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  • 1
    Publication Date: 2013-12-07
    Description: In individual cells, transcription is a random process obeying single-molecule kinetics. Often, it occurs in a bursty, intermittent manner. The frequency and size of these bursts affect the magnitude of temporal fluctuations in messenger RNA and protein content within a cell, creating variation or "noise" in gene expression. It is still unclear to what degree transcriptional kinetics are specific to each gene and determined by its promoter sequence. Alternative scenarios have been proposed, in which the kinetics of transcription are governed by cellular constraints and follow universal rules across the genome. Evidence from genome-wide noise studies and from systematic perturbations of promoter sequences suggest that both scenarios-namely gene-specific versus genome-wide regulation of transcription kinetics-may be present to different degrees in bacteria, yeast, and animal cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045091/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045091/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanchez, Alvaro -- Golding, Ido -- R01 GM082837/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 6;342(6163):1188-93. doi: 10.1126/science.1242975.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24311680" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Escherichia coli/genetics/metabolism ; Eukaryota/genetics/metabolism ; *Gene Expression Regulation ; Genome ; Kinetics ; Models, Genetic ; Promoter Regions, Genetic ; RNA, Messenger/genetics/metabolism ; Single-Cell Analysis ; Stochastic Processes ; *Transcription, Genetic ; Yeasts/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2015-09-04
    Description: MYC (also known as c-MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. MYC is a transcription factor, and many of its pro-tumorigenic functions have been attributed to its ability to regulate gene expression programs. Notably, oncogenic MYC activation has also been shown to increase total RNA and protein production in many tissue and disease contexts. While such increases in RNA and protein production may endow cancer cells with pro-tumour hallmarks, this increase in synthesis may also generate new or heightened burden on MYC-driven cancer cells to process these macromolecules properly. Here we discover that the spliceosome is a new target of oncogenic stress in MYC-driven cancers. We identify BUD31 as a MYC-synthetic lethal gene in human mammary epithelial cells, and demonstrate that BUD31 is a component of the core spliceosome required for its assembly and catalytic activity. Core spliceosomal factors (such as SF3B1 and U2AF1) associated with BUD31 are also required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces an increase in total precursor messenger RNA synthesis, suggesting an increased burden on the core spliceosome to process pre-mRNA. In contrast to normal cells, partial inhibition of the spliceosome in MYC-hyperactivated cells leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of many essential cell processes. Notably, genetic or pharmacological inhibition of the spliceosome in vivo impairs survival, tumorigenicity and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing, and that components of the spliceosome may be therapeutic entry points for aggressive MYC-driven cancers.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hsu, Tiffany Y-T -- Simon, Lukas M -- Neill, Nicholas J -- Marcotte, Richard -- Sayad, Azin -- Bland, Christopher S -- Echeverria, Gloria V -- Sun, Tingting -- Kurley, Sarah J -- Tyagi, Siddhartha -- Karlin, Kristen L -- Dominguez-Vidana, Rocio -- Hartman, Jessica D -- Renwick, Alexander -- Scorsone, Kathleen -- Bernardi, Ronald J -- Skinner, Samuel O -- Jain, Antrix -- Orellana, Mayra -- Lagisetti, Chandraiah -- Golding, Ido -- Jung, Sung Y -- Neilson, Joel R -- Zhang, Xiang H-F -- Cooper, Thomas A -- Webb, Thomas R -- Neel, Benjamin G -- Shaw, Chad A -- Westbrook, Thomas F -- 1F30CA180447/CA/NCI NIH HHS/ -- 1R01CA178039-01/CA/NCI NIH HHS/ -- P30 AI036211/AI/NIAID NIH HHS/ -- P30CA125123/CA/NCI NIH HHS/ -- R01 AR045653/AR/NIAMS NIH HHS/ -- R01 AR060733/AR/NIAMS NIH HHS/ -- R01 CA140474/CA/NCI NIH HHS/ -- R01 HL045565/HL/NHLBI NIH HHS/ -- S10 RR024574/RR/NCRR NIH HHS/ -- U54-CA149196/CA/NCI NIH HHS/ -- England -- Nature. 2015 Sep 17;525(7569):384-8. doi: 10.1038/nature14985. Epub 2015 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA. ; Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA. ; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA. ; Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada. ; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Physics, University of Illinois, Urbana, Illinois 61801, USA. ; Center for Chemical Biology, Bioscience Division, SRI International, Menlo Park, California 94025, USA. ; The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Medical Biophysics, University of Toronto, Toronto M5S 2J7, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26331541" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breast Neoplasms/*drug therapy/*genetics/pathology ; Cell Line, Tumor ; Cell Survival/drug effects ; Cell Transformation, Neoplastic/drug effects ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Genes, myc/*genetics ; HeLa Cells ; Humans ; Introns/genetics ; Mice ; Mice, Nude ; Neoplasm Metastasis/drug therapy ; Nuclear Proteins/metabolism ; Phosphoproteins/metabolism ; Proto-Oncogene Proteins c-myc/genetics/metabolism ; RNA Precursors/biosynthesis/genetics ; RNA Splicing/drug effects ; RNA, Messenger/biosynthesis/genetics ; Ribonucleoprotein, U2 Small Nuclear/metabolism ; Ribonucleoproteins/metabolism ; Spliceosomes/*drug effects/*metabolism ; Xenograft Model Antitumor Assays
