A novel mechanism of epigenetic regulation: nucleosome-space occupancy

Biochemical and Biophysical Research Communications
Peng CuiJun Yu

Abstract

Nucleosome positioning around the gene space (or transcriptional unit) plays a crucial role for gene regulation but we do not know if the spatial organization--nucleosome-space occupancy or nucleosome density in a defined sequence unit length--contributes to the regulation complexity of mammalian gene expression. Using our own rmRNA-Seq (ribosomal RNA-minus RNA sequencing) and publically available ChIP-Seq (H3) data from mouse stem cells, we discovered a non-random distribution of nucleosomes along chromosomes, and further genome-wide studies on histone modifications, DNA methylation, transcriptional activity, gene density, and base compositional dynamics, demonstrated that nucleosome-space occupancy of genomic regions--clustered genes and their intergenic spaces--show distinctive features, where a high occupancy coincides with active transcription, intensive histone modifications, poor DNA methylation, and higher GC contents as compared to the nucleosome-poor regions. We therefore proposed that nucleosome-space occupancy as a novel mechanism of epigenetic gene regulation, creating a vital environment for transcriptional activation.

References

Feb 10, 1995·The Journal of Biological Chemistry·S M Berget
May 1, 1994·Journal of Cellular Biochemistry·Q LuS C Elgin
Mar 21, 2003·Current Biology : CB·Natasha Thorne, Hubert Amrein
Mar 12, 2005·The Journal of Biological Chemistry·Andrew J BannisterTony Kouzarides
Apr 9, 2005·Briefings in Functional Genomics & Proteomics·Sari PenningsColin S Davey
Jan 25, 2006·Proceedings of the National Academy of Sciences of the United States of America·Serge SaxonovDouglas L Brutlag
Oct 13, 2006·Molecular and Cellular Biology·Christopher R VakocGerd A Blobel
Feb 27, 2007·Cell·Bradley E BernsteinEric S Lander
Feb 27, 2007·Cell·Tony Kouzarides
Mar 11, 2008·Cell·Dustin E SchonesKeji Zhao
Jun 3, 2008·Nature Methods·Nicole CloonanSean M Grimmond
Dec 17, 2008·Journal of Molecular Biology·Ho-Ryun Chung, Martin Vingron
Feb 11, 2009·Nature Reviews. Genetics·Cizhong Jiang, B Franklin Pugh
Jul 1, 2009·BMC Developmental Biology·Ke ZhengPeijing Jeremy Wang
Aug 19, 2009·Genome Research·Robin AnderssonJan Komorowski

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Citations

Aug 1, 2012·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Tonglaga BaoGuoqing Liu
Mar 23, 2011·Ecotoxicology·Michiel B Vandegehuchte, Colin R Janssen
Oct 23, 2012·Nature Structural & Molecular Biology·Vladimir B TeifKarsten Rippe
Nov 17, 2011·Genes & Development·Sheila S Teves, Steven Henikoff
Nov 17, 2011·Genes & Development·Katharine Compton AbruzziMichael Rosbash
Oct 22, 2013·Mutation Research. Genetic Toxicology and Environmental Mutagenesis·Leda Mirbahai, James K Chipman
Jul 10, 2012·Genomics, Proteomics & Bioinformatics·Jun Yu
Apr 29, 2014·Genomics, Proteomics & Bioinformatics·Jiayan WuJun Yu
Dec 19, 2012·Epigenomics·Luca MagnaniMathieu Lupien
Oct 7, 2017·Epigenetics & Chromatin·Vincenzo Cavalieri, Giovanni Spinelli
Sep 25, 2020·Journal of Translational Medicine·Cristina Maccalli
Oct 30, 2010·Current Opinion in Endocrinology, Diabetes, and Obesity

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