells. We also discuss a recent study examining the effect of culture conditions on the genetic integrity of hPSCs. Finally, we present a set of sensible guidelines for minimizing the tumorigenic potential of hPSC-derived cells. © 2016 The Authors. Inside the Cell published by Wiley Periodicals, Inc. hPSC-derived cells have the potential to cause tumors during cell therapy but simple steps can be taken to minimize the risk. 1) Genomic analysis to ensure the cells' genetic integrity. 2) Purging contaminating undifferentiated and progenitor cells after differentiation. 3) In vivo testing to demonstrate that the cells aren't tumorigenic.

Description: Disabled-2 (Dab2) is a multimodular scaffold protein with signaling roles in the domains of cell growth, trafficking, differentiation, and homeostasis. Emerging evidences place Dab2 as a novel modulator of cell–cell interaction; however, its mode of action has remained largely elusive. In this review, we highlight the relevance of Dab2 function in cell signaling and development and provide the most recent and comprehensive analysis of Dab2's action as a mediator of homotypical and heterotypical interactions. Accordingly, Dab-2 controls the extent of platelet aggregation through various motifs within its N-terminus. Dab2 interacts with the cytosolic tail of the integrin receptor blocking inside-out signaling, whereas extracellular Dab2 competes with fibrinogen for integrin α IIb β 3 receptor binding and, thus, modulates outside-in signaling. An additional level of regulation results from Dab2's association with cell surface lipids, an event that defines the extent of cell–cell interactions. As a multifaceted regulator, Dab2 acts as a mediator of endocytosis through its association with the [FY]xNPx[YF] motifs of internalized cell surface receptors, phosphoinositides, and clathrin. Other emerging roles of Dab2 include its participation in developmental mechanisms required for tissue formation and in modulation of immune responses. This review highlights the various novel mechanisms by which Dab2 mediates an array of signaling events with vast physiological consequences. Disabled-2 (Dab2) is a multimodular scaffold protein and a putative tumor suppressor involved in a wide array of physiological processes. This review highlights the latest findings involving Dab2 in protein trafficking, immune response, and development, placing emphasis on the recently reported modulatory role of Dab2 in cell-cell interactions.

Description: Depletion of mitochondrial endo/exonuclease G-like (EXOG) in cultured neonatal cardiomyocytes stimulates mitochondrial oxygen consumption rate (OCR) and induces hypertrophy via reactive oxygen species (ROS). Here, we show that neurohormonal stress triggers cell death in endo/exonuclease G-like-depleted cells, and this is marked by a decrease in mitochondrial reserve capacity. Neurohormonal stimulation with phenylephrine (PE) did not have an additive effect on the hypertrophic response induced by endo/exonuclease G-like depletion. Interestingly, PE-induced atrial natriuretic peptide (ANP) gene expression was completely abolished in endo/exonuclease G-like-depleted cells, suggesting a reverse signaling function of endo/exonuclease G-like. Endo/exonuclease G-like depletion initially resulted in increased mitochondrial OCR, but this declined upon PE stimulation. In particular, the reserve capacity of the mitochondrial respiratory chain and maximal respiration were the first indicators of perturbations in mitochondrial respiration, and these marked the subsequent decline in mitochondrial function. Although pathological stimulation accelerated these processes, prolonged EXOG depletion also resulted in a decline in mitochondrial function. At early stages of endo/exonuclease G-like depletion, mitochondrial ROS production was increased, but this did not affect mitochondrial DNA (mtDNA) integrity. After prolonged depletion, ROS levels returned to control values, despite hyperpolarization of the mitochondrial membrane. The mitochondrial dysfunction finally resulted in cell death, which appears to be mainly a form of necrosis. In conclusion, endo/exonuclease G-like plays an essential role in cardiomyocyte physiology. Loss of endo/exonuclease G-like results in diminished adaptation to pathological stress. The decline in maximal respiration and reserve capacity is the first sign of mitochondrial dysfunction that determines subsequent cell death. Mitochondrial Endonuclease G-like-1 (EXOG) modulates mitochondrial respiration and hypertrophy in cardiomyocytes. Here we show that pathological stimulation of EXOG depleted cardiomyocytes results in a diminished mitochondrial reserve capacity, which marks subsequent cell death. EXOG is therefore essential in pathological stress adaptation and to maintain cell viability.

