The long-term goal of this project is to understand the interactions between RNA polymerase II, its basal transcription factors, and the chromatin template that lead to accurate transcription initiation. The yeast Saccharomyces cerevisiae will be used as a model system for an integrated approach to the problem. Genetic approaches such as screens and selections for mutants, second-site suppressors, and synthetic lethality will be used to identify and verify in vivo interactions. Chromatin immunoprecipitation will analyze in vivo localization of factors. In vitro analysis of wild-type and mutant transcription factors will be performed using protein biochemical techniques (including affinity purification, enzymatic assays, reconstituted transcription, immobilized template assays, gel shift analysis, and footprinting). In the next period of the project, four major aims are proposed. (1) We will continue our analysis of the structure and function of basal factor TFIID (TATA-Binding Protein and its associated factors). Having developed an efficient TFIID purification, the role of several posttranslational modifications and TFIID-associated proteins will be studied. (2) A similar analysis will be carried out for TFIIH, allowing analysis of the interactions between its kinase and helicase activities. With efficient purifications of TFIID and TFIIH, we will continue our studies of yeast initiation complexes. (3) We will continue our studies of the TFIID-associated factor Bdf1. Having established that Bdf1 bromodomains interact with histone H4, we will study how this interaction affects transcription. We have recently discovered that Bdfl is phosphorylated by the kinase CK2 and that phosphorylation is required for Bdf1 function in vivo. The function of this modification will be studied in vivo and in vitro. (4) Yeast contains a RNA polymerase II-associated kinase known as Bur1 which resembles mammalian cdk9. However, our recent studies suggest that Bur1 may phosphorylate a substrate other than the CTD. Genetic data suggests that Bur1 is necessary to assist in transcription through chromatin and we will work to find the relevant Bur1 substrate(s) to determine its molecular function. Our work will help us understand the basic mechanisms of gene expression in all eukaryotic cells. Since improper gene expression is often at the root of cancer and developmental diseases, a clear understanding of the gene expression machinery will be required to develop effective therapeutics.
| Joo, Yoo Jin; Ficarro, Scott B; Soares, Luis M et al. (2017) Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation. Genes Dev 31:2162-2174 |
| Woo, Hyeonju; Dam Ha, So; Lee, Sung Bae et al. (2017) Modulation of gene expression dynamics by co-transcriptional histone methylations. Exp Mol Med 49:e326 |
| Soares, Luis M; He, P Cody; Chun, Yujin et al. (2017) Determinants of Histone H3K4 Methylation Patterns. Mol Cell 68:773-785.e6 |
| Kim, Ji Hyun; Lee, Bo Bae; Oh, Young Mi et al. (2016) Modulation of mRNA and lncRNA expression dynamics by the Set2-Rpd3S pathway. Nat Commun 7:13534 |
| Hahn, Steven; Buratowski, Stephen (2016) Structural biology: Snapshots of transcription initiation. Nature 533:331-2 |
| Soares, Luis M; Radman-Livaja, Marta; Lin, Sherry G et al. (2014) Feedback control of Set1 protein levels is important for proper H3K4 methylation patterns. Cell Rep 6:961-972 |
| Marquardt, Sebastian; Escalante-Chong, Renan; Pho, Nam et al. (2014) A chromatin-based mechanism for limiting divergent noncoding transcription. Cell 157:1712-23 |
| Suh, Hyunsuk; Hazelbaker, Dane Z; Soares, Luis M et al. (2013) The C-terminal domain of Rpb1 functions on other RNA polymerase II subunits. Mol Cell 51:850-8 |
| Soares, Luis M; Buratowski, Stephen (2013) Histone Crosstalk: H2Bub and H3K4 Methylation. Mol Cell 49:1019-20 |
| van Werven, Folkert J; Neuert, Gregor; Hendrick, Natalie et al. (2012) Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell 150:1170-81 |
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