MECHANISMS OF EUKARYOTIC TRANSCRIPTIONAL REGULATION

Summary

Principal Investigator: Michael R Green
Abstract: DESCRIPTION (provided by applicant): Mechanisms of Eukaryotic Transcriptional Regulation Abstract In eukaryotes, gene regulation is largely controlled at the transcriptional level through multiple, distinct mechanisms. Transcription initiation by RNA polymerase II involves the assembly of general transcription factors on the core promoter to form a preinitiation complex (PIC). A variety of studies indicate that promoter-specific activator proteins (activators) work, at least in part, by increasing PIC assembly, which results from a direct interaction between the activator and one or more components of the transcription machinery. It has become increasingly evident that transcription is also regulated by alterations in the general transcription machinery. Our laboratory was the first to identify a vertebrate-specific TATA-box-binding protein (TBP)-related factor, TRF3. During the past funding period we have found that Trf3-depleted zebrafish embryos exhibit multiple developmental defects and, in particular, fail to undergo hematopoiesis. We have identified a single TRF3 target gene, mespa, which is required for early embryonic development and commitment of mesoderm to the hematopoietic lineage. We will continue to study the role of TRF3 and TRF3-containing complexes in transcription regulation, early development and hematopoiesis. We seek to understand how TRF3 is selectively recruited to specific target genes, identify the components of the TRF3 complex, and determine how TRF3 and TBP are incorporated into distinct multisubunit complexes. Recently, we have found that alterations in the general transcription machinery may play an important role in human embryonic stem cells (hESCs). Specifically, we have obtained several lines of evidence that hESCs lack the canonical TFIID complex and instead use an "alternative TFIID complex" for expression of protein- coding genes. Experiments are proposed to characterize and study this alternative TFIID complex and its role in hESC biology. We will determine the composition of the alternative TFIID complex, and the role of its individual components in hESC self- renewal and differentiation. In mammalian cells, the transcriptional activity of many genes is controlled by epigenetic mechanisms that involve histone modifications and DNA methylation. The detailed mechanisms and pathways by which epigenetic repression is established and maintained on specific genes remain to be elucidated. During the past funding period, we have performed a genome-wide shRNA screen to identify 28 factors required for epigenetic silencing of Fas, and a select group of other genes, in ras-transformed NIH 3T3 cells. This model system, in conjunction with the experimental reagents we have developed, provides a unique opportunity to study the detailed mechanisms by which an epigenetically repressed state is established and maintained on a select group of genes. Experiments are proposed to understand how multiple factors act cooperatively to establish and maintain an epigenetically repressed state and the basis by which only a small subset of genes are silenced. PUBLIC HEALTH RELEVANCE: In eukaryotes, gene regulation is largely controlled at the transcriptional level through multiple, distinct mechanisms. Transcriptional regulation is highly relevant to numerous human diseases, including inborn errors of metabolism, birth defects, viral infections and cancer. The experiments proposed in this application will increase our understanding of eukaryotic transcriptional regulatory mechanisms. A specific objective of the application is to study the mechanism by which tumor suppressor genes become transcriptionally silenced during cancer development.
Funding Period: 1990-07-01 - 2015-03-31
more information: NIH RePORT

Top Publications

  1. pmc An elaborate pathway required for Ras-mediated epigenetic silencing
    Claude Gazin
    Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
    Nature 449:1073-7. 2007
  2. pmc Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans
    Giorgio Pistis
    Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
    PLoS ONE 8:e69206. 2013
  3. pmc MEN1 is a melanoma tumor suppressor that preserves genomic integrity by stimulating transcription of genes that promote homologous recombination-directed DNA repair
    Minggang Fang
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Mol Cell Biol 33:2635-47. 2013
  4. pmc GABP transcription factor is required for development of chronic myelogenous leukemia via its control of PRKD2
    Zhong fa Yang
    Division of Hematology Oncology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
    Proc Natl Acad Sci U S A 110:2312-7. 2013
  5. pmc A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells
    Li Xie
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    PLoS Genet 8:e1003151. 2012
  6. pmc Non-canonical TAF complexes regulate active promoters in human embryonic stem cells
    Glenn A Maston
    Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, United States Howard Hughes Medical Institute, Chevy Chase, United States
    elife 1:e00068. 2012
  7. ncbi Characterization of enhancer function from genome-wide analyses
    Glenn A Maston
    Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Annu Rev Genomics Hum Genet 13:29-57. 2012
  8. pmc Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4
    Ling Lin
    Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Proc Natl Acad Sci U S A 109:1997-2002. 2012
  9. pmc Maternal Rnf12/RLIM is required for imprinted X-chromosome inactivation in mice
    Jongdae Shin
    Program in Gene Function and Expression, University of Massachusetts Medical School UMMS, Worcester, Massachusetts 01605, USA
    Nature 467:977-81. 2010
  10. pmc ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
    Lihua J Zhu
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    BMC Bioinformatics 11:237. 2010