Description: Positive transcription elongation factor b (P-TEFb), which comprises cyclin-dependent kinase 9 (CDK9) kinase and cyclin T subunits, is an essential kinase complex in human cells. Phosphorylation of the negative elongation factors by P-TEFb is required for productive elongation of transcription of protein-coding genes by RNA polymerase II (pol II). In addition, P-TEFb-mediated phosphorylation of the carboxyl-terminal domain (CTD) of the largest subunit of pol II mediates the recruitment of transcription and RNA processing factors during the transcription cycle. CDK9 also phosphorylates p53, a tumor suppressor that plays a central role in cellular responses to a range of stress factors. Many viral factors affect transcription by recruiting or modulating the activity of CDK9. In this review, we will focus on how the function of CDK9 is regulated by viral gene products. The central role of CDK9 in viral life cycles suggests that drugs targeting the interaction between viral products and P-TEFb could be effective anti-viral agents. Many viruses subvert transcription elongation factor b (P-TEFb) function to facilitate viral gene expression. P-TEFb is integral to the replication of a range of viruses, including herpes simplex virus, Kaposi sarcoma-associated herpesvirus, human cytomegalovirus, Epstein–Barr virus, human immunoficiency virus, human t-lymphotropic virus type 1, adenovirus, influenza A and dengue virus.

Description: Abnormalities in the ability of cells to properly degrade proteins have been identified in many neurodegenerative diseases. Recent work has implicated synaptojanin 1 (SynJ1) in Alzheimer's disease and Parkinson's disease, although the role of this polyphosphoinositide phosphatase in protein degradation has not been thoroughly described. Here, we dissected in vivo the role of SynJ1 in endolysosomal trafficking in zebrafish cone photoreceptors using a SynJ1-deficient zebrafish mutant, nrc a14 . We found that loss of SynJ1 leads to specific accumulation of late endosomes and autophagosomes early in photoreceptor development. An analysis of autophagic flux revealed that autophagosomes accumulate because of a defect in maturation. In addition we found an increase in vesicles that are highly enriched for PI(3)P, but negative for an early endosome marker in nrc a14 cones. A mutational analysis of SynJ1 enzymatic domains found that activity of the 5'phosphatase, but not the Sac1 domain, is required to rescue both aberrant late endosomes and autophagosomes. Finally, modulating activity of the PI(4,5)P 2 regulator, Arf6, rescued the disrupted trafficking pathways in nrc a14 cones. Our study describes a specific role for SynJ1 in autophagosomal and endosomal trafficking and provides evidence that PI(4,5)P 2 participates in autophagy in a neuronal cell type. Loss of synaptojanin 1 (SynJ1) causes late endosomal and autophagic defects in cone photoreceptors. Modulating the activity of the PI(4,5)P 2 regulator Arf6a rescues autophagy defects in the absence of SynJ1. We propose that SynJ1 negatively regulates the formation of autophagosome precursors through actions on membrane PI(4,5)P 2 .

Description: Enhancers can stimulate transcription by a number of different mechanisms which control different stages of the transcription cycle of their target genes, from recruitment of the transcription machinery to elongation by RNA polymerase. These mechanisms may not be mutually exclusive, as a single enhancer may act through different pathways by binding multiple transcription factors. Multiple enhancers may also work together to regulate transcription of a shared target gene. Most of the evidence supporting different enhancer mechanisms comes from the study of single genes, but new high-throughput experimental frameworks offer the opportunity to integrate and generalize disparate mechanisms identified at single genes. This effort is especially important if we are to fully understand how sequence variation within enhancers contributes to human disease. Enhancers are regulatory elements that bind transcription factors and activate expression of their target genes by stimulating specific steps in the RNA polymerase II transcription cycle. Here we review the mechanisms of enhancer action and highlight opportunities for new insights from high-throughput experimental technologies such as massively parallel reporter assays.

Description: 5-methylcytosine (5mC) was long thought to be the only enzymatically created modified DNA base in mammalian cells. The discovery of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine as reaction products of the TET family 5mC oxidases has prompted extensive searches for proteins that specifically bind to these oxidized bases. However, only a few of such “reader” proteins have been identified and verified so far. In this review, we discuss potential biological functions of oxidized 5mC as well as the role the presumed reader proteins may play in interpreting the genomic signals of 5mC oxidation products. Oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine by TET proteins can lead to DNA demethylation. However, the oxidized 5mC bases are rather stable and may function as negative marks for 5mC readers. Intriguingly, proteins that bind to oxidized 5mC have now been identified and characterized by structural studies.

