Nascent transcript sequencing visualizes transcription at nucleotide resolution (original) (raw)
Moore, M. J. & Proudfoot, N. J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell136, 688–700 (2009) ArticleCAS Google Scholar
Preker, P. et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science322, 1851–1854 (2008) ArticleADSCAS Google Scholar
Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature457, 1033–1037 (2009) ArticleADSCAS Google Scholar
Neil, H. et al. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature457, 1038–1042 (2009) ArticleADSCAS Google Scholar
Rougvie, A. E. & Lis, J. T. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D.melanogaster is transcriptionally engaged. Cell54, 795–804 (1988) ArticleCAS Google Scholar
Proshkin, S., Rahmouni, A. R., Mironov, A. & Nudler, E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science328, 504–508 (2010) ArticleADSCAS Google Scholar
Kassavetis, G. A. & Chamberlin, M. J. Pausing and termination of transcription within the early region of bacteriophage T7 DNA in vitro . J. Biol. Chem.256, 2777–2786 (1981) CASPubMed Google Scholar
Shaevitz, J. W., Abbondanzieri, E. A., Landick, R. & Block, S. M. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature426, 684–687 (2003) ArticleADSCAS Google Scholar
Herbert, K. M. et al. Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell125, 1083–1094 (2006) ArticleCAS Google Scholar
Hodges, C., Bintu, L., Lubkowska, L., Kashlev, M. & Bustamante, C. Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science325, 626–628 (2009) ArticleADSCAS Google Scholar
Kireeva, M. L. & Kashlev, M. Mechanism of sequence-specific pausing of bacterial RNA polymerase. Proc. Natl Acad. Sci. USA106, 8900–8905 (2009) ArticleADSCAS Google Scholar
Kireeva, M. L. et al. Nature of the nucleosomal barrier to RNA polymerase II. Mol. Cell18, 97–108 (2005) ArticleCAS Google Scholar
Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature436, 876–880 (2005) ArticleADSCAS Google Scholar
Lefrançois, P. et al. Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics10, 37 (2009) Article Google Scholar
Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science322, 1845–1848 (2008) ArticleADSCAS Google Scholar
Rodríguez-Gil, A. et al. The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors. Nucl. Acids Res.38, 4651–4664 (2010) Article Google Scholar
Cai, H. & Luse, D. S. Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation, and elongation complexes. J. Biol. Chem.262, 298–304 (1987) CASPubMed Google Scholar
Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature456, 53–59 (2008) ArticleADSCAS Google Scholar
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science324, 218–223 (2009) ArticleADSCAS Google Scholar
Markham, R. & Smith, J. D. The structure of ribonucleic acids. I. Cyclic nucleotides produced by ribonuclease and by alkaline hydrolysis. Biochem. J.52, 552–557 (1952) ArticleCAS Google Scholar
Seila, A. C. et al. Divergent transcription from active promoters. Science322, 1849–1851 (2008) ArticleADSCAS Google Scholar
Seila, A. C., Core, L. J., Lis, J. T. & Sharp, P. A. Divergent transcription: a new feature of active promoters. Cell Cycle8, 2557–2564 (2009) ArticleCAS Google Scholar
Weiner, A., Hughes, A., Yassour, M., Rando, O. J. & Friedman, N. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res.20, 90–100 (2010) ArticleCAS Google Scholar
Pokholok, D. K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell122, 517–527 (2005) ArticleCAS Google Scholar
Carrozza, M. J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell123, 581–592 (2005) ArticleCAS Google Scholar
Keogh, M. C. et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell123, 593–605 (2005) ArticleCAS Google Scholar
Li, B. et al. Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription. J. Biol. Chem.284, 7970–7976 (2009) ArticleCAS Google Scholar
Pinskaya, M., Gourvennec, S. & Morillon, A. H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation. EMBO J.28, 1697–1707 (2009) ArticleCAS Google Scholar
Govind, C. K. et al. Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Mol. Cell39, 234–246 (2010) ArticleCAS Google Scholar
Krogan, N. J. et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell. Biol.23, 4207–4218 (2003) ArticleCAS Google Scholar
Nudler, E., Mustaev, A., Lukhtanov, E. & Goldfarb, A. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell89, 33–41 (1997) ArticleCAS Google Scholar
Izban, M. G. & Luse, D. S. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem.267, 13647–13655 (1992) CASPubMed Google Scholar
Reines, D., Conaway, R. C. & Conaway, J. W. Mechanism and regulation of transcriptional elongation by RNA polymerase II. Curr. Opin. Cell Biol.11, 342–346 (1999) ArticleCAS Google Scholar
Kulish, D. & Struhl, K. TFIIS enhances transcriptional elongation through an artificial arrest site in vivo . Mol. Cell. Biol.21, 4162–4168 (2001) ArticleCAS Google Scholar
Nechaev, S. et al. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila . Science327, 335–338 (2010) ArticleADSCAS Google Scholar
Sigurdsson, S., Dirac-Svejstrup, A. B. & Svejstrup, J. Q. Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability. Mol. Cell38, 202–210 (2010) ArticleCAS Google Scholar
Li, B., Carey, M. & Workman, J. The role of chromatin during transcription. Cell128, 707–719 (2007) ArticleCAS Google Scholar
Petesch, S. J. & Lis, J. T. Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell134, 74–84 (2008) ArticleCAS Google Scholar
Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature458, 362–366 (2009) ArticleADSCAS Google Scholar
Hall, M. A. et al. High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nature Struct. Mol. Biol.16, 124–129 (2009) ArticleCAS Google Scholar
Arigo, J. T., Eyler, D. E., Carroll, K. L. & Corden, J. L. Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol. Cell23, 841–851 (2006) ArticleCAS Google Scholar
Vasiljeva, L., Kim, M., Mutschler, H., Buratowski, S. & Meinhart, A. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nature Struct. Mol. Biol.15, 795–804 (2008) ArticleCAS Google Scholar
Unrau, P. J. & Bartel, D. P. RNA-catalysed nucleotide synthesis. Nature395, 260–263 (1998) ArticleADSCAS Google Scholar
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol.10, R25 (2009) Article Google Scholar
Crooks, G. E., Hon, G., Chandonia, J. M. & Brenner, S. E. WebLogo: a sequence logo generator. Genome Res.14, 1188–1190 (2004) ArticleCAS Google Scholar