Hahn, S. & Young, E. T. Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics 189, 705–736 (2011).
Article CAS PubMed PubMed Central Google Scholar
Cairns, B. R. The logic of chromatin architecture and remodelling at promoters. Nature 461, 193–198 (2009).
Article CAS PubMed Google Scholar
Li, B., Carey, M., & Workman, J. L.The role of chromatin during transcription. Cell 128, 707–719 (2007).
Article CAS PubMed Google Scholar
Patel, A. B., Greber, B. J. & Nogales, E. Recent insights into the structure of TFIID, its assembly, and its binding to core promoter. Curr. Opin. Struct. Biol. 61, 17–24 (2020).
Article CAS PubMed Google Scholar
Malik, S. & Roeder, R. G. Mediator: a drawbridge across the enhancer–promoter divide. Mol. Cell 64, 433–434 (2016).
Article CAS PubMed PubMed Central Google Scholar
Allen, B. L. & Taatjes, D. J. The Mediator complex: a central integrator of transcription. Nat. Rev. Mol. Cell Biol. 16, 155–166 (2015).
Article CAS PubMed PubMed Central Google Scholar
Karr, J. P., Ferrie, J. J., Tjian, R. & Darzacq, X. The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer-promoter communication. Genes Dev. 36, 7–16 (2022).
Article CAS PubMed PubMed Central Google Scholar
Ptashne, M. & Gann, A. Transcriptional activation by recruitment. Nature 386, 569–577 (1997).
Article CAS PubMed Google Scholar
Ptashne, M. Regulation of transcription: from lambda to eukaryotes. Trends Biochem. Sci. 30, 275–279 (2005).
Article CAS PubMed Google Scholar
Zhang, H. et al. Mediator structure and conformation change. Mol. Cell 81, 1781–1788 (2021).
Article CAS PubMed Google Scholar
Mittal, C., Culbertson, S. J. & Shogren-Knaak, M. A. Distinct requirements of linker DNA and transcriptional activators in promoting SAGA-mediated nucleosome acetylation. J. Biol. Chem. 293, 13736–13749 (2018).
Article CAS PubMed PubMed Central Google Scholar
Soffers, J. H. M. & Workman, J. L. The SAGA chromatin-modifying complex: the sum of its parts is greater than the whole. Genes Dev. 34, 1287–1303 (2020).
Article CAS PubMed PubMed Central Google Scholar
Huisinga, K. L. & Pugh, B. F. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13, 573–585 (2004).
Article CAS PubMed Google Scholar
Grant, P. A. et al. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11, 1640–1650 (1997).
Article CAS PubMed Google Scholar
Baptista, T. et al. SAGA is a general cofactor for RNA polymerase II transcription. Mol. Cell 68, 130–143 (2017).
Article CAS PubMed PubMed Central Google Scholar
Mittal, C., Lang, O., Lai, W. K. M. & Pugh, B. F. An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters. Genes Dev. 36, 985–1001 (2022).
CAS PubMed PubMed Central Google Scholar
Utley, R. T. et al. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature 394, 498–502 (1998).
Article CAS PubMed Google Scholar
Vignali, M., Steger, D. J., Neely, K. E., & Workman, J. L.Distribution of acetylated histones resulting from Gal4–VP16 recruitment of SAGA and NuA4 complexes. EMBO J. 19, 2629–2640 (2000).
Article CAS PubMed PubMed Central Google Scholar
Chen, X. F. et al. Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function. Cell Rep. 2, 1061–1067 (2012).
Article CAS PubMed PubMed Central Google Scholar
Sikorski, T. W. et al. Proteomic analysis demonstrates activator- and chromatin-specific recruitment to promoters. J. Biol. Chem. 287, 35397–35408 (2012).
Article CAS PubMed PubMed Central Google Scholar
Kuo, M. H., vom Baur, E., Struhl, K. & Allis, C. D. Gcn4 activator targets Gcn5 histone acetyltransferase to specific promoters independently of transcription. Mol. Cell 6, 1309–1320 (2000).
Article CAS PubMed Google Scholar
Bhaumik, S. R. & Green, M. R. SAGA is an essential in vivo target of the yeast acidic activator Gal4p. Genes Dev. 15, 1935–1945 (2001).
Article CAS PubMed PubMed Central Google Scholar
Larschan, E. & Winston, F. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev. 15, 1946–1956 (2001).
Article CAS PubMed PubMed Central Google Scholar
Govind, C. K., Zhang, F., Qiu, H., Hofmeyer, K. & Hinnebusch, A. G. Gcn5 promotes acetylation, eviction, and methylation of nucleosomes in transcribed coding regions. Mol. Cell 25, 31–42 (2007).
Article CAS PubMed Google Scholar
Friedman, L. J., Chung, J. & Gelles, J. Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence. Biophys. J. 91, 1023–1031 (2006).
Article CAS PubMed PubMed Central Google Scholar
Friedman, L. J. & Gelles, J. Multi-wavelength single-molecule fluorescence analysis of transcription mechanisms. Methods 86, 27–36 (2015).
Article CAS PubMed PubMed Central Google Scholar
Keppler, A. et al. A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat. Biotechnol. 21, 86–89 (2003).
Article CAS PubMed Google Scholar
Keppler, A. et al. Labeling of fusion proteins of O6-alkylguanine-DNA alkyltransferase with small molecules in vivo and in vitro. Methods 32, 437–444 (2004).
Article CAS PubMed Google Scholar
Baek, I. et al. A set of Saccharomyces cerevisiae integration vectors for fluorescent dye labeling of proteins. G3 (Bethesda) 12, jkac201 (2022).
Article CAS PubMed Google Scholar
Baek, I., Friedman, L. J., Gelles, J. & Buratowski, S. Single-molecule studies reveal branched pathways for activator-dependent assembly of RNA polymerase II pre-initiation complexes. Mol. Cell 81, 3576–3588 (2021).
留言 (0)