Description: On pages 618–626 , Schmidt et al. discuss the concept of cofactor squelching in light of recent evidence from genome-wide studies indicating that such competition for a limiting amount of coactivators is a general mechanism of transcriptional repression by signal-dependent transcription factors (TFs). They further discuss how TF cooperativity in so-called hotspots and super-enhancers may sensitize these enhancers to cofactor squelching. The cover illustrates how signal dependent TFs can be regarded as the ‘Robin Hoods’ of the genome, redistributing cofactors (gold coins) from the wealthy super-enhancers (stacks of gold coins). Cover design: Andreas N. Grøntved.

Description: Pluripotency can be considered a functional characteristic of pluripotent stem cells (PSCs) populations and their niches, rather than a property of individual cells. In this view, individual cells within the population independently adopt a variety of different expression states, maintained by different signaling, transcriptional, and epigenetics regulatory networks. In this review, we propose that generation of integrative network models from single cell data will be essential for getting a better understanding of the regulation of self-renewal and differentiation. In particular, we suggest that the identification of network stability determinants in these integrative models will provide important insights into the mechanisms mediating the transduction of signals from the niche, and how these signals can trigger differentiation. In this regard, the differential use of these stability determinants in subpopulation-specific regulatory networks would mediate differentiation into different cell fates. We suggest that this approach could offer a promising avenue for the development of novel strategies for increasing the efficiency and fidelity of differentiation, which could have a strong impact on regenerative medicine. Computational modeling of heterogeneity in pluripotent cells, integrating single-cell measurements at the signaling, transcriptional, and epigenetics levels will be essential for understanding the regulation of self-renewal and differentiation. Here we discuss on how computational modeling could be useful for developing efficient strategies for improving the efficiency and fidelity of differentiation.

Description: Comparative mapping and sequencing show that turnover of sex determining genes and chromosomes, and sex chromosome rearrangements, accompany speciation in many vertebrates. Here I review the evidence and propose that the evolution of therian mammals was precipitated by evolution of the male-determining SRY gene, defining a novel XY sex chromosome pair, and interposing a reproductive barrier with the ancestral population of synapsid reptiles 190 million years ago (MYA). Divergence was reinforced by multiple translocations in monotreme sex chromosomes, the first of which supplied a novel sex determining gene. A sex chromosome-autosome fusion may have separated eutherians (placental mammals) from marsupials 160 MYA. Another burst of sex chromosome change and speciation is occurring in rodents, precipitated by the degradation of the Y. And although primates have a more stable Y chromosome, it may be just a matter of time before the same fate overtakes our own lineage. Also watch the video abstract . Sex chromosome turnover is rare in mammals, but major changes in sex chromosomes characterise the three branches of mammals. Here I propose that sex chromosome turnover following SRY evolution, as well as XY-autosome fusions and translocations, interposed mating barriers that precipitated divergence of monotremes, marsupials and placental mammals.

Description: Both W9 and OP3-4 were known to bind the receptor activator of NF-κB ligand (RANKL), inhibiting osteoclastogenesis. Recently, both peptides were shown to stimulate osteoblast differentiation; however, the mechanism underlying the activity of these peptides remains to be clarified. A primary osteoblast culture showed that rapamycin, an mTORC1 inhibitor, which was recently demonstrated to be an important serine/threonine kinase for bone formation, inhibited the peptide-induced alkaline phosphatase activity. Furthermore, both peptides promoted the phosphorylation of Akt and S6K1, an upstream molecule of mTORC1 and the effector molecule of mTORC1, respectively. In the in vivo calvarial defect model, W9 and OP3-4 accelerated BMP-2-induced bone formation to a similar extent, which was confirmed by histomorphometric analyses using fluorescence images of undecalcified sections. Our data suggest that these RANKL-binding peptides could stimulate the mTORC1 activity, which might play a role in the acceleration of BMP-2-induced bone regeneration by the RANKL-binding peptides. Micro CT and fluorescent images revealed that two RANKL-binding peptides, W9 and OP3-4, could equally accelerate BMP-2-induced local bone regeneration in a murine calvarial defect model. The yellow line shows the site of the reconstruction images in the middle panel. White lines show the size of the original defect.

Description: Frequent evolutionary birth and death events have created a large quantity of biologically important, lineage-specific DNA within mammalian genomes. The birth and death of DNA sequences is so frequent that the total number of these insertions and deletions in the human population remains unknown, although there are differences between these groups, e.g. transposable elements contribute predominantly to sequence insertion. Functional turnover – where the activity of a locus is specific to one lineage, but the underlying DNA remains conserved – can also drive birth and death. However, this does not appear to be a major driver of divergent transcriptional regulation. Both sequence and functional turnover have contributed to the birth and death of thousands of functional promoters in the human and mouse genomes. These findings reveal the pervasive nature of evolutionary birth and death and suggest that lineage-specific regions may play an important but previously underappreciated role in human biology and disease. Lineage-specific elements within mammalian genomes have been created by evolutionary birth and death events, which are driven by frequent sequence and functional turnover. Regulatory elements, such as promoters and enhancers, are particularly evolutionarily volatile but their association with divergent transcription and human biology and disease is as yet unclear.

