Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

Kwak, Ho Young; Fuda, Nicholas J.; Core, Leighton J.; Lis, John T.

doi:10.1126/science.1229386

Cited by 686 publications

(813 citation statements)

References 28 publications

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“…Histone modifications such as H3K36me3, which we found positively correlated with resistant nucleosomes, are also thought to contribute to nucleosome stability and maintenance of transcription fidelity (Lieb and Clarke 2005;Lickwar et al 2009). Together, our measurements agree with an emerging picture of highly regulated nucleosome stability throughout the genome, which is likely critical for regulation of DNA templated events like transcription, splicing, and DNA replication (Tilgner et al 2009;Eaton et al 2010;Bintu et al 2011;Kwak et al 2013). …”

Section: Mnase-resistant Nucleosomes Tend To Be In Gene Bodies and Cosupporting

confidence: 82%

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans

Jeffers

Lieb

2016

Genome Res.

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Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability of the underlying histone-DNA interactions affect the access of regulatory proteins to DNA. Both stability and position are regulated through DNA sequence, histone post-translational modifications, histone variants, chromatin remodelers, and transcription factors. Here, we explored the functional implications of nucleosome properties on gene expression and development in Caenorhabditis elegans embryos. We performed a time-course of micrococcal nuclease (MNase) digestion and measured the relative sensitivity or resistance of nucleosomes throughout the genome. Fragile nucleosomes were defined by nucleosomal DNA fragments that were recovered preferentially in early MNase-digestion time points. Nucleosome fragility was strongly and positively correlated with the AT content of the underlying DNA sequence. There was no correlation between promoter nucleosome fragility and the levels of histone modifications or histone variants. Genes with fragile nucleosomes in their promoters tended to be lowly expressed and expressed in a contextspecific way, operating in neuronal response, the immune system, and stress response. In addition to DNA-encoded nucleosome fragility, we also found fragile nucleosomes at locations where we expected to find destabilized nucleosomes, for example, at transcription factor binding sites where nucleosomes compete with DNA-binding factors. Our data suggest that in C. elegans promoters, nucleosome fragility is in large part DNA-encoded and that it poises genes for future context-specific activation in response to environmental stress and developmental cues.[Supplemental material is available for this article.]The fundamental unit of eukaryotic chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around an octamer of histone proteins (Luger et al. 1997). Nucleosomes have important structural and regulatory functions in organizing the genome and restricting access of regulatory factors to the DNA sequence (Henikoff 2008). As such, the interactions between nucleosomes and DNA strongly influence the regulation of gene expression by determining DNA accessibility for transcription factors (TFs) and RNA polymerase. In addition to regulated nucleosome assembly and disassembly through the action of histone chaperones and chromatin remodelers, nucleosome stability is influenced by histone modifications, histone variants, DNA features encoded in cis, and competition with DNA-binding factors in trans . A complete picture of the mechanisms governing nucleosome stability is fundamental to understanding how gene expression is dynamically regulated.Nucleosome stability has been studied in vitro using sensitivity to enzymatic digestion or salt concentration (Bloom and Anderson 1978;Burton et al. 1978;Li et al. 1993;Polach and Widom 1995;Wu and Travers 2004;Jin and Felsenfeld 2007). Genome-wide adaptations of these methods have been used to identify nuc...

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Section: Mnase-resistant Nucleosomes Tend To Be In Gene Bodies and Cosupporting

confidence: 82%

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans

Jeffers

Lieb

2016

Genome Res.

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“…Supporting this observation, recent genome-wide analyses revealed that pausing sites distribute over an extended distance after initiation (51). These findings suggest that stable RNA structures are only surrogate markers for pausing rather than stalling RNAPII by themselves.…”

Section: Discussionmentioning

confidence: 71%

Genetic Analysis of the Structure and Function of 7SK Small Nuclear Ribonucleoprotein (snRNP) in Cells

Fujinaga

Luo

Peterlin

2014

Journal of Biological Chemistry

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“…A similar bias of RNAPII enrichment at exons is evident throughout the genome (data not shown), consistent with ChIP and GRO-seq results from other experimental systems. [48][49][50][51][52] At the 3 0 end of the soc-2 gene total RNAPII and Ser2p signal accumulate just upstream of the termination site presumably due to a strong pause at the site of 3 0 end formation as seen previously. 20,28 In order to determine whether these patterns are similar across C. elegans genes, we created metagenes using a list of 1,691 expressed and isolated genes greater than 2 kb in length.…”

Section: Rnapii Distribution On C Elegans Single Genesmentioning

confidence: 99%

Localization of RNAPII and 3′ end formation factor CstF subunits onC. elegansgenes and operons

2016

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Transcription termination is mechanistically coupled to pre-mRNA 3 0 end formation to prevent transcription much beyond the gene 3 0 end. C. elegans, however, engages in polycistronic transcription of operons in which 3 0 end formation between genes is not accompanied by termination. We have performed RNA polymerase II (RNAPII) and CstF ChIP-seq experiments to investigate at a genome-wide level how RNAPII can transcribe through multiple poly-A signals without causing termination. Our data shows that transcription proceeds in some ways as if operons were composed of multiple adjacent single genes. Total RNAPII shows a small peak at the promoter of the gene cluster and a much larger peak at 3 0 ends. These 3 0 peaks coincide with maximal phosphorylation of Ser2 within the C-terminal domain (CTD) of RNAPII and maximal localization of the 3 0 end formation factor CstF. This pattern occurs at all 3 0 ends including those at internal sites in operons where termination does not occur. Thus the normal mechanism of 3 0 end formation does not always result in transcription termination. Furthermore, reduction of CstF50 by RNAi did not substantially alter the pattern of CstF64, total RNAPII, or Ser2 phosphorylation at either internal or terminal 3 0 ends. However, CstF50 RNAi did result in a subtle reduction of CstF64 binding upstream of the site of 3 0 cleavage, suggesting that the CstF50/CTD interaction may facilitate bringing the 3 0 end machinery to the transcription complex.

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Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

Cited by 686 publications

References 28 publications

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans

Genetic Analysis of the Structure and Function of 7SK Small Nuclear Ribonucleoprotein (snRNP) in Cells

Localization of RNAPII and 3′ end formation factor CstF subunits onC. elegansgenes and operons

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