|
      |
|
Protein Complexes that Modify Chromatin and Regulate Gene Transcription. Eukaryotic chromosomes comprise DNA that is complexed with small basic proteins, histones, and other proteins to generate chromatin. The tight association of these proteins with DNA provides a level of transcription control and contributes to epigenetic mechanisms of gene regulation. For example, the amino-terminal tail domains of the core histone proteins are sights of numerous post-translational modifications. In addition to potential effects on chromatin structure, these modifications act as binding sites/receptors for protein complexes that activate or repress gene transcription. Thus, histone modification can be used to generate a "code" of signals on the surface of the chromosome fiber, which provides regulatory information above that contained in the DNA sequence. Our laboratory is focused on studying the protein complexes that carry out these histone modifications and those that recognize the resulting signals. Our laboratory discovered several yeast histone acetyltransferase complexes including the first transcription coactivator HAT complexes. Since joining the Stowers Institute we have made several novel findings regarding the functions of these complexes. For example, the SAS complex was found to specifically acetylate histone H4 lysine 16 (a modification thought to decondense chromatin structure) at subtelomeric regions which facilitates the insertion of the histone variant Htz and counters the spread of heterochromatin. We found that the 19S proteosome regulatory particle enhances the binding of the SAGA complex to activation domains of transcription factors hastening its recruitment to promoters. SAGA recruitment brings about de-ubiquitination of H2B, through its Sgf11 and Ubp8 subunits, and acetylation of H3. Histone acetylation and contact with transcription activation domains drive displacement of promoter nucleosomes by the Swi/Snf nucleosome remodeling complex. A new area of our work is the function of histone modifications during transcription elongation. We found that histone acetylation can facilitate the passage of RNA polymerase II past nucleosomes through the action of the RSC remodeling complex. We have also discovered a pathway by which RNA polymerase II signals for histone deacetylation. The Set2 methyltransferase binds the elongating form of RNA pol. II and co-transcriptionally methylates histone H3 on K36. H3 K36 methylated nucleosomes are recognized and deacetylated by the Rpd3S complex. This recognition requires the combinatorial action of domains from two Rpd3S subunits. In the absence of this pathway ORFs remain acetylated and 20% of yeast genes suffer cryptic transcription initiation from sites in the body of the genes. Thus, the Set2/Rpd3S pathway is crucial to block cryptic transcription and limit transcription initiation to promoters. Selected publications Weake VM, Lee KK, Guelman S, Lin CH, Seidel C, Abmayr SM, Workman JL. SAGA-mediated H2B deubiquitination controls the development of neuronal connectivity in the Drosophila visual system. Embo J. 2008;27:394-405. Abstract Li B, Gogol M, Carey M, Pattenden SG, Seidel C, Workman JL. Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription. Genes Dev. 2007;21:1422-1430. Abstract Li B, Gogol M, Carey M, Lee D, Seidel C, Workman JL. Combined Action of PHD and Chromo Domains Directs the Rpd3S HDAC to Transcribed Chromatin. Science. 2007;316:1050-1054. Abstract Gutierrez JL, Chandy M, Carrozza MJ, Workman JL. Activation domains drive nucleosome eviction by SWI/SNF. Embo J. 2007;26:730-740. Abstract Carey M, Li B, Workman JL. Guelman S, Suganuma T, Florens L, Weake V, Shia WJ, Li B, Workman JL. SAS-mediated acetylation of histone H4 Lys 16 is required for H2A.Z incorporation at subtelomeric regions in Saccharomyces cerevisiae. Genes Dev. 2006;20:2507-2512. Abstract Guelman S, Suganuma T, Florens L, Swanson SK, Kiesecker CL, Kusch T, Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription. Cell. 2005;123:581-592. Abstract Lee D, Ezhkova E, Li B, Pattenden SG, Tansey WP, Workman JL. The Proteasome Regulatory Particle Alters the SAGA Coactivator to Enhance Its Interactions with Transcriptional Activators. Cell. 2005;123:423-436. Lee KK, Florens L, Li B, Pattenden SG, Lee D, Gutierrez J, Chen J, Seidel C, Gerton J, Workman JL. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc Natl Acad Sci U S A. 2005. Abstract Shia WJ, Osada S, Florens L, Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates Iii JR, Abmayr SM, Washburn MP, Workman JL. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science. 2004;306:2084-2087. Abstract Kusch T, Guelman S, Abmayr SM, Workman JL. Two Drosophila Ada2 homologues function in different multiprotein complexes. Mol Cell Biol. 2003;23:3305-3319. Abstract Li B, Howe L, |
Workman
Lab