Description: Mitotic entry and exit are switch-like transitions that are driven by the activation and inactivation of Cdk1 and mitotic cyclins. This simple on/off reaction turns out to be a complex interplay of various reversible reactions, feedback loops, and thresholds that involve both the direct regulators of Cdk1 and its counteracting phosphatases. In this review, we summarize the interplay of the major components of the system and discuss how they work together to generate robustness, bistability, and irreversibility. We propose that it may be beneficial to regard the entry and exit reactions as two separate reversible switches that are distinguished by differences in the state of phosphatase activity, mitotic proteolysis, and a dramatic rearrangement of cellular components after nuclear envelope breakdown, and discuss how the major Cdk1 activity thresholds could be determined for these transitions. A complex cell cycle control network is responsible for mitotic entry and exit. This system is based on Cdk1 activation and inactivation and behaves like a bistable switch. We are discussing the various control elements in this system and their contribution to the thresholds that ultimately determine bistability.

Description: Eukaryotic mRNAs are monocistronic, and therefore mechanisms exist that coordinate the synthesis of multiprotein complexes in order to obtain proper stoichiometry at the appropriate intracellular locations. RNA-binding proteins containing low-complexity sequences are prone to generate liquid droplets via liquid-liquid phase separation, and in this way create cytoplasmic assemblages of functionally related mRNAs. In a recent iCLIP study, we showed that the Drosophila RNA-binding protein Imp, which exhibits a C-terminal low-complexity sequence, increases the formation of F-actin by binding to 3′ untranslated regions of mRNAs encoding components participating in F-actin biogenesis. We hypothesize that phase transition is a mechanism the cell employs to increase the local mRNA concentration considerably, and in this way synchronize protein production in cytoplasmic territories, as discussed in the present review. RNA-binding proteins containing low-complexity sequences are prone to generate cytoplasmic assemblages of functionally related mRNAs within liquid droplets. Such a partitioning mechanism coordinates local post-transcriptional regulation and ensures proximity of synthesized proteins in response to environmental cues, as illustrated for F-actin biogenesis during cellular migration.

Description: Mitochondrial respiration is the predominant source of ATP. Excessive rates of electron transport cause a higher production of harmful reactive oxygen species (ROS). There are two regulatory mechanisms known. The first, according to Mitchel , is dependent on the mitochondrial membrane potential that drives ATP synthase for ATP production, and the second, the Kadenbach mechanism, is focussed on the binding of ATP to Cytochrome c Oxidase (CytOx) at high ATP/ADP ratios, which results in an allosteric conformational change to CytOx, causing inhibition. In times of stress, ATP-dependent inhibition is switched off and the activity of CytOx is exclusively determined by the membrane potential, leading to an increase in ROS production. The second mechanism for respiratory control depends on the quantity of electron transfer to the Heme aa3 of CytOx. When ATP is bound to CytOx the enzyme is inhibited, and ROS formation is decreased, although the mitochondrial membrane potential is increased. ATP-binding inhibits Cytochrome c Oxidase, and ROS formation is decreased. This mechanism depends on the quantity of electron transfer to the Heme aa3 of CytOx. In times of stress, ATP-dependent inhibition is switched off and activity of CytOx is exclusively determined by the membrane potential, leading to increased ROS production.

Description: Mutations in growth factor receptor signaling pathways are common in cancer cells, including the highly lethal brain tumor glioblastoma (GBM) where they drive tumor growth through mechanisms including altering the uptake and utilization of nutrients. However, the impact of changes in micro-environmental nutrient levels on oncogenic signaling, tumor growth, and drug resistance is not well understood. We recently tested the hypothesis that external nutrients promote GBM growth and treatment resistance by maintaining the activity of mechanistic target of rapamycin complex 2 (mTORC2), a critical intermediate of growth factor receptor signaling, suggesting that altered cellular metabolism is not only a consequence of oncogenic signaling, but also potentially an important determinant of its activity. Here, we describe the studies that corroborate the hypothesis and propose others that derive from them. Notably, this line of reasoning raises the possibility that systemic metabolism may contribute to responsiveness to targeted cancer therapies. We propose that in glioblastoma, and possibly other cancers, abundant glucose or acetate, which are readily available to tumor cells in their native environment, facilitate biochemical modification of a core component of the growth factor receptor signaling pathway, mTOR complex 2, driving growth and rendering tumors resistant to drugs that target upstream components of growth factor signaling pathways.

