H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions in the human genome

By C. Jin, Chongzhi Zang, Gang Wei, Kairong Cui, Weiqun Peng, Keji Zhao, G. Felsenfeld. Nature Genetics, 2009

791 citations recorded by the source corpus.

To understand how chromatin structure is organized by different histone variants, we have measured the genome-wide distribution of nucleosome core particles (NCPs) containing the histone variants H3.3 and H2A.Z in human cells. We find that a special class of NCPs containing both variants is enriched at 'nucleosome-free regions' of active promoters, enhancers and insulator regions. We show that preparative methods used previously in studying nucleosome structure result in the loss of these unstable double-variant NCPs. It seems likely that this instability facilitates the access of transcription factors to promoters and other regulatory sites in vivo. Other combinations of variants have different distributions, consistent with distinct roles for histone variants in the modulation of gene expression.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f0d276ff7a5a30e8619ba20fe36210829da2b8f0

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Citations in the corpus

Comprehensive analysis of the chromatin landscape in Drosophila (2010, background): “35);thus, further integration of such data in the same cell type may resolve additional functional features.”
Histone variants — ancient wrap artists of the epigenome (2010, neutral): “3 nucleosomes in human NDRs, which are not uniformly positioned 68 , probably represent nucleosomes that are in the process of being disrupted.”
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. (2013, neutral): “These results indicate that the identified clusters are biologically relevant, as the genomic loci they occupy are enriched in conserved sequences, and in established promoter and enhancer marks (Barski et al., 2007; Heintzman et al., 2007; Jin et al., 2009).”
Modification of enhancer chromatin: what, how and why? (2013, background): “Z, which are deposited at chromatin in a replication-independent manner (Goldberg et al., 2010; Jin et al., 2009).”
Enhancer function: new insights into the regulation of tissue-specific gene expression (2011, positive): “Z-containing nucleosome core particles are enriched at the nucleosome-free regions of regulatory elements across the genom”
Distinct factors control histone variant H3.3 localization at specific genomic regions (2010, methodology): “3 enrichment has recently been shown at TFBS in Drosophila and human cells (Jin et al., 2009; Mito et al., 2007).”
Epigenetic regulation of gene responsiveness in Arabidopsis (2014, positive): “Z/H3 in human cells (Jin and Felsenfeld, 2007; Jin et al., 2009).”
Pioneer transcription factors: establishing competence for gene expression. (2011, background): “Z, at promoters can also destabilize nucleosomes (Zhang et al. 2005; Jin and Felsenfeld 2007; Jin et al. 2009).”