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Research Paper

Distinct roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation

, , , , , ORCID Icon & show all
Pages 1642-1652 | Received 11 Sep 2020, Accepted 01 Dec 2020, Published online: 28 Jan 2021

References

  • Butler JE, Kadonaga JT. The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev. 2002;16:2583–2592.
  • Lenhard B, Sandelin A, Carninci P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev. 2012;13:233–245.
  • Smale ST, Kadonaga JT. The RNA polymerase II core promoter. Annu Rev Biochem. 2003;72:449–479.
  • Kadonaga JT. Perspectives on the RNA polymerase II core promoter. WIRES Dev Biol. 2012;1:40–51.
  • Haberle V, Li N, Hadzhiev Y, et al. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature. 2014;507:381–385.
  • Lu Z, Lin Z. Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae. Genome Res. 2019;29:1198–1210.
  • Carninci P, Kasukawa T, Katayama S, et al. The transcriptional landscape of the mammalian genome. Science. 2005;309:1559–1563.
  • Hoskins RA, Landolin JM, Brown JB, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011;21:182–192.
  • Schor IE, Degner JF, Harnett D, et al. Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet. 2017;49:550–558.
  • LuZ, LinZ. The origin and evolution of a distinct mechanism of transcription initiation in yeasts. Genome Res. 2020 Nov 20:gr.264325.120. doi:10.1101/gr.264325.120
  • Qiu C, Jin H, Vvedenskaya I, et al. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biol. 2020;21:132.
  • Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast TATA box-containing genes. Cell. 2004;116:699–709.
  • Carninci P, Sandelin A, Lenhard B, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet. 2006;38:626–635.
  • Kapranov P, Cheng J, Dike S, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007;316:1484–1488.
  • Struh l K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol. 2007;14:103–105.
  • Xu Z, Wei W, Gagneur J, et al. Bidirectional promoters generate pervasive transcription in yeast. Nature. 2009;457:1033–1037.
  • Shen X, Mizuguchi G, Hamiche A, et al. A chromatin remodelling complex involved in transcription and DNA processing. Nature. 2000;406:541–544.
  • True JD, Muldoon JJ, Carver MN, et al. The modifier of transcription 1 (Mot1) ATPase and Spt16 histone chaperone co-regulate transcription through preinitiation complex assembly and nucleosome organization. J Biol Chem. 2016;291:15307–15319.
  • Xue Y, Pradhan SK, Sun F, et al. Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mol Cell. 2017;67:594–607 e4.
  • Poorey K, Sprouse RO, Wells MN, et al. RNA synthesis precision is regulated by preinitiation complex turnover. Genome Res. 2010;20:1679–1688.
  • Shilatifard A. Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem. 2006;75:243–269.
  • Kim JH, Lee BB, Oh YM, et al. Modulation of mRNA and lncRNA expression dynamics by the Set2-Rpd3S pathway. Nat Commun. 2016;7:13534.
  • Venkatesh S, Li H, Gogol MM, et al. Selective suppression of antisense transcription by Set2-mediated H3K36 methylation. Nat Commun. 2016;7(1):13610.
  • Marquardt S, Escalante-Chong R, Pho N, et al. A chromatin-based mechanism for limiting divergent noncoding transcription. Cell. 2014;157:1712–1723.
  • Takahashi H, Lassmann T, Murata M, et al. 5ʹ end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc. 2012;7:542–561.
  • Haruki H, Nishikawa J, Laemmli UK. The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. Mol Cell. 2008;31:925–932.
  • Challal D, Barucco M, Kubik S, et al. General regulatory factors control the fidelity of transcription by restricting non-coding and ectopic initiation. Mol Cell. 2018;72:955–69 e7.
  • Kubik S, Bruzzone MJ, Challa l D, et al. Opposing chromatin remodelers control transcription initiation frequency and start site selection. Nat Struct Mol Biol. 2019;26:744–754.
  • MalabatC, FeuerbachF, MaL, et al. 2015. Quality control of transcription start site selection by nonsense-mediated-mRNA decay. eLife. 4:e06722.
  • Tirosh I, Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res. 2008;18:1084–1091.
  • van Bakel H, Tsui K, Gebbia M, et al. A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. PLoS Genet. 2013;9:e1003479.
  • Zentner GE, Henikoff S. Mot1 redistributes TBP from TATA-containing to TATA-less promoters. Mol Cell Biol. 2013;33:4996–5004.
  • Jensen TH, Jacquier A, Libri D. Dealing with pervasive transcription. Mol Cell. 2013;52:473–484.
  • Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, et al. Detecting expressed genes using CAGE. Methods Mol Biol. 2014;1164:67–85.
  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–360.
  • Lademann CA, Renkawitz J, Pfander B, et al. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 2017;19:1294–1303.
  • Shin H, Liu T, Manrai AK, et al. CEAS: cis-regulatory element annotation system. Bioinformatics. 2009;25:2605–2606.

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