Robert G. Roeder

Arnold and Mabel Beckman Professor of Biochemistry and Molecular Biology

The Rockefeller University, New York NY 10065

BIOGRAPHICAL SKETCH

NAME:  Robert G. Roeder

eRA COMMONS USER NAME (credential, e.g., agency login): RGROEDER

POSITION TITLE: Professor and Head, Laboratory of Biochemistry and Molecular Biology

EDUCATION/TRAINING

Differential gene expression underlies key events in development, cell growth and differentiation, homeostasis, and pathologies such as cancer -- and is controlled primarily at the level of transcription. The execution and regulation of transcription is effected through a complex array of RNA polymerases, general initiation and elongation factors, gene- and cell-specific DNA-binding regulatory factors, and an increasingly complex array of cofactors that act either on the general transcription machinery or indirectly through chromosomal histone modifications. Over the past 50 years, I have made seminal contributions to both the discovery and an understanding of the structure, function, mechanism of action and regulation of many of these factors. These studies have emphasized the development and application of powerful cell-free transcription systems, reconstituted with purified factors and recombinant DNA or chromatin templates, in order to uniquely, and unequivocally, establish direct functions and mechanisms of action of specific factors on specific genes. At the same time, the biochemical studies have been complemented with cell-based and mouse genetic analyses, along with state of the art genomic and proteomic technologies, both to validate and to guide the in vitro studies. These complementary studies have led to significant new insights into transcriptional regulation in relation to physiological processes that include metabolism and homeostasis, cell growth and differentiation, and cancer (through studies of nuclear hormone receptors, tumor suppressor p53, B cell factors, and leukemic fusion proteins). Recent representative papers:

 • M. Shimada, W.-Y. Chen, T. Nakadai, T. Onikubo, M. Guermah, D. Rhodes and R.G. Roeder. Genespecific

H1 eviction through a transcriptional activator-p300-NAP1-H1 pathway. Molec. Cell 2019, in press.

• M. Jishage, X. Yu, Y. Shi, S.J. Ganesan, A. Sali, B.T. Chait, FJ. Asturias and R.G. Roeder.  Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nat. Struct. Mol. Biol. 25:859-867, 2018.

• S. P. Wang, Z. Tang, C. W. Chen, M. Shimada, R. P. Koche, L. H. Wang, T. Nakadai, A. Chramiec, A. V. Krivtsov, S. A. Armstrong and R. G. Roeder.  A UTX-MLL4-p300 transcriptional regulatory network coordinately shapes active enhancer landscapes for eliciting transcription. Mol. Cell, 67:308-321, 2017. PMC5574165

Ÿ S. Z. Josefowicz, M. Shimada, A. Armache, C. H. Li, R. M. Miller, S. Lin, A. Yang, B. D. Dill, H. Molina, H.-S.

Park, B. A. Garcia, J. Taunton, R. G. Roeder*, C. D. Allis*.  Chromatin kinases act on transcription factors and

 histone tails to regulate inducible transcription. Mol. Cell, 64:347-361, 2016. PMC5081221 *co-corres. authors.

 

B. Positions

1965-1969 Predoctoral Fellow of the USPHS with W. J. Rutter

Department of Biochemistry - University of Washington, Seattle, WA.

1969-1971 Postdoctoral Fellow of the American Cancer Society with D.D. Brown.

Department of Embryology - Carnegie Institute of Washington. Baltimore, MD.

1971-1982  Assistant (‘71-’75), Associate (‘75-’76), and Professor (‘76-’82) of Biological Chemistry.  Professor of Genetics (‘78-82) and J.S. McDonnell Professor of Biochemical Genetics (‘78-’82).

Washington University School of Medicine, St. Louis, MO.