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2011-12-14
    Description: Myc is an oncogenic transcription factor frequently dysregulated in human cancer. To identify pathways supporting the Myc oncogenic program, we used a genome-wide RNA interference screen to search for Myc-synthetic lethal genes and uncovered a role for the SUMO-activating enzyme (SAE1/2). Loss of SAE1/2 enzymatic activity drives synthetic lethality with Myc. Inactivation of SAE2 leads to mitotic catastrophe and cell death upon Myc hyperactivation. Mechanistically, SAE2 inhibition switches a transcriptional subprogram of Myc from activated to repressed. A subset of these SUMOylation-dependent Myc switchers (SMS genes) is required for mitotic spindle function and to support the Myc oncogenic program. SAE2 is required for growth of Myc-dependent tumors in mice, and gene expression analyses of Myc-high human breast cancers suggest that low SAE1 and SAE2 abundance in the tumors correlates with longer metastasis-free survival of the patients. Thus, inhibition of SUMOylation may merit investigation as a possible therapy for Myc-driven human cancers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059214/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059214/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kessler, Jessica D -- Kahle, Kristopher T -- Sun, Tingting -- Meerbrey, Kristen L -- Schlabach, Michael R -- Schmitt, Earlene M -- Skinner, Samuel O -- Xu, Qikai -- Li, Mamie Z -- Hartman, Zachary C -- Rao, Mitchell -- Yu, Peng -- Dominguez-Vidana, Rocio -- Liang, Anthony C -- Solimini, Nicole L -- Bernardi, Ronald J -- Yu, Bing -- Hsu, Tiffany -- Golding, Ido -- Luo, Ji -- Osborne, C Kent -- Creighton, Chad J -- Hilsenbeck, Susan G -- Schiff, Rachel -- Shaw, Chad A -- Elledge, Stephen J -- Westbrook, Thomas F -- CA149196/CA/NCI NIH HHS/ -- P30 CA125123/CA/NCI NIH HHS/ -- P50 CA058183/CA/NCI NIH HHS/ -- R01 GM082837/GM/NIGMS NIH HHS/ -- R01GM082837/GM/NIGMS NIH HHS/ -- T32CA090221-09/CA/NCI NIH HHS/ -- T32HD05520/HD/NICHD NIH HHS/ -- U54 CA149196/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Jan 20;335(6066):348-53. doi: 10.1126/science.1212728. Epub 2011 Dec 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22157079" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breast Neoplasms/*genetics/metabolism/mortality/pathology ; Cell Cycle ; Cell Line, Tumor ; *Cell Transformation, Neoplastic ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; *Genes, myc ; Humans ; Mammary Neoplasms, Experimental/genetics/metabolism/mortality/pathology ; Mice ; Mice, Nude ; Mitosis ; Neoplasm Transplantation ; Proto-Oncogene Proteins c-myc/*metabolism ; RNA Interference ; RNA, Small Interfering ; Spindle Apparatus/physiology ; Sumoylation ; *Transcription, Genetic ; Transplantation, Heterologous ; Ubiquitin-Activating Enzymes/antagonists & inhibitors/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2015-03-21
    Description: Base-pairing interactions between nucleic acids mediate target recognition in many biological processes. We developed a super-resolution imaging and modeling platform that enabled the in vivo determination of base pairing-mediated target recognition kinetics. We examined a stress-induced bacterial small RNA, SgrS, which induces the degradation of target messenger RNAs (mRNAs). SgrS binds to a primary target mRNA in a reversible and dynamic fashion, and formation of SgrS-mRNA complexes is rate-limiting, dictating the overall regulation efficiency in vivo. Examination of a secondary target indicated that differences in the target search kinetics contribute to setting the regulation priority among different target mRNAs. This super-resolution imaging and analysis approach provides a conceptual framework that can be generalized to other small RNA systems and other target search processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410144/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410144/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fei, Jingyi -- Singh, Digvijay -- Zhang, Qiucen -- Park, Seongjin -- Balasubramanian, Divya -- Golding, Ido -- Vanderpool, Carin K -- Ha, Taekjip -- GM 112659/GM/NIGMS NIH HHS/ -- GM065367/GM/NIGMS NIH HHS/ -- GM082837/GM/NIGMS NIH HHS/ -- GM092830/GM/NIGMS NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- R01 GM082837/GM/NIGMS NIH HHS/ -- R01 GM092830/GM/NIGMS NIH HHS/ -- R01 GM112659/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Mar 20;347(6228):1371-4. doi: 10.1126/science.1258849.