Exploration of nucleosome positioning patterns in transcription factor function

Scientific Reports
Kazumitsu Maehara, Yasuyuki Ohkawa

Abstract

The binding of transcription factors (TFs) triggers activation of specific chromatin regions through the recruitment and activation of RNA polymerase. Unique nucleosome positioning (NP) occurs during gene expression and has been suggested to be involved in various other chromatin functions. However, the diversity of NP that can occur for each function has not been clarified. Here we used MNase-Seq data to evaluate NP around 258 cis-regulatory elements in the mouse genome. Principal component analysis of the 258 elements revealed that NP consisted of five major patterns. Furthermore, the five NP patterns had predictive power for the level of gene expression. We also demonstrated that selective NP patterns appeared around TF binding sites. These results suggest that the NP patterns are correlated to specific functions on chromatin.

References

Aug 11, 2001·Science·T Jenuwein, C D Allis
Aug 28, 2003·Nature Structural Biology·Stephen Buratowski
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Jun 18, 2005·Science·Guo-Cheng YuanOliver J Rando
Dec 31, 2005·Nucleic Acids Research·V MatysE Wingender
Jul 25, 2006·Nature·Eran SegalJonathan Widom
Dec 30, 2006·The Journal of Biological Chemistry·Yasuyuki OhkawaAnthony N Imbalzano
Feb 27, 2007·Cell·Bing LiJerry L Workman
Apr 15, 2008·Nature·Travis N MavrichB Franklin Pugh
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Nov 8, 2008·PLoS Computational Biology·Yair FieldEran Segal
Feb 11, 2009·Nature Reviews. Genetics·Cizhong Jiang, B Franklin Pugh
Apr 21, 2009·Nature Structural & Molecular Biology·Maarten KruithofJohn van Noort
Feb 18, 2010·PloS One·Desiree TilloTimothy R Hughes
Mar 9, 2010·Nature Genetics·Housheng Hansen HeX Shirley Liu
Oct 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Xiaochun FanKevin Struhl
Oct 16, 2010·Methods in Enzymology·Oliver J Rando
Jan 6, 2011·PloS One·Ho-Ryun ChungMartin Vingron
Jan 19, 2011·Cell·Zhenhai Zhang, B Franklin Pugh
May 10, 2011·Proceedings of the National Academy of Sciences of the United States of America·Patrik AspBrian David Dynlacht
May 24, 2011·Nature·Anton ValouevArend Sidow
Oct 26, 2011·Proceedings of the National Academy of Sciences of the United States of America·Jorja G HenikoffSteven Henikoff
May 10, 2012·The EMBO Journal·Akihito HaradaYasuyuki Ohkawa
Aug 15, 2012·Genome Biology·UNKNOWN Mouse ENCODE ConsortiumLeslie B Adams
Oct 23, 2012·Nature Structural & Molecular Biology·Vladimir B TeifKarsten Rippe
Jul 13, 2013·Bioinformatics·Robert SchöpflinGero Wedemann
May 23, 2015·Bioinformatics·Kazumitsu Maehara, Yasuyuki Ohkawa

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Citations

Jul 12, 2019·Frontiers in Microbiology·Anthony J SaviolaSeth Frietze
Nov 23, 2020·Journal of Molecular Biology·Daniël P Melters, Yamini Dalal

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Datasets Mentioned

BETA
DRA001262

Methods Mentioned

BETA
MNase-Seq
ChIP-seq
PCR
chemical modifications
immunoprecipitation
electrophoresis

Software Mentioned

R
tfbsConsSites
UCSC
liftOver
MACS
Bowtie2
agplus

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