Description: Cells live in dynamic environments that necessitate perpetual adaptation. Since cells have limited resources to monitor external inputs, they are required to maximize the information content of perceived signals. This challenge is not unique to microscopic life: Animals use senses to perceive inputs and adequately respond. Research showed that sensory-perception is actively shaped by learning and expectation allowing internal cognitive models to “fill in the blanks” in face of limited information. We propose that cells employ analogous strategies and use internal models shaped through the long process of evolutionary adaptation. Given this perspective, we postulate that cells are prone to “misperceptions,” analogous to visual illusions, leading them to incorrectly decode patterns of inputs that lie outside of their evolutionary experience. Mapping cellular misperception can serve as a fundamental approach for dissecting regulatory networks and could be harnessed to modulate cell behavior, a potentially new avenue for therapy. Cells use regulatory networks to guide their responses after changes in their environments. In extreme cases, the mapping between external stimuli and downstream responses can be incorrect and culminate in adverse fitness effects. We propose that the mapping cellular “misperceptions” can serve as a fundamental approach for dissecting regulatory networks.

Description: Long non-coding RNAs (lncRNAs) have recently gained increasing attention because of their crucial roles in gene regulatory processes. Functional studies using mammalian skin as a model system have revealed their role in controlling normal tissue homeostasis as well as the transition to a diseased state. Here, we describe how lncRNAs regulate differentiation to preserve an undifferentiated epidermal progenitor compartment, and to maintain a functional skin permeability barrier. Furthermore, we will reflect on recent work analyzing the impact of lncRNAs on the progression from normal epithelium to the development of skin disorders and cancer. Long non-coding RNAs (lncRNAs) have recently been shown to control a wide variety of gene regulatory processes. In mammalian skin, lncRNAs appear to regulate the intricate balance between progenitor cells undergoing continual regeneration in the basal layer and highly differentiated cells forming the epidermal permeability barrier.

Description: General mechanism for exaggerated sexuallyselected traits. Many animals wield sexually-selected exaggerated traits. ‘Classic’ examples include the peacock's train, and the antlers observed in male deer, as well as fiddler crabs with enlarged claws, and the enlarged head-horns of rhinoceros beetles ( Trypoxylus dichotomus , cover). These traits are used for mate choice, or to deter rival males, because they act as unusually reliable signals of the condition of individual males: only the best-quality animals produce full-sized signal structures. But what keeps their expression honest? How can signal traits evolve that are resistant to invasion by cheaters who fake attractive signals? The answer may lie in the ancient insulin-like signalling pathway, which is found in all animals and directly links individual condition to growth in a dose dependent manner. Warren et al. discuss recent evidence suggesting that exaggerated sexually-selected signal traits arise when specific structures become extra-sensitive to physiological signals like insulins or insulin-like growth factors (pages 889–899 ).

Description: mRNA synthesis in all organisms is performed by RNA polymerases, which work as nanomachines on DNA templates. The rate at which their product is made is an important parameter in gene expression. Transcription rate encompasses two related, yet different, concepts: the nascent transcription rate, which measures the in situ mRNA production by RNA polymerase, and the rate of synthesis of mature mRNA, which measures the contribution of transcription to the mRNA concentration. Both parameters are useful for molecular biologists, but they are not interchangeable and they are expressed in different units. It is important to distinguish when and where each one should be used. We propose that for functional genomics the use of nascent transcription rates should be restricted to the evaluation of the transcriptional process itself, whereas mature mRNA synthesis rates should be employed to address the transcriptional input to mRNA concentration balance leading to variation of gene expression. Transcription rate encompasses two related, yet different, concepts: the nascent transcription rate, which measures the in situ mRNA production by RNA polymerase, and the rate of synthesis of mature mRNA, which measures the contribution of transcription to the mRNA concentration. It is important to distinguish when to use each one.

