Transcription-induced nucleosome ‘splitting’: an underlying structure for DNase I sensitive chromatin.

Lee, Myeong Sok; Garrard, William T.

doi:10.1002/j.1460-2075.1991.tb07988.x

Cited by 137 publications

(112 citation statements)

References 65 publications

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“…Our observation of half-nucleosome footprints at asymmetric +1 positions is similar to an earlier observation by Lee and Garrard at a transcriptionally active locus, which they attributed to nucleosome splitting (Lee and Garrard 1991). Tracking ''old'' and ''new'' histones had also demonstrated splitting of nucleosomes in yeast (Katan-Khaykovich and Struhl 2011) and in human cells (Huang et al 2013).…”

Section: Discussionsupporting

confidence: 89%

Asymmetric nucleosomes flank promoters in the budding yeast genome

2014

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Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have asymmetric histone-DNA interactions. These asymmetric interactions are enriched at nucleosome positions that flank promoters. Micrococcal nuclease (MNase) sequencebased profiles of asymmetric nucleosome positions revealed a corresponding asymmetry in MNase protection near the dyad axis, suggesting that the loss of DNA contacts around H4S47 is accompanied by protection of the DNA from MNase. Chromatin immunoprecipitation mapping of selected nucleosome remodelers indicated that asymmetric nucleosomes are bound by the RSC chromatin remodeling complex, which is required for maintaining nucleosomes at asymmetric positions. These results imply that the asymmetric nucleosome-RSC complex is a metastable intermediate representing partial unwrapping and protection of nucleosomal DNA on one side of the dyad axis during chromatin remodeling.[Supplemental material is available for this article.]Nucleosomes, the fundamental units of chromatin, are dynamic structures characterized by spontaneous conformational fluctuations that lead to reversible loss of histone-DNA and histone-histone contacts. Every nucleosome in the genome has to disassemble at least once during the cell cycle to allow for passage of the DNA replication machinery (Annunziato 2005), and nucleosomes at active regions might turn over several times during each cell cycle (Dion et al. 2007;Deal et al. 2010). Intrinsic to nucleosome dynamics is the formation of nucleosomal intermediates with alternative structures. However, the nature of such intermediate nucleosome structures formed in vivo is not known.Intermediate nucleosome structures can potentially be identified in vivo using base-pair resolution methods that interrogate histone-DNA contacts genome-wide. The traditional method for high-resolution mapping of nucleosomes is to use micrococcal nuclease (MNase) digestion, which digests away linker regions between nucleosomes (Reeves and Jones 1976). Subjecting MNase-digested DNA fragments to paired-end sequencing (MNase-seq) results in a high-resolution map of nucleosome positions (Hughes and Rando 2014). An alternative method for mapping nucleosomes is H4S47C-anchored cleavage mapping (Brogaard et al. 2012b), which has been used to determine the precise position of nucleosomes in yeast genomes (Brogaard et al. 2012a;Moyle-Heyrman et al. 2013). In this method, histone H4 mutant S47C is derivatized ex vivo with a phenanthroline ligand, converting H4 into a site-specific DNA cleavage agent. Using a modified library preparation and a structural model for H4S47C-anchored cleavage, we extended this method to determine the precise position and orientation of half-nucleosomes (hemisomes) at centromeres (Henikoff et al. 2014), thus showing that alternative nucle...

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Section: Discussionsupporting

confidence: 89%

Asymmetric nucleosomes flank promoters in the budding yeast genome

2014

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“…This exposure, with consequences in factor accessibility to the DNA, has functional consequences in gene regulation. This important observation was proposed to explain the subnucleosomal structures observed upon transcriptional activation of the heat-shock inducible HSP82 gene in yeast (75). Interestingly, a recent genome-wide analysis in budding yeast has provided further support to the idea of a widespread presence of these (and other) subnucleosomal particles (76).…”

Section: Discussionmentioning

confidence: 83%

Quantitative Mass Spectrometry Reveals Changes in Histone H2B Variants as Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation

Rea

Eleazer

Eckstein

et al. 2016

Molecular & Cellular Proteomics

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Exposure to inorganic arsenic, a ubiquitous environmental toxic metalloid, leads to carcinogenesis. However, the mechanism is unknown. Several studies have shown that inorganic arsenic exposure alters specific gene expression patterns, possibly through alterations in chromatin structure. While most studies on understanding the mechanism of chromatin-mediated gene regulation have focused on histone post-translational modifications, the role of histone variants remains largely unknown. Incorporation of histone variants alters the functional properties of chromatin. To understand the global dynamics of chromatin structure and function in arsenic-mediated carcinogenesis, analysis of the histone variants incorporated into the nucleosome and their covalent modifications is required. Here we report the first global mass spectrometric analysis of histone H2B variants as cells undergo arsenic-mediated epithelial to mesenchymal transition. We used electron capture dissociation-based top-down tandem mass spectrometry analysis validated with quantitative reverse transcription real-time polymerase chain reaction to identify changes in the expression levels of H2B variants in inorganic arsenic-mediated epithelial-mesenchymal transition. We identified changes in the expression levels of specific histone H2B variants in two cell types, which are dependent on dose and length of exposure of inorganic arsenic. In particular, we found increases in H2B variants H2B1H/1K/1C/1J/1O and H2B2E/2F, and significant decreases in H2B1N/1D/1B as cells undergo inorganic arsenic-mediated epithelial-mesenchymal transition. The analysis of these histone vari-

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“…How the presence of nucleosomes on chromatin allows its replication and transcription to take place is an important and interesting question. Although both the status of nucleosomes and the role of histones in transcription initiation are becoming more and more clear (Grunstein, 1990b;Laybourn & Kadonaga, 1991;Workman et al, 1991), the status of nucleosomes during transcription elongation remains controversial (Lorch et al, 1988;Grunstein, 1990b;Clark & Felsenfeld, 1991 ;Kornberg & Lorch, 1991;Lee & Garrard, 1991;Thoma, 1991;Felsenfeld, 1992). The answer to this question spans two extremes: nucleosomes either dismantle or remain intact.…”

Section: ~~mentioning

confidence: 99%

Dynamics of interaction of RNA polymerase II with nucleosomes. I. Effect of salts

Bhargava

1993

Protein Science

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Mononucleosomes were labeled with the sulfhydryl-specific fluorescence probe 1,5-IAEDANS (5-(2-((iodoacety1)amino)ethyl)amino-naphthalene-1-sulfonic acid) by attaching the dye to the single cysteine of H3 through a covalent linkage. The enzyme RNA polymerase I1 (pol 11) utilized the native and the reconstituted fluorescent nucleosomes as templates with greatest efficiency when 0.2 M potassium acetate (AcOK) was used as the supporting salt; 0.2 M NaCl was found to be very much inhibitory. Measurement of polarity of the microenvironment of the dye at its binding site in the nucleosome showed the conformation to be more open in the presence of AcOK, compared to that in 0.1 or 0.2 M NaCl. The binding of pol I1 to the nucleosome resulted in a relatively more compact structure when measured in terms of the polarity of the microenvironment of the dye in various salt-dependent conformations of the nucleosomes. Time-resolved fluorescence spectroscopy showed that the probe molecule at its binding site undergoes certain excited-state processes, and the presence/absence or rate of these excited-state processes depends on the conformation of nucleosomes, which in turn depends on the type and concentration of the ion present in the medium. Time-resolved emission spectra showed that binding of nucleosomes by pol 11 established some new contacts that resulted in inaccessibility of the dye to the bulk solvent, reflecting a more hydrophobic environment for the dye in the steady-state spectra. Thus, binding or transcription of nucleosomes by pol I1 did not break open their structure. Rather, some transient internal adjustments within the histone octamer may take place to accommodate the bulky pol I1 molecule.

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Transcription-induced nucleosome ‘splitting’: an underlying structure for DNase I sensitive chromatin.

Cited by 137 publications

References 65 publications

Asymmetric nucleosomes flank promoters in the budding yeast genome

Asymmetric nucleosomes flank promoters in the budding yeast genome

Quantitative Mass Spectrometry Reveals Changes in Histone H2B Variants as Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation

Dynamics of interaction of RNA polymerase II with nucleosomes. I. Effect of salts

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