1982- Professor and Head of the Laboratory of Biochemistry and Molecular Biology

The Rockefeller University, New York, NY

           Arnold and Mabel Beckman Professor, The Rockefeller University, New York, NY

B. Honors

NIH Research Career Development Awardee, 1972-1978 • American Chemical Society Eli Lilly Award in Biological Chemistry, 1977 • Dreyfus Foundation Teacher-Scholar Award, 1976-1981 • National Academy of Sciences U.S. Steel Award in Molecular Biology, 1986 • Member, National Academy of Sciences, 1988 • NIH/NCI Outstanding Investigator Award, 1986-2000 • Fellow of the American Association for the Advancement of Science • Lewis S. Rosenstiel Award for Distinguished Work in Basic Medical Sciences, 1995 • Passano Award, 1995 • Fellow of the New York Academy of Sciences, 1995 • Fellow of the American Academy of Arts and Sciences, 1995 • General Motors Cancer Research Foundation’s Alfred P. Sloan Prize, 1999 • Louisa Gross Horwitz Prize, 1999 • Gairdner Foundation International Award, 2000 • The Dickson Prize in Medicine, 2001 • ASBMB Merck Award, 2002 • Associate Member, European Molecular Biology Organization, 2003 • Albert Lasker Award for Basic Medical Research, 2003 •  Salk Institute Medal for Research Excellence, 2010 • Albany Medical Center Prize In Medicine and Biomedical Research, 2012 • Thomas Reuters Citation Laureate, 2014 • Hope Funds for Cancer Research Award in Basic Science, 2015 • ASBMB Herbert Tabor Research Award, 2016 • Howard Taylor Ricketts Award, 2018.

 

C. Contributions to Science

1. Discovery of nuclear RNA polymerases I, II, and III and establishment of their distinct multi-subunit structures and their distinct functions in the synthesis of the major classes of RNA. The paramount factor for transcription is of course the RNA polymerase; and studies in the late1960s had demonstrated a 5-subunit structure for the single E. coli RNA polymerase and an RNA polymerase activity in mammalian cell extracts that was otherwise completely uncharacterized. At the same time, there was an appreciation of three major classes of RNA (rRNAs, tRNAs and (pre)mRNAs) in animal cells but no information on corresponding enzymology and no cloned genes or information on DNA regulatory elements.  In 1969, the PI succeeded in the quantitative solubilization and identification of three nuclear RNA polymerases (I, II, III), with distinct chromatographic and enzymatic properties and sub-nuclear localizations, in organisms ranging from yeast to mammals.  This seminal study is generally regarded as the principal starting point for mechanistic analyses of transcription in eukaryotes.  In subsequent studies, the three enzymes were shown to have complex subunit structures with both distinct and common polypeptides, allowing the possibility of both distinct functions and distinct regulatory properties. The subsequent discovery of differential sensitivities of the three enzymes to the mushroom toxin a-amanatin, the ability to monitor specific transcription from endogenous templates in isolated nuclei, and the nucleolar localization of Pol I allowed an initial assignment of the general functions of Pols I, II and III in the synthesis of the large ribosomal RNAs, pre-mRNAs and 5S and tRNAs, respectively. This in turn set the stage for studies of transcription mechanisms and regulation for specific genes.

Ÿ R.G. Roeder and W.J. Rutter.  Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms.  Nature  224: 234-237, 1969.

Ÿ V.E.F. Sklar, L.B. Schwartz and R.G. Roeder.  Distinct molecular structures of nuclear class I, II and III DNA-dependent RNA polymerases. Proc. Natl. Acad. Sci. USA  72: 348-352, 1975.

Ÿ R. Weinmann and R.G. Roeder.  Role of DNA-dependent RNA polymerase III in the transcription of the tRNA and 5S RNA genes. Proc. Natl. Acad. Sci. USA  71: 1790-1794, 1974.

Ÿ R. Weinmann, H.J. Raskas and R.G. Roeder.  Role of DNA-dependent RNA polymerases II and III in transcription of the adenovirus genome late in productive infection. Proc. Natl. Acad. Sci. USA  71: 3426-3430, 1974.

2. Establishment of cell-free systems for the accurate transcription of purified genes by purified RNA polymerases, leading to the discovery of cognate classes of general initiation factors and their mechanisms of action in pre-initiation complex (PIC) formation and function. As studies in several labs in the late 1970s began to identify transcription start sites in viral and cellular genes, it became possible to test the physiological functions of the eukaryotic RNA polymerases in vitro. Quite surprisingly, in view of precedent from studies of the bacterial RNA polymerase (which directly recognizes promoter elements) and the extreme structural complexity of the eukaryotic enzymes (up to 17 subunits), the PI showed that accurate transcription of corresponding cloned genes by purified human RNA polymerases requires additional factors that are ubiquitous and specific to each polymerase.  While their activities were initially detected in cellular extracts, these factors were ultimately purified and cognate cDNAs cloned through the efforts of many laboratories (including that of the PI). Prototype studies of the Pol III factors on tRNA genes established an ordered PIC assembly pathway involving sequential binding of TFIIIC (which directly recognizes core promoter elements), TFIIIB and Pol III. Subsequent studies (Roeder, Sharp, and Reinberg labs) of the Pol II factors on the strong adenovirus 2 major late promoter established a parallel assembly pathway involving sequential binding of TFIID (which recognizes core promoter elements), TFIIA, TFIIB, TFIIF/Pol II, TFIIE and TFIIH -- forming a final PIC with 44 distinct polypeptides. Many studies of these pathways, including recent X-ray/cryo EM structural studies (Kornberg, Nogales, Cramer labs) have provided deep insights into underlying mechanisms and potential points of regulation by various cell- and gene-specific regulatory factors and cofactors. Notably, the PI’s studies established a promoter recognition paradigm distinct from that in bacteria, where RNA polymerase directly recognizes the core promoter element. Also notable from the earliest studies from the PI's laboratory is the finding that cell-specific genes (e.g., adenovirus late and beta-globin) were robustly transcribed (from DNA templates) in extracts from non-specialized cells and in systems reconstituted with purified Pol II and cognate general initiation factors, which led to our prediction of both a generalized repression mechanism (such as chromatin) and cell-specific factors to reverse this repression in a cell-specific manner.

Ÿ P.A. Weil, D.S. Luse, J. Segall and R.G. Roeder.  Selective and accurate initiation of transcription at the Ad2 major late promoter in a soluble system dependent on purified RNA polymerase II and DNA. Cell 18: 469-484, 1979.

Ÿ T. Matsui, J. Segall, P.A. Weil and R.G. Roeder.  Multiple factors required for accurate initiation of transcription by purified RNA polymerase II. J. Biol. Chem. 255:11992-11996, 1980.

Ÿ J. Segall, T. Matsui and R.G. Roeder.  Multiple factors are required for the accurate transcription of purified genes by RNA polymerase III. J. Biol. Chem. 255:11986-11991, 1980.

Ÿ A.B. Lassar, P.L. Martin and R.G. Roeder.  Transcription of class III genes: formation of preinitiation complexes. Science 222:740-748, 1983.

3. Discovery of the first gene-specific transcriptional activator (and prototype zinc finger protein) in eukaryotes and establishment of mechanisms of action of gene-specific activators through the general transcription machinery. Although gene- and cell-specific transcriptional factors that act at enhancers and promoters to regulate key biological processes are now taken for granted, they were an unknown entity in eukaryotes in the 1970s and there was considerable speculation, given the presence and extensive turnover of heterogeneous nuclear RNA and the discovery of RNA splicing, that cell-specific RNAs may be derived largely from selective splicing and stabilization of RNAs rather than gene-specific transcription. However, our 1979 discovery of the prototype gene-specific transcriptional regulatory factor (TFIIIA) in eukaryotes, as well as a mechanism involving site-specific promoter binding and recruitment of general initiation factors that in turn recruit the cognate RNA polymerase, established the fundamentally important paradigm that gene-specific RNA production in eukaryotes can involve selective gene transcription, rather than global transcription followed by selective RNA processing and stabilization. This seminal observation prompted subsequent studies, in our own and many other laboratories, that led to the identification of gene-specific factors for the more numerous (~25,000) Pol II-transcribed genes and demonstrations of their direct functions on target gene promoters in cell free transcription assays -- further supporting models for cell-specific gene expression through cell-specific gene transcription.  Notably, whereas the factors for Pol II-transcribed genes may more generally effect the function of the general transcription machinery through various cofactors (below), a number of early studies from our own and other laboratories indicated direct interactions of activators with components (including TFIID) of the general transcription machinery; and our more recent and very rigorous biochemical and cell-based assays have provided unequivocal evidence for the function of these interactions and a mechanism involving enhanced TFIID binding and PIC formation. These studies continue to serve as precedent for studies of the thousands of DNA-binding regulatory factors whose mechanisms remain to be established.

Ÿ D.R. Engelke, S.-Y. Ng, B.S. Shastry and R.G. Roeder.  Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell 19:717-728, 1980.

Ÿ A.M. Ginsberg, B.O. King and R.G. Roeder.  Xenopus 5S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development. Cell 39:479-489, 1984.

Ÿ M. Sawadogo and R.G. Roeder.  Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell 43:165-175, 1985.

