ALBERT

Description: Dominant mutations in transactive response DNA-binding protein-43 (TDP-43) cause amyotrophic lateral sclerosis. TDP-43 inclusions occur in neurons, glia and muscle in this disease and in sporadic and inherited forms of frontotemporal lobar degeneration. Cytoplasmic localization, cleavage, aggregation and phosphorylation of TDP-43 at the Ser409/410 epitope have been associated with disease pathogenesis. TDP-43 aggregation is not a common feature of mouse models of TDP-43 proteinopathy, and TDP-43 is generally not thought to acquire an amyloid conformation or form fibrils. A number of putative TDP-43 kinases have been identified, but whether any of these functions to regulate TDP-43 phosphorylation or toxicity in vivo is not known. Here, we demonstrate that human TDP-43 Q331K undergoes cytoplasmic localization and aggregates when misexpressed in Drosophila when compared with wild-type and M337V forms. Coexpression of Q331K with doubletime (DBT), the fly homolog of casein kinase I (CKI), enhances toxicity. There is at best modest basal phosphorylation of misexpressed human TDP-43 in Drosophila , but coexpression with DBT increases Ser409/410 phosphorylation of all TDP-43 isoforms tested. Phosphorylation of TDP-43 in the fly is specific for DBT, as it is not observed using the validated tau kinases GSK-3β, PAR-1/MARK2 or CDK5. Coexpression of DBT with TDP-43 Q331K enhances the formation of high-molecular weight oligomeric species coincident with enhanced toxicity, and treatment of recombinant oligomeric TDP-43 with rat CKI strongly enhances its toxicity in mammalian cell culture. These data identify CKI as a potent TDP-43 kinase in vivo and implicate oligomeric species as the toxic entities in TDP-43 proteinopathies.

Description: A transcriptional attenuation mechanism regulates expression of the bacterial tnaCAB operon. This mechanism requires ribosomal arrest induced by the regulatory nascent TnaC peptide in response to free L-tryptophan (L-Trp). In this study we demonstrate, using genetic and biochemical analyses, that in Escherichia coli , TnaC residue I19 and 23S rRNA nucleotide A2058 are essential for the ribosome’s ability to sense free L-Trp. We show that the mutational change A2058U in 23S rRNA reduces the concentration dependence of L-Trp-mediated tna operon induction, whereas the TnaC I19L change suppresses this phenotype, restoring the sensitivity of the translating A2058U mutant ribosome to free L-Trp. These findings suggest that interactions between TnaC residue I19 and 23S rRNA nucleotide A2058 contribute to the creation of a regulatory L-Trp binding site within the translating ribosome.

Description: Poly(ADP-ribose) polymerases (PARP) attach poly(ADP-ribose) (PAR) chains to various proteins including themselves and chromatin. Topoisomerase I (Top1) regulates DNA supercoiling and is the target of camptothecin and indenoisoquinoline anticancer drugs, as it forms Top1 cleavage complexes (Top1cc) that are trapped by the drugs. Endogenous and carcinogenic DNA lesions can also trap Top1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1), a key repair enzyme for trapped Top1cc, hydrolyzes the phosphodiester bond between the DNA 3'-end and the Top1 tyrosyl moiety. Alternative repair pathways for Top1cc involve endonuclease cleavage. However, it is unknown what determines the choice between TDP1 and the endonuclease repair pathways. Here we show that PARP1 plays a critical role in this process. By generating TDP1 and PARP1 double-knockout lymphoma chicken DT40 cells, we demonstrate that TDP1 and PARP1 are epistatic for the repair of Top1cc. The N-terminal domain of TDP1 directly binds the C-terminal domain of PARP1, and TDP1 is PARylated by PARP1. PARylation stabilizes TDP1 together with SUMOylation of TDP1. TDP1 PARylation enhances its recruitment to DNA damage sites without interfering with TDP1 catalytic activity. TDP1–PARP1 complexes, in turn recruit X-ray repair cross-complementing protein 1 (XRCC1). This work identifies PARP1 as a key component driving the repair of trapped Top1cc by TDP1.

Description: Chromosomes within eukaryotic cell nuclei at interphase are not positioned at random, since gene-rich chromosomes are predominantly found towards the interior of the cell nucleus across a number of cell types. The physical mechanisms that could drive and maintain the spatial segregation of chromosomes based on gene density are unknown. Here, we identify a mechanism for such segregation, showing that the territorial organization of chromosomes, another central feature of nuclear organization, emerges naturally from our model. Our computer simulations indicate that gene density-dependent radial segregation of chromosomes arises as a robust consequence of differences in non-equilibrium activity across chromosomes. Arguing that such differences originate in the inhomogeneous distribution of ATP-dependent chromatin remodeling and transcription machinery on each chromosome, we show that a variety of non-random positional distributions emerge through the interplay of such activity, nuclear shape and specific interactions of chromosomes with the nuclear envelope. Results from our model are in reasonable agreement with experimental data and we make a number of predictions that can be tested in experiments.

Description: We present results from our Giant Metrewave Radio Telescope (GMRT) H i observations of the interacting pair Arp 202 (NGC 2719 and NGC 2719A). Earlier deep ultraviolet ( Galaxy Evolution Explorer ) observations of this system revealed a tidal-tail-like extension with a diffuse object towards its end, proposed as a tidal dwarf galaxy (TDG) candidate. We detect H i emission from the Arp 202 system, including H i counterparts for the tidal tail and the TDG candidate. Our GMRT H i morphological and kinematic results clearly link the H i tidal tail and the H i TDG counterparts to the interaction between NGC 2719 and NGC 2719A, thus strengthening the case for the TDG. The Arp 202 TDG candidate belongs to a small group of TDG candidates with extremely blue colours. In order to gain a better understanding of this group we carried out a comparative study of their properties from the available data. We find that H i (and probably stellar) masses of this extremely blue group are similar to the lowest H i mass TDGs in the literature. However the number of such blue TDG candidates examined so far is too small to conclude whether or not their properties justify them to be considered as a subgroup of TDGs.

