Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in Pigs

Animals : an Open Access Journal From MDPI
Haifei WangWenbin Bao

Abstract

Porcine epidemic diarrhea virus (PEDV) is currently detected as the main pathogen causing severe diarrhea in pig farms. The phenotypic alterations induced by pathogenic infections are usually tightly linked with marked changes in epigenetic modification and gene expression. We performed global mapping of H3K4 trimethylation (H3K4me3) and transcriptomic analyses in the jejunum of PEDV-infected and healthy piglets using chromatin immunoprecipitation sequencing and RNA-seq techniques. A total of 1885 H3K4me3 peaks that are associated with 1723 genes were characterized. Moreover, 290 differentially expressed genes were identified, including 104 up-regulated and 186 down-regulated genes. Several antiviral genes including 2'-5'-oligoadenylate synthetase 1 (OAS1), 2'-5'-oligoadenylate synthetase 2 (OAS2), ephrin B2 (EFNB2), and CDC28 protein kinase regulatory subunit 1B (CKS1B) with higher H3K4me3 enrichment and expression levels in PEDV-infected samples suggested the potential roles of H3K4me3 deposition in promoting their expressions. Transcription factor annotation analysis highlighted the potential roles of two transcription factors interferon regulatory factor 8 (IRF8) and Kruppel like factor 4 (KLF4) in modulating the differenti...Continue Reading

References

Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Apr 28, 2004·Cell·Matthias W HentzeNancy C Andrews
Aug 2, 2005·Cell Metabolism·Adriana DonovanNancy C Andrews
Aug 26, 2006·Nature Reviews. Immunology·Kenya Honda, Tadatsugu Taniguchi
Jan 18, 2007·Proceedings of the National Academy of Sciences of the United States of America·Deborah J LenschowHerbert Whiting Virgin
Jul 4, 2007·Journal of the American Veterinary Medical Association·Adam J Moeser, Anthony T Blikslager
Jun 26, 2008·Nature Reviews. Immunology·Anthony J Sadler, Bryan R G Williams
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Apr 11, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sung-Woo ParkDavid J Erle
May 12, 2009·Nature Reviews. Microbiology·Stanley Perlman, Jason Netland
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Rosa KarlićMartin Vingron
Feb 19, 2011·Bioinformatics·Charles E GrantWilliam Stafford Noble
Mar 9, 2011·The Journal of Immunology : Official Journal of the American Association of Immunologists·Taku KobayashiScott E Plevy
Aug 22, 2013·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Gregory W StevensonKyoungjin J Yoon
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Dec 23, 2014·Cellular & Molecular Immunology·Wei-Wei LuoShu Li
Mar 20, 2015·Journal of Virology·Chang LiuFang Li
Nov 6, 2015·The Journal of Veterinary Medical Science·Dongbo SunLi Feng
Feb 5, 2016·The Journal of Immunology : Official Journal of the American Association of Immunologists·Ming YanHerbert C Morse
Jul 14, 2017·Journal of Autoimmunity·Kerstin KleinCaroline Ospelt

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Citations

Mar 13, 2021·Frontiers in Genetics·Mengqi Wang, Eveline M Ibeagha-Awemu
Jun 23, 2020·Pharmacological Research : the Official Journal of the Italian Pharmacological Society·Esther C W de BoerMarit J van Gils

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Methods Mentioned

BETA
immunoprecipitation
RNA-seq
PCR
RNA Assay
ChIP
ChIP-seq

Software Mentioned

skewer
in
FIMO
MACS2
DESeq of R
BWA
HTSeq
KOBAS
TopHat2
house Perl scripts

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