Defining mechanisms that regulate RNA polymerase II transcription in vivo

By Nicholas J Fuda, M. Ardehali, J. Lis. Nature, 2009

614 citations recorded by the source corpus.

In the eukaryotic genome, the thousands of genes that encode messenger RNA are transcribed by a molecular machine called RNA polymerase II. Analysing the distribution and status of RNA polymerase II across a genome has provided crucial insights into the long-standing mysteries of transcription and its regulation. These studies identify points in the transcription cycle where RNA polymerase II accumulates after encountering a rate-limiting step. When coupled with genome-wide mapping of transcription factors, these approaches identify key regulatory steps and factors and, importantly, provide an understanding of the mechanistic generalities, as well as the rich diversities, of gene regulation.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a1d9002beb8a069cb3b6ea7b02928bc0baf2f978

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Citations in the corpus

Discovery and Characterization of Super-Enhancer Associated Dependencies in Diffuse Large B-Cell Lymphoma (2013, neutral): “The subsequent recruitment of multiprotein complexes leads to local remodeling of chromatin, which establishes mitotic memory, and transmission of transcriptional signals to RNA polymerase II poised at genes associated with growth and survival (Fuda et al., 2009; Schreiber and Bernstein, 2002).”
Histone Marks in the 'Driver's Seat': Functional Roles in Steering the Transcription Cycle. (2017, background): “While it is estimated that the GTFs and the Mediator complex are composed of about 60 proteins in yeast [12], many more additional factors help regulate transcription [11].”
Enhancer decommissioning by LSD1 during embryonic stem cell differentiation (2012, neutral): “Transcription factors bind to enhancer elements and recruit coactivators and chromatin-modifying enzymes to facilitate transcription initiatio”
c-Myc regulates transcriptional pause release (2010, background): “The large subunit of Pol II contains a C-terminal domain (CTD) that is modified at various stages of transcription; Pol II is recruited into the preinitiation complex with a hypophosphorylated CTD, the CTD is phosphorylated on Serine 5 (Ser5P) during initiation and then on Serine 2 (Ser2P) during el”
Control of Embryonic Stem Cell State (2011, background): “Control of RNA Polymerase II Transcription factors control at least two major steps in gene expression (Fuda et al., 2009; Peterlin and Price, 2006; Rahl et al., 2010).”
Molecular Architecture of the Mammalian Circadian Clock (2013, background): “Phosphorylation of the RNAPII C-terminal domain at serine 5 (RNAPII-Ser5P) correlates with promoter escape and transcriptional initiation [76].”
Transcriptional Regulation and its Misregulation in Disease (2013, neutral): “…leading to a present-day consensus model for selective gene control (Adelman and Lis, 2012; Bannister and Kouzarides, 2011; Bonasio et al., 2010; Conaway and Conaway, 2011; Fuda et al., 2009; Ho and Crabtree, 2010; Roeder, 2005; Spitz and Furlong, 2012; Taatjes, 2010; Zhou et al., 2012b).”
Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. (2010, background): “The large subunit of Pol II contains a CTD that is modified at various stages of transcription; Pol II is recruited into the preinitiation complex with a hypophosphorylated CTD, and the CTD is phosphorylated on serine 5 (Ser5P) during initiation and then on serine 2 (Ser2P) during elongation (Fuda e”
Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put (2013, background): “Ultimately, the myriad decisions that create cellular on/off profiles rely on mechanisms that impact nucleosomes (Cairns, 2009; Fuda et al., 2009; Li et al., 2007; Weake and Workman, 2010), the universal packagingmaterial of eukaryotic genomes.”