Research Grants

  1. Mechanism of Chromatin Organization and Dynamics in Development
    Xiaole Shirley Liu; Fiscal Year: 2013
  2. Cadiorenal and Metabolic Diseases Research Center
    John E Hall; Fiscal Year: 2013
  3. Histone Modifications During Embryogenesis
    Alexander F Schier; Fiscal Year: 2013

Detail Information

Publications14

  1. pmc An elaborate pathway required for Ras-mediated epigenetic silencing
    Claude Gazin
    Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
    Nature 449:1073-7. 2007
    ..Our results show that Ras-mediated epigenetic silencing occurs through a specific, complex, pathway involving components that are required for maintenance of a fully transformed phenotype...
  2. pmc Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans
    Giorgio Pistis
    Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
    PLoS ONE 8:e69206. 2013
    ..Finally, TAF3 represents a potential candidate or a modifier gene for disorders of red cell membrane. ..
  3. pmc MEN1 is a melanoma tumor suppressor that preserves genomic integrity by stimulating transcription of genes that promote homologous recombination-directed DNA repair
    Minggang Fang
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Mol Cell Biol 33:2635-47. 2013
    ..Collectively, our results indicate that MEN1 is a melanoma tumor suppressor that functions by stimulating the transcription of genes involved in HR-directed DNA repair...
  4. pmc GABP transcription factor is required for development of chronic myelogenous leukemia via its control of PRKD2
    Zhong fa Yang
    Division of Hematology Oncology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
    Proc Natl Acad Sci U S A 110:2312-7. 2013
    ..Thus, GABP is required for HSC cell cycle entry and CML development through its control of PRKD2. This offers a potential therapeutic target in leukemia...
  5. pmc A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells
    Li Xie
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    PLoS Genet 8:e1003151. 2012
    ..Our collective results identify a regulatory pathway involving ETV1, ATR, and TERT that is preferentially important for proliferation of diverse p53- cancer cells...
  6. pmc Non-canonical TAF complexes regulate active promoters in human embryonic stem cells
    Glenn A Maston
    Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, United States Howard Hughes Medical Institute, Chevy Chase, United States
    elife 1:e00068. 2012
    ..Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew.DOI:http://dx.doi.org/10.7554/eLife.00068.001...
  7. ncbi Characterization of enhancer function from genome-wide analyses
    Glenn A Maston
    Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Annu Rev Genomics Hum Genet 13:29-57. 2012
    ..Going forward, the integration of multiple genome-wide data sets should become a standard approach to elucidate higher-order regulatory interactions...
  8. pmc Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4
    Ling Lin
    Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Proc Natl Acad Sci U S A 109:1997-2002. 2012
    ..Finally, we show that although Tra1 is targeted by other activators, these interactions are unaffected by GID mutations, revealing an unanticipated specificity of the Gal4-Tra1 interaction...
  9. pmc Maternal Rnf12/RLIM is required for imprinted X-chromosome inactivation in mice
    Jongdae Shin
    Program in Gene Function and Expression, University of Massachusetts Medical School UMMS, Worcester, Massachusetts 01605, USA
    Nature 467:977-81. 2010
    ..These results assign crucial functions to the maternal deposit of Rnf12/RLIM for the initiation of imprinted XCI...
  10. pmc ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
    Lihua J Zhu
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    BMC Bioinformatics 11:237. 2010
    ..However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome...
  11. pmc Epigenetic silencing of the RASSF1A tumor suppressor gene through HOXB3-mediated induction of DNMT3B expression
    Rajendra Kumar Palakurthy
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
    Mol Cell 36:219-30. 2009
    ..Analysis of human cancer cell lines indicates that the RASSF1A epigenetic silencing mechanism described here may be common in diverse cancer types...
  12. pmc Selective interaction between Trf3 and Taf3 required for early development and hematopoiesis
    Daniel O Hart
    Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Dev Dyn 238:2540-9. 2009
    ..Thus, a selective interaction between Trf3 and Taf3 is required for early zebrafish development and initiation of hematopoiesis. Finally, we provide evidence that TRF3 and TAF3 are also required for hematopoiesis initiation in the mouse...
  13. pmc Initiation of zebrafish haematopoiesis by the TATA-box-binding protein-related factor Trf3
    Daniel O Hart
    Howard Hughes Medical Institute, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
    Nature 450:1082-5. 2007
    ..Thus, in zebrafish, commitment of mesoderm to the haematopoietic lineage occurs through a transcription factor pathway initiated by a TBP-related factor...
  14. pmc Oncogenic RAS directs silencing of tumor suppressor genes through ordered recruitment of transcriptional repressors
    Narendra Wajapeyee
    Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Genes Dev 27:2221-6. 2013
    ....

Research Grants30

  1. Mechanism of Chromatin Organization and Dynamics in Development
    Xiaole Shirley Liu; Fiscal Year: 2013
    ....
  2. Cadiorenal and Metabolic Diseases Research Center
    John E Hall; Fiscal Year: 2013
    ..abstract_text> ..
  3. Histone Modifications During Embryogenesis
    Alexander F Schier; Fiscal Year: 2013
    ..It might even become possible to use the proposed technology to specifically activate disease-protective genes or repress disease-inducing genes. ..