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Genome-wide mapping of yeast RNA polymerase II termination.
Schaughency P, Merran J, Corden JL. Schaughency P, et al. PLoS Genet. 2014 Oct 9;10(10):e1004632. doi: 10.1371/journal.pgen.1004632. eCollection 2014 Oct. PLoS Genet. 2014. PMID: 25299594 Free PMC article.
Yeast RNA polymerase II (Pol II) terminates transcription of coding transcripts through the polyadenylation (pA) pathway and non-coding transcripts through the non-polyadenylation (non-pA) pathway. We have used PAR-CLIP to map the positio
Yeast RNA polymerase II (Pol II) terminates transcription of coding transcripts through the polyad
Transcription-dependent enrichment of the yeast FACT complex influences nucleosome dynamics on the RNA polymerase III-transcribed genes.
Shukla A, Bhalla P, Potdar PK, Jampala P, Bhargava P. Shukla A, et al. RNA. 2020 Dec 4;27(3):273-90. doi: 10.1261/rna.077974.120. Online ahead of print. RNA. 2020. PMID: 33277439 Free PMC article.
The FACT (FAcilitates Chromatin Transactions) complex influences transcription initiation and enables passage of RNA polymerase (pol) II through gene body nucleosomes during elongation. ...As opposed to the enrichment at the 5'-ends of pol II-transcrib …
The FACT (FAcilitates Chromatin Transactions) complex influences transcription initiation and enables passage of RNA polymerase
Gene-specific RNA polymerase II phosphorylation and the CTD code.
Kim H, Erickson B, Luo W, Seward D, Graber JH, Pollock DD, Megee PC, Bentley DL. Kim H, et al. Nat Struct Mol Biol. 2010 Oct;17(10):1279-86. doi: 10.1038/nsmb.1913. Epub 2010 Sep 12. Nat Struct Mol Biol. 2010. PMID: 20835241 Free PMC article.
Phosphorylation of the RNA polymerase (Pol) II C-terminal domain (CTD) repeats (1-YSPTSPS-7) is coupled to transcription and may act as a 'code' that controls mRNA synthesis and processing. To examine the code in budding yeast, we mapped
Phosphorylation of the RNA polymerase (Pol) II C-terminal domain (CTD) repeats (1-YSPTSPS-7) is coupled to trans …
Common genomic elements promote transcriptional and DNA replication roadblocks.
Roy K, Gabunilas J, Gillespie A, Ngo D, Chanfreau GF. Roy K, et al. Genome Res. 2016 Oct;26(10):1363-1375. doi: 10.1101/gr.204776.116. Epub 2016 Aug 18. Genome Res. 2016. PMID: 27540088 Free PMC article.
RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical for the production of stable noncoding RNAs and the control of pervasive transcription in Saccharomyces cerevisiae To uncover d
RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical f
FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.
Jeronimo C, Angel A, Nguyen VQ, Kim JM, Poitras C, Lambert E, Collin P, Mellor J, Wu C, Robert F. Jeronimo C, et al. Mol Cell. 2021 Sep 2;81(17):3542-3559.e11. doi: 10.1016/j.molcel.2021.07.010. Epub 2021 Aug 10. Mol Cell. 2021. PMID: 34380014 Free PMC article.
How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partia …
How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase
Promoter nucleosome dynamics regulated by signalling through the CTD code.
Materne P, Anandhakumar J, Migeot V, Soriano I, Yague-Sanz C, Hidalgo E, Mignion C, Quintales L, Antequera F, Hermand D. Materne P, et al. Elife. 2015 Jun 22;4:e09008. doi: 10.7554/eLife.09008. Elife. 2015. PMID: 26098123 Free PMC article.
The phosphorylation of the RNA polymerase II C-terminal domain (CTD) plays a key role in delineating transcribed regions within chromatin by recruiting histone methylases and deacetylases. Using genome-wide nucleosome mapping, we s …
The phosphorylation of the RNA polymerase II C-terminal domain (CTD) plays a key role in delineating transcribed …
The yeast cap binding complex modulates transcription factor recruitment and establishes proper histone H3K36 trimethylation during active transcription.
Hossain MA, Chung C, Pradhan SK, Johnson TL. Hossain MA, et al. Mol Cell Biol. 2013 Feb;33(4):785-99. doi: 10.1128/MCB.00947-12. Epub 2012 Dec 10. Mol Cell Biol. 2013. PMID: 23230273 Free PMC article.
Recent studies have revealed a close relationship between transcription, histone modification, and RNA processing. In fact, genome-wide analyses that correlate histone marks with RNA processing signals raise the possibility that specific RNA pro …
Recent studies have revealed a close relationship between transcription, histone modification, and RNA processing. In fact, genome
Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation.
Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K. Fan X, et al. Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17945-50. doi: 10.1073/pnas.1012674107. Epub 2010 Oct 4. Proc Natl Acad Sci U S A. 2010. PMID: 20921369 Free PMC article.
Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome format
Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and
Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping.
Voong LN, Xi L, Sebeson AC, Xiong B, Wang JP, Wang X. Voong LN, et al. Cell. 2016 Dec 1;167(6):1555-1570.e15. doi: 10.1016/j.cell.2016.10.049. Epub 2016 Nov 23. Cell. 2016. PMID: 27889238 Free PMC article.
Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising features of nucleosome organization in mouse embryonic stem cells. ...Furthermore, we provide evidence that promoter-proximal nucleosomes, w …
Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising …