Regulatory and evolutionary signatures of sex-biased genes on both the X chromosome and the autosomes

Biology of Sex Differences
Jiangshan J ShenWanling Yang

Abstract

Sex is an important but understudied factor in the genetics of human diseases. Analyses using a combination of gene expression data, ENCODE data, and evolutionary data of sex-biased gene expression in human tissues can give insight into the regulatory and evolutionary forces acting on sex-biased genes. In this study, we analyzed the differentially expressed genes between males and females. On the X chromosome, we used a novel method and investigated the status of genes that escape X-chromosome inactivation (escape genes), taking into account the clonality of lymphoblastoid cell lines (LCLs). To investigate the regulation of sex-biased differentially expressed genes (sDEG), we conducted pathway and transcription factor enrichment analyses on the sDEGs, as well as analyses on the genomic distribution of sDEGs. Evolutionary analyses were also conducted on both sDEGs and escape genes. Genome-wide, we characterized differential gene expression between sexes in 462 RNA-seq samples and identified 587 sex-biased genes, or 3.2% of the genes surveyed. On the X chromosome, sDEGs were distributed in evolutionary strata in a similar pattern as escape genes. We found a trend of negative correlation between the gene expression breadth and non...Continue Reading

References

Nov 5, 1999·Science·B T Lahn, D C Page
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Oct 21, 2006·Laboratory Investigation; a Journal of Technical Methods and Pathology·Julie L RyanMargaret L Gulley
Aug 8, 2007·Nature Reviews. Genetics·Hans Ellegren, John Parsch
Nov 3, 2007·Evolution; International Journal of Organic Evolution·Philip W Hedrick
Jan 4, 2008·The American Naturalist·Judith E MankHans Ellegren
Mar 10, 2009·Genes & Development·Michaela SchwaigerDirk Schübeler
Apr 7, 2009·Current Opinion in Genetics & Development·Ichiro HirataniDavid M Gilbert
May 26, 2009·Nucleic Acids Research·Jing ChenAnil G Jegga
Jun 11, 2010·Molecular Biology and Evolution·Chungoo ParkKateryna D Makova
Jun 16, 2010·Bioinformatics·Anmol Kiran, Pavel V Baranov
Jun 28, 2012·Molecular Medicine Reports·Markku H VaaralaTimo K Paavonen
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 11, 2012·Genome Research·Antigone S DimasEmmanouil T Dermitzakis
Oct 26, 2012·Genome Biology and Evolution·Raquel AssisDoris Bachtrog
Nov 28, 2012·American Journal of Human Genetics·Amnon KorenSteven A McCarroll
Sep 17, 2013·Nature·Tuuli LappalainenEmmanouil T Dermitzakis
Jan 7, 2014·Nature·Yukinori OkadaRobert M Plenge
Feb 11, 2014·Nature Genetics·UNKNOWN DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) ConsortiumAndrew P Morris
Nov 29, 2014·Current Protocols in Bioinformatics·Geraldine A Van der AuweraMark A DePristo
Dec 5, 2014·Epigenetics & Chromatin·Maria Tsompana, Michael J Buck
Jan 9, 2015·PLoS Genetics·Athma A PaiYoav Gilad
Feb 21, 2016·Database : the Journal of Biological Databases and Curation·Javier HerreroPaul Flicek
May 20, 2016·Genome Research·Kimberly R KukurbaStephen B Montgomery
Oct 13, 2017·Nature·Taru TukiainenDaniel G MacArthur

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Citations

Sep 26, 2019·Frontiers in Cell and Developmental Biology·Daniel F Deegan, Nora Engel
Dec 24, 2018·Nutrients·Dolores CorellaJose M Ordovas
Nov 6, 2018·Current Opinion in Rheumatology·Allison C BilliJohann E Gudjonsson
Oct 3, 2018·Cancer Research·Camila M Lopes-RamosJohn Quackenbush
Aug 2, 2020·Trends in Genetics : TIG·Sara Carmela CredendinoIrene Cantone
Jun 15, 2021·Frontiers in Cardiovascular Medicine·Daniel F DeeganNora Engel

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Methods Mentioned

BETA
RNA-Seq
ChipSeq

Software Mentioned

SAMtools
ENCODE
ENSEMBL
TweeDESeq
GATK
Gene Set Enrichment Analysis ( GSEA )
ToppFun
GSEA
R package TweeDESeq
ToppGene suite

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