Ÿ W.-Y. Chen, J. Zhang, H. Geng, Z. Du, T. Nakadai and R.G. Roeder.  A TAF4 coactivator function for E proteins  that involves enhanced TFIID binding. Genes & Development 27:1596-1609, 2013. PMC3731548

4. Discovery of diverse general, gene-specific and cell-specific coactivators, underlying mechanisms of action, and physiological functions. Despite the specificity intrinsic to DNA-binding transcriptional activators and the structural complexity of their ultimate targets, the general transcription machinery, biochemical analyses with highly purified factors uncovered requirements for additional factors (designated cofactors) that are essential for optimal activator function. This included our discovery of the B cell-specific OCA-B, the prototype cell-specific transcriptional co-activator, and a gene-specific activation mechanism involving interactions with a ubiquitous DNA-binding protein -- thus indicating a novel mechanism for cell- and gene-specific transcription. Subsequent genetic analyses established a key role for OCA-B in B cell activation and, in particular, germinal center formation. This is of special relevance in view of recent studies (Bradner laboratory) indicating an important role for OCA-B in germinal center derived lymphomas (DLBCL), especially since it suggests potential therapeutic targets. OCA-B has also served as an important model for other cell-specific/induced coactivators such as PGC-1 (energy metabolism) and FOG-1 (hematopoiesis). Our biochemical studies also led to the discovery, purification, and characterization of the human TRAP/Mediator coactivator complex, counterpart of yeast Mediator, and the first demonstration of a mechanism involving not only Pol II interactions (as first shown by Kornberg and Young in yeast) but direct interactions, through distinct subunits, with different transcriptional activators that are primarily responsible for their recruitment to enhancers and promoters. Notably, the 30-subunit Mediator has proved to be the major conduit for direct communication between diverse transcriptional activators and the general transcriptional machinery; and mutations in various subunits have also been linked (by others) to a variety of pathologies that include cancer and various cardiovascular, neurodevelopmental and behavioral disorders.  Our own studies have established key roles for specific Mediator subunits in p53 function (MED17) and in nuclear receptor function in adipogenesis and obesity (TRAP220/MED1) (thus indicating potential therapeutic targets). Our biochemical analyses also identified other general coactivators such as PC4 and p75/LEDGF, the latter of significance because of its roles in MLL fusion protein function and in directing HIV integrase to transcribed regions.

Ÿ Y. Luo, H. Fujii, T. Gerster and R.G. Roeder.  A novel B cell-derived coactivator potentiates the activation of immunoglobulin promoters by octamer-binding transcription factors. Cell 71:231-241, 1992.

Ÿ M. Meisterernst, A.L. Roy, H.M. Lieu and R.G. Roeder.  Activation of class II gene transcription by regulatory factors is potentiated by a novel activity. Cell 66:981-993, 1991.

Ÿ J.D. Fondell, H. Ge and R.G. Roeder.  Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc. Natl. Acad. Sci. USA 93:8329-8333, 1996.

Ÿ K. Ge, M. Guermah, C.-X. Yuan, M. Ito, A.E. Wallberg, B.M. Spiegelman and R.G. Roeder.  Transcription coactivator TRAP220 is required for PPARg2-stimulated adipogenesis. Nature 417:563-567, 2002.

5. Establishment of biochemically defined cell-free systems for accurate transcription of specific genes within recombinant chromatin templates and utilization of these systems to provide definitive information on the direct functions and mechanisms of action of diverse epigenetic factors and cognate histone modifications. Our studies in 1987-1988 demonstrated that nucleosome assembly on a promoter prevents access to the otherwise promiscuous general transcription machinery, whereas prior formation of a preinitiation complex with promoter-bound TFIID precluded nucleosome assembly-mediated repression -- thus providing critical evidence for a general repressive function of histones (rather than just a DNA packaging function) and insights into derepression mechanisms. Currently, chromatin remodeling and covalent modifications of histones through complex arrays of single and multi-subunit enzyme complexes are believed to play major roles in gene regulation in both normal and pathological states. Our significant contributions in this area have emphasized the use of cell-free transcription systems reconstituted with purified factors and recombinant chromatin templates (assembled with wild type, mutated or pre-modified histones) in order (i) to prove that the functions of various enzyme complexes are due to direct effects on the gene of interest and that the corresponding histone modifications, rather than modifications of other factors, are essential for (rather than simply correlated with) transcription and (ii) to detail the actual mechanism of action of the various factors and histone modifications. The importance of these studies is underscored by our seminal observation, published in 1997, that the prominent “histone” acetyltransferase p300/CBP could also functionally modify p53 and by many subsequent studies documenting functional modifications of many transcription factors/cofactors by histone acetyl- and methyl-transferases. Notably, in support of the conclusions based on correlations in cell-based assays, our in vitro studies have clearly established the direct function in transcription of specific histone modifications, as well as mechanisms (including regulatory factor interactions) for recruitment of histone modifying factors, cooperative functions of these factors, and functions of specific histone modifications through recognition by specific “readers”. In another major advancement, we have reconstructed a completely defined system (over 90 distinct polypeptides) that mediates transcription initiation and elongation on chromatin templates -- thus providing an unparalleled system for detailed mechanistic studies of various histone modifying factors in conjunction with different transcriptional activators.