Description: CALHM1 was recently demonstrated to be a voltage-gated ATP-permeable ion channel and to serve as a bona fide conduit for ATP release from sweet-, umami-, and bitter-sensing type II taste cells. Calhm1 is expressed in taste buds exclusively in type II cells and its product has structural and functional similarities with connexins and pannexins, two families of channel protein candidates for ATP release by type II cells. Calhm1 knockout in mice leads to loss of perception of sweet, umami, and bitter compounds and to impaired gustatory nerve responses to these tastants. These new studies validate the concept of ATP as the primary neurotransmitter from type II cells to gustatory neurons. Furthermore, they identify voltage-gated ATP release through CALHM1 as an essential molecular mechanism of ATP release in taste buds. We discuss these new findings, as well as unresolved issues in peripheral taste signaling that we hope will stimulate future research. Sweetness, umami, and bitterness are transmitted to the nervous system via ion channel-mediated ATP release from taste cells. A recent study demonstrated that CALHM1 is essential for taste cell ATP release and perception of sweetness, umami, and bitterness. We discuss the new findings and unresolved issues in peripheral taste signaling.

Description: The precise orchestration of two opposing protein complexes – one in the cytoplasm (β-catenin destruction complex) and the other at the plasma membrane (LRP6 signaling complex) – is critical for controlling levels of the transcriptional co-factor β-catenin, and subsequent activation of the Wnt/β-catenin signal transduction pathway. The Wnt pathway component Axin acts as an essential scaffold for the assembly of both complexes. How the β-catenin destruction and LRP6 signaling complexes are modulated following Wnt stimulation remains controversial. A recent study in Science by He and coworkers reveals an underlying logic for Wnt pathway control in which Axin phosphorylation toggles a switch between the active and inactive states. This mini-review focuses on this and two other recent studies that provide insight into the initial signaling events triggered by Wnt exposure. We emphasize regulation of the β-catenin destruction and LRP6 signaling complexes and propose a framework for future work in this area. The mechanism by which the Wnt pathway stabilizes β-catenin, a key transcriptional co-factor, remains controversial. Recent studies have revealed that the phosphorylation state of an essential regulator of the pathway, Axin, controls its conformation and, consequently, its availability to scaffold two opposing Wnt pathway protein complexes that regulate β-catenin stability.

Description: Metagenomics is a culture- and PCR-independent approach that is now widely exploited for directly studying microbial evolution, microbial ecology, and developing biotechnologies. Observations and discoveries are critically dependent on DNA extraction methods, sequencing technologies, and bioinformatics tools. The potential pitfalls need to be understood and, to some degree, mastered if the resulting data are to survive scrutiny. In particular, methodological variations appear to affect results from different ecosystems differently, thus increasing the risk of biological and ecological misinterpretation. Part of the difficulty is derived from the lack of knowledge concerning the true microbial diversity and because no approach can guarantee accessing microorganisms in the same proportion in which they exist in the environment. However, the variation between different approaches (e.g. DNA extraction techniques, sequence annotation systems) can be used to evaluate whether observations are meaningful. These methodological variations can be integrated into the error analysis before comparing microbial communities. Metagenomics is a powerful approach targeting environmental nucleic diversity but represents also a methodological jungle where pitfalls are challenging when quantitative observations are desired. Here we describe the effect of critical parameters (especially DNA extraction and annotation stringency) required to represent microbial communities function and structure in the metagenomic era.

Description: Pericytes, typically attached to the walls of microvessels in almost all organs, interact with endothelial cells and take part in diverse biological processes, e.g. blood vessel regulation and tissue repair. This suggests that pericytes harbor a remarkable degree of cellular plasticity, which could potentially be employed for the treatment of diseases affecting diverse tissues such as the skeletal muscle and the central nervous system. Here, we follow pericytes on their journey across Waddington's epigenetic landscape, descending from their origin, along a path guided by environmental signals or ectopic transcription factors, at the end of which they acquire a new identity, e.g. muscle or nerve cells. The central theme of this review is the question of whether pericytes can be enticed to differentiate into whatever cell type is needed, and thus provide an endogenous cellular source for treating as yet incurable diseases – like a magic bullet. Also watch the Video Abstract. http://youtu.be/J4b-cmRWLWI Recent studies show that microvessel-associated pericytes exhibit an unprecedented degree of plasticity and implicate these cells as a physiological cellular source or therapeutic target for tissue repair. They have potential for therapeutic applications in areas ranging from muscle degeneration to heart infarction and CNS injury.

