RRC ID 69010
Author Ishihara S, Sasagawa Y, Kameda T, Yamashita H, Umeda M, Kotomura N, Abe M, Shimono Y, Nikaido I.
Title Local states of chromatin compaction at transcription start sites control transcription levels.
Journal Nucleic Acids Res
Abstract The 'open' and 'compact' regions of chromatin are considered to be regions of active and silent transcription, respectively. However, individual genes produce transcripts at different levels, suggesting that transcription output does not depend on the simple open-compact conversion of chromatin, but on structural variations in chromatin itself, which so far have remained elusive. In this study, weakly crosslinked chromatin was subjected to sedimentation velocity centrifugation, which fractionated the chromatin according to its degree of compaction. Open chromatin remained in upper fractions, while compact chromatin sedimented to lower fractions depending on the level of nucleosome assembly. Although nucleosomes were evenly detected in all fractions, histone H1 was more highly enriched in the lower fractions. H1 was found to self-associate and crosslinked to histone H3, suggesting that H1 bound to H3 interacts with another H1 in an adjacent nucleosome to form compact chromatin. Genome-wide analyses revealed that nearly the entire genome consists of compact chromatin without differences in compaction between repeat and non-repeat sequences; however, active transcription start sites (TSSs) were rarely found in compact chromatin. Considering the inverse correlation between chromatin compaction and RNA polymerase binding at TSSs, it appears that local states of chromatin compaction determine transcription levels.
Volume 49(14)
Pages 8007-8023
Published 2021-8-20
DOI 10.1093/nar/gkab587
PII 6316832
PMID 34233004
PMC PMC8373074
MeSH Centrifugation Chromatin / genetics Chromatin / ultrastructure* Chromatin Assembly and Disassembly / genetics Genome, Human / genetics Histones / genetics Humans Nucleosomes / genetics* Nucleosomes / ultrastructure Protein Binding / genetics Transcription Factors / genetics Transcription Initiation Site* Transcription, Genetic*
IF 11.502
Human and Animal Cells Hep G2