The RNA Polymerase II Transcriptional Machinery and Its Epigenetic Context
RNA polymerase II (Pol II) is the main engine that drives transcription of protein-encoding genes in eukaryotes. Despite its intrinsic subunit complexity, Pol II is subject to a host of factors that regulate the multistep transcription process. Indeed, the hallmark of the transcription cycle is the dynamic association of Pol II with initiation, elongation and other factors. In addition, Pol II transcription is regulated by a series of cofactors (coactivators and corepressors). Among these, the Mediator has emerged as one of the key regulatory factors for Pol II. Transcription by Pol II takes place in the context of chromatin, which is subject to numerous epigenetic modifications. This chapter mainly summarizes the various biochemical mechanisms that determine formation and function of a Pol II preinitiation complex (PIC) and those that affect its progress along the gene body (elongation). It further examines the various epigenetic modifications that the Pol II machinery encounters, especially in certain developmental contexts, and highlights newer evidence pointing to a likely close interplay between this machinery and factors responsible for the chromatin modifications.
KeywordsEmbryonic Stem Cell Transcription Start Site Histone Modification Transcription Elongation Preinitiation Complex
Given the scope of this chapter, citations have been limited to review articles in many cases. We therefore apologize to colleagues whose original publications we could not directly cite. M.J.B is partially supported by the Ramón y Cajal program and by grants RYC-2007-01510 and SAF2009-08588 from the Ministerio de Ciencia e Innovación of Spain. S.M. is partially supported by 1RC1GM09029. M.J.B and S.M. would also like to thank Dr Robert G. Roeder for his support and encouragement.
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