Description: Factors affecting transcriptional elongation have been characterized extensively in in vitro, single cell (yeast) and cell culture systems; however, data from the context of multicellular organisms has been relatively scarce. While studies in homogeneous cell populations have been highly informative about the underlying molecular mechanisms and prevalence of polymerase pausing, they do not reveal the biological impact of perturbing this regulation in an animal. The core components regulating pausing are expressed in all animal cells and are recruited to the majority of genes, however, disrupting their function often results in discrete phenotypic effects. Mutations in genes encoding key regulators of transcriptional pausing have been recovered from several genetic screens for specific phenotypes or interactions with specific factors in mice, zebrafish and flies. Analysis of these mutations has revealed that control of transcriptional pausing is critical for a diverse range of biological pathways essential for animal development and survival. Animal studies reveal that correct regulation of promoter proximal pausing is critical for a diverse range of biological pathways during embryo development and also for health in adult life. This regulation facilitates fine control of gene expression levels and may also act as a barrier to uncontrolled cell proliferation.

Description: Phosphatidylinositol 4,5-bisphosphate (PI4,5P 2 ) is a key lipid signaling molecule that regulates a vast array of biological activities. PI4,5P 2 can act directly as a messenger or can be utilized as a precursor to generate other messengers: inositol trisphosphate, diacylglycerol, or phosphatidylinositol 3,4,5-trisphosphate. PI4,5P 2 interacts with hundreds of different effector proteins. The enormous diversity of PI4,5P 2 effector proteins and the spatio-temporal control of PI4,5P 2 generation allow PI4,5P 2 signaling to control a broad spectrum of cellular functions. PI4,5P 2 is synthesized by phosphatidylinositol phosphate kinases (PIPKs). The array of PIPKs in cells enables their targeting to specific subcellular compartments through interactions with targeting factors that are often PI4,5P 2 effectors. These interactions are a mechanism to define spatial and temporal PI4,5P 2 synthesis and the specificity of PI4,5P 2 signaling. In turn, the regulation of PI4,5P 2 effectors at specific cellular compartments has implications for understanding how PI4,5P 2 controls cellular processes and its role in diseases. Site-directed synthesis of phosphatidylinositol-4,5-bisphosphate (PI4,5P 2 ) at distinct sub-cellular compartments mediates a variety of events, such as migration, cell-cell adhesion, transcription and vesicle trafficking. PI4,5P 2 regulated processes are critical for function at the cellular level, which is evident in neurons, platelet, and macrophage function.

Description: The increased incidence of morbidity and mortality due to Clostridium difficile infection, had led to the emergence of fecal microbial transplantation (FMT) as a highly successful treatment. From this, a 32 strain stool substitute has been derived, and successfully tested in a pilot human study. These approaches could revolutionize not only medical care of infectious diseases, but potentially many other conditions linked to the human microbiome. But a second revolution may be needed in order for regulatory agencies, society and medical practitioners to accept and utilize these interventions, monitor their long term effects, have a degree of control over their use, or at a minimum provide guidelines for donors and recipients. If a simple replacement of your gut microbiota by someone else's could improve your health and ability to function, would you do it? How would you select the donor and would the “authorities” let you perform the transplant? The age of the microbiome is here, but is society ready?

Description: Many species maintain cytosine DNA methyltransferase (MTase) genes belonging to the Dnmt2 family. Prokaryotic modification-restriction systems utilize DNA methylation to distinguish between self and foreign DNA, and cytosine methylation in eukaryotic DNA contributes to epigenetic mechanisms that control gene expression. However, Dnmt2 proteins display only low or no DNA MTase activity, making this protein family the odd and enigmatic family member. Recent evidence showed that Dnmt2 proteins are not DNA but RNA MTases with functions in biological processes as diverse as stress responses and RNA-mediated inheritance. These observations not only raise profound questions regarding the perceived substrate specificities of cytosine MTase, but also suggest links between DNA and RNA modification systems. Here, we speculate that Dnmt2 proteins might be part of an ancient cytosine modification toolbox that is used to successfully respond to environmental challenges, including constantly evolving RNA and DNA substrates. Recent observations indicated that Dnmt2 proteins, which belong to a highly conserved DNA cytosine methyltransferase family, are important for the response to RNA-based stressors, including transposons, viruses, and experimentally introduced small RNAs. Is Dnmt2 part of an ancient defense system that employs nucleotide modifications against invading pathogens?

