Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression

BMC Genomics
Kenneth J Evans

Abstract

On a single strand of genomic DNA the number of As is usually about equal to the number of Ts (and similarly for Gs and Cs), but deviations have been noted for transcribed regions and origins of replication. The mouse genome is shown to have a segmented structure defined by strand bias. Transcription is known to cause a strand bias and numerous analyses are presented to show that the strand bias in question is not caused by transcription. However, these strand bias segments influence the position of genes and their unspliced length. The position of genes within the strand bias structure affects the probability that a gene is switched on and its expression level. Transcription has a highly directional flow within this structure and the peak volume of transcription is around 20 kb from the A-rich/T-rich segment boundary on the T-rich side, directed away from the boundary. The A-rich/T-rich boundaries are SATB1 binding regions, whereas the T-rich/A-rich boundary regions are not. The direct cause of the strand bias structure may be DNA replication. The strand bias segments represent a further biological feature, the chromatin structure, which in turn influences the ease of transcription.

References

Jul 1, 1968·Proceedings of the National Academy of Sciences of the United States of America·R RudnerE Chargaff
Mar 14, 1968·Journal of Molecular Biology·J A Huberman, A D Riggs
May 1, 1996·Molecular Biology and Evolution·J R Lobry
Sep 5, 1997·Science·F R BlattnerY Shao
May 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·J Mrázek, S Karlin
Jun 10, 1998·Nucleic Acids Research·A Grigoriev
Dec 16, 1998·Journal of Molecular Evolution·M J McLeanK M Devine
Feb 3, 1999·Annual Review of Genetics·S KarlinJ Mrázek
Jul 23, 2002·Nature Genetics·Cristian I Castillo-DavisFyodor A Kondrashov
Mar 4, 2003·Nature Genetics·Phil GreenEric D Green
Jul 9, 2003·Nature Genetics·Eduardo P C Rocha, Antoine Danchin
Jul 10, 2003·Trends in Genetics : TIG·Eli Eisenberg, Erez Y Levanon
Jul 26, 2003·American Journal of Human Genetics·Jacek Majewski
Nov 14, 2003·Genome Research·Francesca ChiaromonteEric E Bouhassira
Nov 14, 2003·Genome Research·Elizabeth LouieJacek Majewski
Nov 25, 2003·Journal of Molecular Evolution·Deng K NiuDa-Yong Zhang
Sep 25, 2004·Nucleic Acids Research·Marie TouchonClaude Thermes
Dec 21, 2004·Nucleic Acids Research·Sam Griffiths-JonesAlex Bateman
Mar 1, 2005·BMC Genomics·Shigeo FujimoriMasaru Tomita
Jun 30, 2005·Proceedings of the National Academy of Sciences of the United States of America·Marie TouchonClaude Thermes
Aug 11, 2005·Physical Review Letters·E B Brodie Of BrodieA Arneodo
Mar 18, 2006·PLoS Computational Biology·Gustavo GlusmanArian F A Smit
Jul 18, 2006·Nucleic Acids Research·Philipp W Messer, Peter F Arndt
Nov 14, 2006·Nucleic Acids Research·Tanya BarrettRon Edgar
Nov 16, 2006·Physiological Genomics·Andreas WernerHeiko Peters
Dec 7, 2006·Nucleic Acids Research·T J P HubbardE Birney
Mar 6, 2007·BMC Bioinformatics·Kenneth EvansLorenz Wernisch
Apr 11, 2007·Molecular Biology Reports·Hai-Fang WangDeng-Ke Niu
Jul 6, 2007·Biochemical and Biophysical Research Communications·Shu-Wei LiDeng-Ke Niu
Aug 7, 2007·Genome Research·Maxime HuvetClaude Thermes

❮ Previous
Next ❯

Methods Mentioned

BETA
chip

Software Mentioned

ENSEMBL

Related Concepts

Related Feeds

Ataxia telangiectasia (MDS)

Ataxia telangiectasia is a rare neurodegenerative diseases caused by defects in the ATM gene, which is involved in DNA damage recognition and repair pathways. Here is the latest research on this autosomal recessive disease.

© 2021 Meta ULC. All rights reserved