Determinants of nucleosome positioning
By Kevin Struhl, Eran Segal. Nature Structural &Molecular Biology, 2013
679 citations recorded by the source corpus.
Nucleosome positioning is critical for gene expression and most DNA-related processes. Here we review the dominant patterns of nucleosome positioning that have been observed and summarize the current understanding of their underlying determinants. The genome-wide pattern of nucleosome positioning is determined by the combination of DNA sequence, ATP-dependent nucleosome remodeling enzymes and transcription factors that include activators, components of the preinitiation complex and elongating RNA polymerase II. These determinants influence each other such that the resulting nucleosome positioning patterns are likely to differ among genes and among cells in a population, with consequent effects on gene expression.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/056967d40bfde0c5118925bf903eb41064aa5662
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Citations in the corpus
- Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants (2017, background): “org/publicdomain/ze The structure of chromatin regulates the accessibility of genes for the transcriptional machinery, and is thus an integral part of regulated gene expression in stress responses and development [8, 9].”
- Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape (2016, neutral): “, locations) (Struhl and Segal, 2013).”
- Precise genome-wide mapping of single nucleosomes and linkers in vivo (2018, background): “Our biophysical model explains the salient features of nucleosome positioning genome-wide, while ignoring DNA sequence, thus simplifying our current understanding of the rules for nucleosome positioning [15].”
- Genomic nucleosome organization reconstituted with pure proteins (2016, background): “While transcription is not reconstituted in our systems and thus is not likely to be required for establishing the ground state organizational pattern, we fully expect that transcription initiation and elongation modulates nucleosome positioning (Hughes et al., 2012; Ocampo et al., 2016; Struhl and ”
- High-throughput functional testing of ENCODE segmentation predictions (2014, neutral): “scriptional regulation configure the immediate chromatin environment (Struhl and Segal 2013), leading to the constellation of histone modifications observed in segments with high cis-regulatory activity.”
- Organization of Chromatin by Intrinsic and Regulated Phase Separation (2019, background): “DNA sequences phased in TA:AT:TT:AA dinucleotide base pairs position nucleosomes in vitro and in vivo (Kaplan et al., 2009; Lowary and Widom, 1998; Struhl and Segal, 2013).”