Description: Inflammatory immune cells, when activated, display much the same metabolic profile as a glycolytic tumor cell. This involves a shift in metabolism away from oxidative phosphorylation towards aerobic glycolysis, a phenomenon known as the Warburg effect. The result of this change in macrophages is to rapidly provide ATP and metabolic intermediates for the biosynthesis of immune and inflammatory proteins. In addition, a rise in certain tricarboxylic acid cycle intermediates occurs notably in citrate for lipid biosynthesis, and succinate, which activates the transcription factor Hypoxia-inducible factor. In this review we take a look at the emerging evidence for a role for the Warburg effect in the immune and inflammatory responses. The reprogramming of metabolic pathways in macrophages, dendritic cells, and T cells could have relevance in the pathogenesis of inflammatory and metabolic diseases and might provide novel therapeutic strategies. Recent studies reveal that inflammatory cells, when activated, display similar metabolic traits as cancer cells. During an inflammatory response or infection pro-inflammatory immune cells can shift their metabolism away from oxidative phosphorylation towards a high rate of glycolysis, a phenomenon known as the Warburg effect.

Description: The fast advancing RNA-seq technology has unveiled an unexpected diversity and expression specificity of 3′ untranslated regions (3′UTRs) of mRNAs. In particular, neural mRNAs seem to express significantly longer 3′UTRs, some of which are over 10 kb in length. The extensive elongation of 3′UTRs in neural tissues provides intriguing possibilities for cell type-specific regulations that are governed by miRNAs, RNA-binding proteins and ribonucleoprotein aggregates. In this article, we review recent progress in the characterization of mRNA 3′UTRs and discuss their implications in the understanding of 3′UTR-mediated gene regulation. Differential expression of short and long 3′UTRs, especially in neurons, presents technical challenges for experimental characterization. Such dynamic expression of 3′UTR isoforms, however, provides a mechanism to regulate protein production of both individual and a pool of transcripts in physiological and pathological conditions.

Description: The segregation of damaged components at cell division determines the survival and aging of cells. In cells that divide asymmetrically, such as Saccharomyces cerevisiae , aggregated proteins are retained by the mother cell. Yet, where and how aggregation occurs is not known. Recent work by Zhou and collaborators shows that the birth of protein aggregates, under specific stress conditions, requires active translation, and occurs mainly at the endoplasmic reticulum. Later, aggregates move to the mitochondrial surface through fis1-dependent association. During replicative aging, aggregate association with the mother-cell mitochondria contributes to the asymmetric segregation of aggregates, because mitochondria in the daughter cell do not carry aggregates. With increasing age of mother cells, aggregates lose their connection to the mitochondria, and segregation is less asymmetric. Relating these findings to other mechanisms of aggregate segregation in different organisms, we postulate that fusion between aggregates and their tethering to organelles such as the vacuole, nucleus, ER, or mitochondria are common principles that establish asymmetric segregation during stress resistance and aging. Protein aggregates move by diffusion in the cytoplasm, on the surface of organelles such as mitochondria, or by active transport. Movement of aggregates leads to their fusion with one another, which results in asymmetric segregation at division, where one cell inherits the aggregate while the other one is born clean.

Description: You are what you eat – this well-known phrase properly describes the phenomenon of the effects of diet on acute and chronic inflammation. Several lipids and lipophilic compounds that are delivered with food or are produced in situ in pathological conditions exert immunomodulatory activity due to their interactions with the plasma membrane. This group of compounds includes cholesterol and its oxidized derivatives, fatty acids, α-tocopherol, and polyphenols. Despite their structural heterogeneity, all these compounds ultimately induce changes in plasma membrane architecture and fluidity. By doing this, they modulate the dynamics of plasma membrane receptors, such as TLR4. This receptor is activated by lipopolysaccharide, triggering acute inflammation during bacterial infection, which often leads to sepsis and is linked with diverse chronic inflammatory diseases. In this review, we discuss how the impact on plasma membrane properties contributes to the immunomodulatory activity of dietary compounds, pointing to the therapeutic potential of some of them. Cholesterol, saturated, and trans fatty acids, abundant in “westernized” diet, can impact the architecture of plasma membrane rafts, a process that ultimately potentiates LPS-induced pro-inflammatory signaling of TLR4. A therapeutic effect can be achieved by enrichment of the diet with anti-inflammatory compounds affecting membrane organization, like α-tocopherol, polyunsaturated fatty acids, and polyphenols.

Description: Dynamic interactions with DNA allow replication protein A to direct single-stranded DNA-intermediates into different pathways for synthesis or repair. On pages 1156–1161 , Chen and Wold review recent discoveries that show that replication protein A (RPA), the major eukaryotic single-stranded DNA-binding protein, binds DNA dynamically and that this is important for correct processing of DNA intermediates. The cover shows a model of human RPA interacting with ssDNA based on the known structures of the domains of human RPA and the structure of Ustalago RPA bound to DNA. The three subunits of RPA are shown in blue (RPA1), red (RPA2), and green (RPA3) with ssDNA shown in black.