Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II

Hsieh, Fu-Kai; Fisher, Michael A.; Újvári, Andrea; Studitsky, Vasily M.; Luse, Donal S.

doi:10.1038/embor.2010.113

Cited by 42 publications

(69 citation statements)

References 15 publications

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“…Although facilitating unfolding of critical histone-DNA contacts clearly improves transcription through nucleosomes by pol II, traversal in the in vitro studies just cited remained incomplete and slow relative to transcription of pure DNA templates (21,23 template when it encounters transcriptional barriers, including arrest sites on pure DNA templates (24,25) and nucleosomes (17). Thus, effective nucleosome traversal is likely to require factors that hold pol II in the transcriptionally competent configuration.…”

mentioning

confidence: 99%

“…These contacts are specifically disrupted by point mutations in histone H3 or H4 called Sin mutants (20). We have recently shown that nucleosomes containing Sin mutant histones do provide a significantly lower barrier to nucleosome traversal by pol II (21). Single-nucleosome unfolding studies have demonstrated that removal of the N-terminal tail domains from histones H2A and H2B specifically favors DNA unwrapping 45-55 bp within the nucleosome (22).…”

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confidence: 99%

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Efficient and Rapid Nucleosome Traversal by RNA Polymerase II Depends on a Combination of Transcript Elongation Factors

Luse

Spangler

Újvári

2011

Journal of Biological Chemistry

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The nucleosome is generally found to be a strong barrier to transcript elongation by RNA polymerase II (pol II) in vitro. The elongation factors TFIIF and TFIIS have been shown to cooperate in maintaining pol II in the catalytically competent state on pure DNA templates. We now show that although TFIIF or TFIIS alone is modestly stimulatory for nucleosome traversal, both factors together increase transcription through nucleosomes in a synergistic manner. We also studied the effect of TFIIF and TFIIS on transcription of nucleosomes containing a Sin mutant histone. The Sin point mutations reduce critical histone-DNA contacts near the center of the nucleosome. Significantly, we found that nucleosomes with a Sin mutant histone are traversed to the same extent and at nearly the same rate as equivalent pure DNA templates if both TFIIS and TFIIF are present. Thus, the nucleosome is not necessarily an insurmountable barrier to transcript elongation by pol II. If unfolding of template DNA from the nucleosome surface is facilitated and the tendency of pol II to retreat from barriers is countered, transcription of nucleosomal templates can be rapid and efficient.It is now appreciated that control of transcript elongation is an important aspect of gene regulation (recently reviewed in Ref. 1). A major checkpoint occurs as RNA polymerase II (pol II) 2 passes from initiation into productive transcript elongation, ϳ50 bp downstream of the transcription start site in many genes (2-6). This checkpoint is roughly coincident with the initial contact between pol II and the first nucleosome of the transcription unit (7-9). Once pol II crosses this initial checkpoint, it can elongate transcripts efficiently over hundreds of kilobases of predominantly nucleosomal template (10). The rate of transcript elongation in vivo (10) slightly exceeds the maximum rates reported for transcript elongation by pol II on pure DNA templates in vitro (11,12). To understand both the initial elongation checkpoint and the exceptional efficiency of transcript elongation downstream of that point, it is essential to develop in vitro systems that duplicate these processes. Progress toward this goal has been somewhat limited because even single nucleosomes have generally proven to be strong barriers to transcribing pol II in vitro (11,(13)(14)(15)(16)(17).Given the tight association of all 146 bp of nucleosomal DNA with the histone octamer surface, one might initially imagine that the nucleosome presents an essentially continuous barrier to transcript elongation by pol II. However, studies with templates bearing single, precisely positioned nucleosomes indicated that the transcriptional barrier for pol II is more discrete. The strongest pauses for human pol II typically occur 45-55 bp within the nucleosome. After pol II crosses this barrier and the nucleosome dyad, transcription continues largely uninhibited through the remainder of the nucleosome (13). This suggests that traversal is controlled primarily by the unfolding of the template DNA from the octamer ...

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confidence: 99%

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confidence: 99%

Efficient and Rapid Nucleosome Traversal by RNA Polymerase II Depends on a Combination of Transcript Elongation Factors

Luse

Spangler

Újvári

2011

Journal of Biological Chemistry

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“…They found that for almost all genes, the first nucleosome is a major barrier for the elongation. This fact has been also observed in vitro by other people [1], [2] and mathematical model based on these in vitro results are also introduced [4]. However, in vivo studies show barrier positions that differ from in vitro results [3].…”

Section: Introductionmentioning

confidence: 84%

“…We use a computer code (See supplementary materials) to find these optimal μ in [0.01,0.6] and σ in [1,60] for nucleosomes on different genes (e. g.μ 1 and σ 1 for all +1 nucleosomes, μ 2 and σ 2 for all +2 nucleosomes, and so on). We employ magnitude (M) as another degree of freedom which is unique for any individual nucleosome.…”

Section: Methodsmentioning

confidence: 99%

“…Studies show that RNA Polymerase II elongation is influenced and regulated by nucleosomes. It has been shown that nucleosomes mostly behave as physical barriers in vitro [1], [2], and in vivo [3]; and the strength of this barrier is not constant across one nucleosome or among different nucleosomes. Some of the key elements affecting this barrier strength are believed to be histone tails, histone-DNA contact points, and their connections [4].…”

Section: Introductionmentioning

confidence: 99%

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Modeling in vivo dynamics of RNA polymerase II meeting Nucleosomes

Abedini-Nassab¹,

Zhang²

2016

IJET

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Nucleosomes are shown to be barriers for RNA Polymerase II elongation along DNA, and their entry site behaves as the major obstacle. In this work, based on recent available in vivo data, we introduce a mathematical model for RNA Polymerase II reads. Moreover, as an alternative way, we use Radial Basis Function Network to predict RNA Polymerase II reads. Results of our models are in good agreement with experimental data. Furthermore, we introduce a random walk model which includes stalling, backtracking, and elongation phenomena. This model can predict and simulate the RNA Polymerase II trajectory on DNA, when it meets various nucleosomes.

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Experimental Analysis of hFACT Action During Pol II Transcription In Vitro

Hsieh

Kulaeva

Studitsky

2015

Methods in Molecular Biology

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Summary FACT (facilitates chromatin transcription) is a histone chaperone that facilitates transcription through chromatin and promotes histone recovery during transcription. Here, we describe a highly purified experimental system that recapitulates many important properties of transcribed chromatin and the key aspects of hFACT action during this process in vitro. We present the protocols describing how to prepare different forms of nucleosomes, including intact nucleosome, covalently conjugated nucleosome, nucleosome missing one of the two H2A/2B dimers (hexasome) and tetrasome (a nucleosome missing both H2A/2B dimers). These complexes allow analysis of various aspects of FACT’s function. These approaches and other methods described below can also be applied to the study of other chromatin remodelers and chromatin-targeted factors.

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Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II

Cited by 42 publications

References 15 publications

Efficient and Rapid Nucleosome Traversal by RNA Polymerase II Depends on a Combination of Transcript Elongation Factors

Efficient and Rapid Nucleosome Traversal by RNA Polymerase II Depends on a Combination of Transcript Elongation Factors

Modeling in vivo dynamics of RNA polymerase II meeting Nucleosomes

Experimental Analysis of hFACT Action During Pol II Transcription In Vitro

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