High Stability of the Epigenome in Drosophila Interspecific Hybrids.
Drosophila
deregulation
epigenome
histone methylation
interspecific hybrids
transposable elements
Journal
Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707
Informations de publication
Date de publication:
04 02 2022
04 02 2022
Historique:
accepted:
02
02
2022
pubmed:
11
2
2022
medline:
1
4
2022
entrez:
10
2
2022
Statut:
ppublish
Résumé
Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F1 hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis-trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.
Identifiants
pubmed: 35143649
pii: 6526395
doi: 10.1093/gbe/evac024
pmc: PMC8872975
pii:
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Brief Funct Genomics. 2012 Jul;11(4):319-31
pubmed: 22806479
PLoS Biol. 2012;10(11):e1001428
pubmed: 23189033
PLoS One. 2014 Feb 20;9(2):e88992
pubmed: 24586475
Bioinformatics. 2011 Jun 15;27(12):1691-2
pubmed: 21493652
Genome Res. 2002 Apr;12(4):656-64
pubmed: 11932250
Mol Biol Evol. 2021 Jun 25;38(7):3022-3027
pubmed: 33892491
Genome Biol Evol. 2014 Dec 31;7(1):349-66
pubmed: 25552534
Genomics. 2019 Mar;111(2):177-185
pubmed: 29432976
Genome Res. 2010 Jun;20(6):816-25
pubmed: 20354124
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Genome Biol. 2009;10(3):R25
pubmed: 19261174
PLoS One. 2016 Jan 26;11(1):e0147903
pubmed: 26812285
Mol Biol Evol. 2007 Jan;24(1):137-45
pubmed: 17032727
Plant J. 2005 Dec;44(5):707-17
pubmed: 16297064
Genome Res. 2014 Jul;24(7):1125-37
pubmed: 24840603
Plant Cell. 2010 Jan;22(1):17-33
pubmed: 20086188
Genetics. 2005 Dec;171(4):1813-22
pubmed: 16143608
Nat Biotechnol. 2011 May 15;29(7):644-52
pubmed: 21572440
BMC Evol Biol. 2008 Mar 10;8:82
pubmed: 18331635
PLoS Genet. 2015 Oct 28;11(10):e1005462
pubmed: 26509888
Mol Biol Evol. 2014 May;31(5):1188-99
pubmed: 24505119
Genetics. 2006 Jan;172(1):507-17
pubmed: 16172500
Cytogenet Genome Res. 2005;110(1-4):462-7
pubmed: 16093699
Genome Biol. 2017 Aug 22;18(1):157
pubmed: 28830561
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Genetics. 2009 Oct;183(2):547-61, 1SI-21SI
pubmed: 19667135
BMC Genomics. 2017 Feb 7;18(1):137
pubmed: 28173754
J Hered. 2019 Jan 7;110(1):124-136
pubmed: 30107415
Mol Ecol. 2021 Jan;30(2):517-527
pubmed: 33179328
Science. 2010 Dec 24;330(6012):1787-97
pubmed: 21177974
Mol Biol Evol. 1999 Jul;16(7):931-7
pubmed: 10406110
PLoS Genet. 2011 Dec;7(12):e1002380
pubmed: 22194694
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nature. 1996 Jun 27;381(6585):807-10
pubmed: 8657287
Bioinformatics. 2019 Jun 1;35(12):2084-2092
pubmed: 30395178
Genetica. 2007 Jan;129(1):71-81
pubmed: 17043744
Curr Biol. 2020 Feb 24;30(4):573-588.e7
pubmed: 32004456
Genome Biol. 2017 Aug 4;18(1):148
pubmed: 28778180
Plant J. 2011 Aug;67(4):691-700
pubmed: 21554454
Genome Biol. 2012 Dec 19;13(12):R117
pubmed: 23253144
Elife. 2016 Jan 27;5:
pubmed: 26814573
Sci Rep. 2017 Jan 16;7:40618
pubmed: 28091568
Genome Biol Evol. 2018 Jun 1;10(6):1403-1415
pubmed: 29788048
Genome Biol Evol. 2019 Mar 1;11(3):660-677
pubmed: 30689829
Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14471-6
pubmed: 18791071
BMC Genomics. 2019 Oct 12;20(1):732
pubmed: 31606030
Behav Brain Res. 2001 Nov 1;125(1-2):279-84
pubmed: 11682119
Genome Biol Evol. 2016 Feb 12;8(3):556-61
pubmed: 26872773
Genetics. 1996 Jul;143(3):1243-55
pubmed: 8807297
Mol Biol Evol. 2016 Apr;33(4):984-94
pubmed: 26685177
Sci Rep. 2018 Aug 15;8(1):12197
pubmed: 30111890
Heredity (Edinb). 1991 Aug;67 ( Pt 1):57-72
pubmed: 1917552
Nucleic Acids Res. 2017 Feb 28;45(4):e17
pubmed: 28204592
Nature. 2004 Jul 1;430(6995):85-8
pubmed: 15229602
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Chromosome Res. 2006;14(4):377-92
pubmed: 16821134
Mol Biol Evol. 2003 Jul;20(7):1070-6
pubmed: 12777520
BMC Bioinformatics. 2015 Apr 29;16:137
pubmed: 25924884
Mol Phylogenet Evol. 2012 Sep;64(3):533-44
pubmed: 22634936
Genome Res. 2011 Feb;21(2):147-63
pubmed: 21177972
PLoS Genet. 2014 Mar 20;10(3):e1004240
pubmed: 24651406
PLoS One. 2012;7(9):e44253
pubmed: 22962605
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Genome Biol Evol. 2014 Jun 24;6(7):1806-17
pubmed: 24966182
Annu Rev Entomol. 2007;52:171-92
pubmed: 16881818
Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489
pubmed: 33237286
Genetica. 2011 Apr;139(4):465-77
pubmed: 21424276
Genome Biol Evol. 2017 Jun 1;9(6):1450-1470
pubmed: 28854624
Mob Genet Elements. 2014 Aug 08;4:e34394
pubmed: 25136509
Genome Biol. 2013 Jun 12;14(6):R57
pubmed: 23758703
Trends Genet. 2017 Jan;33(1):68-80
pubmed: 27914620
Bioinformatics. 2011 Mar 15;27(6):863-4
pubmed: 21278185
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genes Dev. 2004 Jun 1;18(11):1263-71
pubmed: 15175259
Cell. 2010 Oct 15;143(2):212-24
pubmed: 20888037
Genome Res. 2004 Mar;14(3):373-9
pubmed: 14962989
Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):E468-77
pubmed: 23329330
Biotechniques. 2011 Apr;50(4):247-50
pubmed: 21548908
Evolution. 1993 Oct;47(5):1616-1624
pubmed: 28564907
Elife. 2020 Sep 21;9:
pubmed: 32955438
Nat Methods. 2013 Jan;10(1):71-3
pubmed: 23160280
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Mol Genet Genomics. 2015 Aug;290(4):1471-83
pubmed: 25711309
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Mol Biol Evol. 2003 Mar;20(3):410-23
pubmed: 12644562
Heredity (Edinb). 2012 May;108(5):461-8
pubmed: 21971178
J Hered. 1998 Jul-Aug;89(4):336-9
pubmed: 9703688
Philos Trans R Soc Lond B Biol Sci. 2014 Aug 5;369(1648):
pubmed: 24958919
Genes (Basel). 2020 Feb 19;11(2):
pubmed: 32092860