Description: Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto–Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India.

Description: A major fraction of the transcriptome of higher organisms comprised an extensive repertoire of long non-coding RNA (lncRNA) which express in a cell type and development stage-specific manner. While lncRNAs are a proven component of epigenetic gene expression modulation, epigenetic regulation of lncRNA itself remains poorly understood. Here we have analysed pan-genomic DNA methylation and histone modification marks (H3K4me3, H3K9me3, H3K27me3 and H3K36me3) associated with transcription start site (TSS) of lncRNA in four different cell types and three different tissue types representing various cellular stages. We observe that histone marks associated with active transcription H3K4me3 and H3K36me3 along with the repressive histone mark H3K27me3 have similar distribution pattern around TSS irrespective of cell types. Also, the density of these marks correlates well with expression of protein-coding and lncRNA genes. In contrast, the lncRNA genes harbour higher methylation density around TSS than protein-coding genes regardless of their expression status. Furthermore, we found that DNA methylation along with the other repressive histone mark H3K9me3 does not seem to play a role in lncRNA expression. Thus, our observation suggests that epigenetic regulation of lncRNA shares common features with mRNA except the role of DNA methylation which is markedly dissimilar.

Description: An exposure of polyphase, Neoarchaean–early Palaeoproterozoic basement rocks has been identified in the northeastern part (10°53·44'N, 78°22·88'E) of the Madurai Province. The dominant migmatitic charnockite contains older enclaves of isoclinally folded syenitic biotite gneiss and boudinaged mafic dykes. A highly evolved (Mg# 10) and high field strength element (HFSE) + rare earth element (REE)-enriched ferroan basic dyke body exhibits a distinct mineralogical zonation produced during intense syn-boudinage infiltration metasomatism, coeval with high-grade metamorphism and anatexis of the host charnockite. Core domains that preserve an anhydrous granulite assemblage (domain A: garnet, clinopyroxene and minor plagioclase) grade through a narrow mineralogical transition zone (domain B) into a broad amphibole-rich rind (domain C: ferropargasite + K-feldspar ± plagioclase, quartz). Pseudosection modelling and thermobarometry yields P – T estimates of ~800 °C, 8 kbar for the granulite-facies metamorphism (M 1 ) and ~730 °C, 7 kbar for the high-grade metasomatism (M 2 ). The changes in fabric, mineral assemblage and whole-rock chemistry across domains A to C reveal near-isovolumetric–isochoric conditions of infiltration-driven metasomatism and an unusual enrichment in large ion lithophile elements (LILE), REE, and HFSE, causing prolific neoblastesis of apatite and zircon, and attest attainment of chemical equilibrium. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) trace element analyses for major constituents and accessory phases in the metasomatic domains provide a new set of equilibrium distribution coefficients for the REE. LA-ICP-MS spot analyses of zircon in well-documented microstructural settings identified the following events: ~2·67 Ga: intrusions of foid-bearing syenite and ferroan basic dykes during crustal extension; ~2·6 Ga: high-grade metamorphism M 1 ; ~2·6 Ga: emplacement of voluminous arc-type intrusions (the protolith of charnockite); ~2·48 Ga: high-grade metamorphism and anatexis M 2 of the charnockite protolith and metasomatism of the ferroan metabasite. A distinct Pan-African overprint (M 3 , ~610 Ma, 520 Ma) of the Palaeoproterozoic high-pressure rocks is manifested by hydration related to the exhumation of the deep-seated granulites to mid-crustal levels. This study confirms the continuation of Neoarchaean crust farther south beyond the perceived Palghat Cauvery shear zone system and contradicts the view that this shear zone system represents the Neoproterozoic–Cambrian suture zone along which the Mozambique Ocean was closed.

Description: Topoisomerase 1 (Top1) is essential for removing the DNA supercoiling generated during replication and transcription. Anticancer drugs like camptothecin (CPT) and its clinical derivatives exert their cytotoxicity by reversibly trapping Top1 in covalent complexes on the DNA (Top1cc). Poly(ADP-ribose) polymerase (PARP) catalyses the addition of ADP-ribose polymers (PAR) onto itself and Top1. PARP inhibitors enhance the cytotoxicity of CPT in the clinical trials. However, the molecular mechanism by which PARylation regulates Top1 nuclear dynamics is not fully understood. Using live-cell imaging of enhanced green fluorescence tagged-human Top1, we show that PARP inhibitors (Veliparib, ABT-888) delocalize Top1 from the nucleolus to the nucleoplasm, which is independent of Top1–PARP1 interaction. Using fluorescence recovery after photobleaching and subsequent fitting of the data employing kinetic modelling we demonstrate that ABT-888 markedly increase CPT-induced bound/immobile fraction of Top1 (Top1cc) across the nuclear genome, suggesting Top1-PARylation counteracts CPT-induced stabilization of Top1cc. We further show Trp205 and Asn722 of Top1 are critical for subnuclear dynamics. Top1 mutant (N722S) was restricted to the nucleolus in the presence of CPT due to its deficiency in the accumulation of CPT-induced Top1-PARylation and Top1cc formation. This work identifies ADP-ribose polymers as key determinant for regulating Top1 subnuclear dynamics.