Ÿ J.L. Workman and R.G. Roeder.  Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell 51:613-622, 1987.

Ÿ W. An, J. Kim and R.G. Roeder. Cooperative ordered functions of p300, PRMT1 and CARM1 in transcriptional activation by p53. Cell 117:735-748, 2004.

Ÿ J. Kim, M. Guermah and R.G. Roeder. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Cell 140:491-503, 2010. PMC2853908

Ÿ Z. Tang, W.-Y. Chen, M. Shimada, U.T.T. Nguyen, J. Kim, X.-J. Sun, T. Sengoku, R.K. McGinty, J.P. Fernandez, T.W. Muir and R.G. Roeder. SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53. Cell, 154:297-310, 2013. PMC4023349

 

Complete List of Published Work in My Bibliography: http://www.ncbi.nlm.nih.gov/sites/myncbi/robert.roeder.1/bibliography/41160557/public/?sort=date&direction=ascending

 

D. Research Support

Ongoing Research Support

 

NIH/NCI R01 CA234575  1/1/19 – 12/31/24 PI: R. Roeder

“Molecular mechanisms of estrogen receptor-dependent transcription regulation” The proposal will use a variety of approaches to understand ERalpha-coactivator interactions at the structural and functional levels, towards developing novel therapies against breast cancer.

 

NIH/NCI RO1 CA178765  8/1/13 – 5/31/19 PI: R. Roeder

“Transcriptional regulatory mechanisms in B cell development and leukemogenesis”. Investigation of the function of transcription factor E2A and cognate leukemic fusion proteins, through co-activator TAF4/TFIID and p300 interactions, in B cell development and related leukemias.

 

NIH/NCI R01 CA163086 9/14/11 – 8/31/22 PI: R. Roeder

“Function and targeting of a stable transcription factor complex in leukemia”. Investigation of the mechanism of action of the leukemogenic fusion protein AML1-ETO, including identification of specific target genes, and identification of peptidomimetic inhibitors of critical AML1-ETO interactions.

 

NIH/NCI R01 CA202245 12/1/15 – 8/31/20 PI: R. Roeder

“Biological roles and Mediator-dependent transcription mechanisms of RNA polymerase II(G)”. Investigation of fundamental aspects of the mechanism of action and biological functions of a new repressed form of RNA polymerase II whose function is critically dependent upon the multi-subunit Mediator coactivator complex.

 

NIH/NCI R01 CA204639 3/1/16-2/28/21 PI: C.D. Allis, co-PI: R. Roeder, S. Armstrong

 “Functional and Mechanistic Study of Histone Crotonylation in Hematological Malignancies”

This proposal concerns studies of the role of newly described histone acylations in MLL-rearranged leukemias.

 

Starr Cancer Consortium I12-0063 1/1/2019-12/31/2021 PI: K. Birsoy; co-PI: O. Abdel-Wahab, R. Roeder, G. Inghrami

“Identification of transcriptional determinants of asparaginase sensitivity in leukemias”

The major aim is to understand the mechanisms by which the transcription cofactor ZBTB1 enables acute lymphoblastic leukemias to survive under asparagine depletion.

 

Title: Mechanisms of transcriptional regulation through diverse coactivators

Transcriptional regulation by gene- and cell-specific DNA-binding factors underlies key events in development, cell differentiation and cell transformation. However, their effects on specific genes depend upon complex arrays of cofactors (coactivators and co-repressors) that include both chromatin remodeling/histone modifying factors (e.g., the p300/CBP histone acetyl-transferases and the SET1/MLL H3K4 methyl-transferases) and other general (e.g., Mediator, TAFs) and cell-specific (e.g., OCA-B, PGC-1) that facilitate more direct communication between enhancer-bound regulatory factors and the general transcription machinery at core promoters/transcription start sites. Emphasizing complementary biochemical, cell-based and genetic analyses, the functions of selected co-activators will be discussed in relation to gene regulation by selected gene-specific activators (p53, nuclear receptors, B cell factors, or leukemic fusion proteins). This may include studies of p300-dependent activation of chromatin templates through novel acylation marks as well as cooperative,activator-directed functions of p300 and MLL complexes in establishment of active chromatin templates.