Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages

Scientific Reports
Cheng WangColin Logie

Abstract

Glucocorticoid receptor is a transcription factor that is ubiquitously expressed. Glucocorticoids are circadian steroids that regulate a wide range of bodily functions, including immunity. Here we report that synthetic glucocorticoids affect 1035 mRNAs in isolated healthy human blood monocytes but only 165 in the respective six day-old monocyte-derived macrophages. The majority of the glucocorticoid response in monocytes concerns genes that are dynamic upon monocyte to macrophage differentiation, whereby macrophage-like mRNA levels are often reached in monocytes within four hours of treatment. Concomitantly, over 5000 chromosomal H3K27ac regions undergo remodelling, of which 60% involve increased H3K27ac signal. We find that chromosomal glucocorticoid receptor binding sites correlate with positive but not with negative local epigenomic effects. To investigate further we assigned our data to topologically associating domains (TADs). This shows that about 10% of macrophage TADs harbour at least one GR binding site and that half of all the glucocorticoid-induced H3K27ac regions are confined to these TADs. Our analyses are therefore consistent with the notion that TADs naturally accommodate information from sets of distal glucocort...Continue Reading

References

Feb 1, 1985·The Journal of Clinical Investigation·T R CuppsA S Fauci
Apr 13, 2000·European Journal of Immunology·M K MatyszakP Ricciardi-Castagnoli
Jun 17, 2000·Journal of Leukocyte Biology·A van der GoesC D Dijkstra
Aug 28, 2004·Molecular Endocrinology·Julien GrenierCharbel Massaad
Sep 28, 2005·Proceedings of the National Academy of Sciences of the United States of America·Cosima FonteCharbel Massaad
Oct 22, 2005·Molecular Endocrinology·Weiwei ChenMichael J Garabedian
Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
Feb 6, 2007·The Journal of Biological Chemistry·Latika DhawanMark B Taubman
May 4, 2007·The Journal of Steroid Biochemistry and Molecular Biology·Cosima FonteCharbel Massaad
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Apr 18, 2009·Science·Sebastiaan H MeijsingKeith R Yamamoto
May 12, 2009·Nucleic Acids Research·Yuan-Bin XieHueng-Sik Choi
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jul 28, 2009·Cellular and Molecular Life Sciences : CMLS·Tomoshige KinoGeorge P Chrousos
Apr 24, 2010·Nature Reviews. Immunology·Christopher K Glass, Kaoru Saijo
May 13, 2010·Journal of Visualized Experiments : JoVE·Nynke L van BerkumEric S Lander
Dec 15, 2010·The Journal of Immunology : Official Journal of the American Association of Immunologists·Faoud T IshmaelCristiana Stellato
Jan 13, 2011·Autoimmunity Reviews·Margherita ZenAndrea Doria
Jan 25, 2011·Nature Genetics·Sam JohnJohn A Stamatoyannopoulos
Jul 14, 2011·Genome Research·Nagesha A S RaoHendrik G Stunnenberg
Jan 4, 2012·Pharmacology & Therapeutics·Andrew R Clark, Maria G Belvisi
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard

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Citations

Sep 12, 2019·Frontiers in Immunology·Jan M EhrchenKatarzyna Barczyk-Kahlert
May 20, 2020·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·Rafal MorgaJoanna Pera
Jun 26, 2020·Frontiers in Immunology·Dieuwertje M MosselJulia Kzhyshkowska
Feb 16, 2021·Frontiers in Immunology·Rebecca ShepherdBoris Novakovic
Apr 10, 2021·Nucleic Acids Research·Daniela RovitoDaniel Metzger
Jan 19, 2022·Journal of Leukocyte Biology·Laszlo A GrohNiels P Riksen

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Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
RNA-seq
acetylation
ChIP
HiC
RNAseq
ELISA
electrophoresis
PCR

Software Mentioned

GMQL
4Cseqpipe
package SVA
MoMf
Ensembl
Deeptools
DESeq2
UCSC genome browser
UCSC
Homer

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