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. ; Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA. ; Department of Microbiology, University of Illinois, Urbana, IL, USA. ; Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA. ; Department of Microbiology, University of Illinois, Urbana, IL, USA. tjha@illinois.edu cvanderp@life.uiuc.edu. ; Center for the Physics of Living Cells, Department of Physics, University of Illinois, Urbana, IL, USA. Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL, USA. Carl R. Woese Institute for Genomic Biology, Howard Hughes Medical Institute, Urbana, IL, USA. Howard Hughes Medical Institute, Urbana, IL, USA. tjha@illinois.edu cvanderp@life.uiuc.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25792329" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Pairing ; Endoribonucleases/chemistry/genetics ; Escherichia coli/genetics/metabolism ; Kinetics ; Molecular Imaging/*methods ; Mutation ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics ; *RNA Stability ; RNA, Messenger/*chemistry ; RNA, Small Untranslated/*chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2016-03-12
    Description: In vivo mapping of transcription-factor binding to the transcriptional output of the regulated gene is hindered by probabilistic promoter occupancy, the presence of multiple gene copies, and cell-to-cell variability. We demonstrate how to overcome these obstacles in the lysogeny maintenance promoter of bacteriophage lambda, P(RM). We simultaneously measured the concentration of the lambda repressor CI and the number of messenger RNAs (mRNAs) from P(RM) in individual Escherichia coli cells, and used a theoretical model to identify the stochastic activity corresponding to different CI binding configurations. We found that switching between promoter configurations is faster than mRNA lifetime and that individual gene copies within the same cell act independently. The simultaneous quantification of transcription factor and promoter activity, followed by stochastic theoretical analysis, provides a tool that can be applied to other genetic circuits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806797/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806797/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sepulveda, Leonardo A -- Xu, Heng -- Zhang, Jing -- Wang, Mengyu -- Golding, Ido -- R01 GM082837/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 Mar 11;351(6278):1218-22. doi: 10.1126/science.aad0635. Epub 2016 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA. ; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA. Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA. ; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA. Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA. Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. golding@bcm.edu igolding@illinois.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26965629" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/genetics ; Escherichia coli/genetics/virology ; Gene Dosage ; *Gene Expression Regulation ; Lysogeny/genetics ; Models, Theoretical ; Probability ; Promoter Regions, Genetic/*physiology ; RNA, Messenger/biosynthesis ; Repressor Proteins/metabolism ; Single-Cell Analysis ; Stochastic Processes ; Transcription Factors/*metabolism ; Transcription, Genetic ; Viral Regulatory and Accessory Proteins/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Electronic Resource
    Electronic Resource
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1019-1020 
    ISSN: 1600-5759
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
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  • 7
    Publication Date: 2005-06-30
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 8
    Publication Date: 2004-07-26
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
    Publication Date: 2012-06-07
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2015-12-02
    Description: DksA is an auxiliary transcription factor that interacts with RNA polymerase and influences gene expression. Depending on the promoter, DksA can be a positive or negative regulator of transcription initiation. Moreover, DksA has a substantial effect on transcription elongation where it prevents the collision of transcription and replication machineries, plays a key role in maintaining transcription elongation when translation and transcription are uncoupled and has been shown to be involved in transcription fidelity. Here, we assessed the role of DksA in transcription fidelity by monitoring stochastic epigenetic switching in the lac operon (with and without an error-prone transcription slippage sequence), partial phenotypic suppression of a lacZ nonsense allele, as well as monitoring the number of lacI mRNA transcripts produced in the presence and absence of DksA via an operon fusion and single molecule fluorescent in situ hybridization studies. We present data showing that DksA acts to maintain transcription fidelity in vivo and the role of DksA seems to be distinct from that of the GreA and GreB transcription fidelity factors.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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