Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth.
Journal
Science advances
ISSN: 2375-2548
Titre abrégé: Sci Adv
Pays: United States
ID NLM: 101653440
Informations de publication
Date de publication:
12 2020
12 2020
Historique:
received:
18
05
2020
accepted:
19
10
2020
entrez:
3
12
2020
pubmed:
4
12
2020
medline:
16
4
2022
Statut:
epublish
Résumé
While a genetic component of preterm birth (PTB) has long been recognized and recently mapped by genome-wide association studies (GWASs), the molecular determinants underlying PTB remain elusive. This stems in part from an incomplete availability of functional genomic annotations in human cell types relevant to pregnancy and PTB. We generated transcriptome (RNA-seq), epigenome (ChIP-seq of H3K27ac, H3K4me1, and H3K4me3 histone modifications), open chromatin (ATAC-seq), and chromatin interaction (promoter capture Hi-C) annotations of cultured primary decidua-derived mesenchymal stromal/stem cells and in vitro differentiated decidual stromal cells and developed a computational framework to integrate these functional annotations with results from a GWAS of gestational duration in 56,384 women. Using these resources, we uncovered additional loci associated with gestational duration and target genes of associated loci. Our strategy illustrates how functional annotations in pregnancy-relevant cell types aid in the experimental follow-up of GWAS for PTB and, likely, other pregnancy-related conditions.
Identifiants
pubmed: 33268355
pii: 6/49/eabc8696
doi: 10.1126/sciadv.abc8696
pmc: PMC7710387
pii:
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Medical Research Council
ID : MC_PC_19009
Pays : United Kingdom
Organisme : NIDDK NIH HHS
ID : R01 DK114661
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH110531
Pays : United States
Organisme : Medical Research Council
ID : MC_PC_15018
Pays : United Kingdom
Organisme : Medical Research Council
ID : G9815508
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NHLBI NIH HHS
ID : R01 HL129735
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL128075
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL119577
Pays : United States
Informations de copyright
Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).
Références
Endocr Rev. 2014 Dec;35(6):851-905
pubmed: 25141152
Epigenomics. 2018 Sep;10(9):1243-1257
pubmed: 30212243
Nat Rev Genet. 2018 Aug;19(8):491-504
pubmed: 29844615
Int J Epidemiol. 2013 Feb;42(1):111-27
pubmed: 22507743
Endocrinology. 2000 Sep;141(9):3510-3
pubmed: 10965925
Science. 2012 Sep 7;337(6099):1190-5
pubmed: 22955828
Nat Commun. 2019 Sep 2;10(1):3927
pubmed: 31477735
Mol Endocrinol. 2014 Oct;28(10):1656-69
pubmed: 25073104
Semin Cell Dev Biol. 2016 Sep;57:57-67
pubmed: 27364700
FASEB J. 2018 May;32(5):2467-2477
pubmed: 29259032
Fertil Steril. 2013 Jan;99(1):248-255.e2
pubmed: 23036802
Am J Hum Genet. 2018 Oct 4;103(4):509-521
pubmed: 30245028
PLoS Genet. 2007 Jul;3(7):e114
pubmed: 17676998
Int J Mol Sci. 2020 Mar 13;21(6):
pubmed: 32183093
Nature. 2012 Nov 1;491(7422):56-65
pubmed: 23128226
J Clin Endocrinol Metab. 2003 Dec;88(12):6029-33
pubmed: 14671207
Am J Obstet Gynecol. 2007 Feb;196(2):107-18
pubmed: 17306646
Endocrinology. 2015 Jun;156(6):2239-53
pubmed: 25781565
Genome Biol. 2016 Jun 15;17(1):127
pubmed: 27306882
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Mol Endocrinol. 2015 Mar;29(3):421-33
pubmed: 25584414
Biostatistics. 2007 Apr;8(2):485-99
pubmed: 17189563
Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130022
pubmed: 24218635
Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):E8468-E8477
pubmed: 28923940
Genome Biol. 2014;15(12):550
pubmed: 25516281
Elife. 2018 Jul 10;7:
pubmed: 29988018
Med Mol Morphol. 2013 Jun;46(2):61-8
pubmed: 23381604
Genome Res. 2015 Apr;25(4):582-97
pubmed: 25752748
Nat Genet. 2015 Jun;47(6):598-606
pubmed: 25938943
Bioinformatics. 2016 Jan 15;32(2):283-5
pubmed: 26395773
Mol Hum Reprod. 2017 Oct 1;23(10):708-724
pubmed: 28962035
PLoS One. 2017 Feb 22;12(2):e0172642
pubmed: 28225815
Mol Endocrinol. 2013 Dec;27(12):2041-54
pubmed: 24176914
Cell Commun Signal. 2011 May 14;9:12
pubmed: 21569606
Nucleic Acids Res. 2014 Dec 1;42(21):
pubmed: 25294822
Nat Genet. 2016 Oct;48(10):1193-203
pubmed: 27526324
Cold Spring Harb Perspect Med. 2015 Apr 27;5(11):
pubmed: 25918180
Lancet. 2008 Jan 19;371(9608):261-9
pubmed: 18207020
Am J Hum Genet. 2014 Apr 3;94(4):559-73
pubmed: 24702953
Reprod Biol Endocrinol. 2018 Feb 07;16(1):12
pubmed: 29415736
Reprod Sci. 2018 Feb;25(2):166-173
pubmed: 28826363
PLoS Genet. 2011 Apr;7(4):e1001365
pubmed: 21533219
Nature. 2015 Feb 19;518(7539):317-30
pubmed: 25693563
BJOG. 2005 Mar;112 Suppl 1:28-31
pubmed: 15715591
Scand J Public Health. 2001 Dec;29(4):300-7
pubmed: 11775787
Genet Epidemiol. 2009 Jan;33(1):79-86
pubmed: 18642345
Genet Med. 2005 Nov-Dec;7(9):593-604
pubmed: 16301860
Int J Epidemiol. 2013 Feb;42(1):97-110
pubmed: 22507742
Mol Endocrinol. 2011 Nov;25(11):1892-903
pubmed: 21903722
N Engl J Med. 2017 Sep 21;377(12):1156-1167
pubmed: 28877031
Bioinformatics. 2015 Mar 1;31(5):782-4
pubmed: 25338720
Mol Endocrinol. 2015 Jun;29(6):882-95
pubmed: 25875046
Nat Genet. 2015 Nov;47(11):1228-35
pubmed: 26414678
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Genome Res. 2002 Jun;12(6):996-1006
pubmed: 12045153
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Am J Hum Genet. 2016 Jun 2;98(6):1114-1129
pubmed: 27236919
Cell Rep. 2016 Oct 25;17(5):1414-1425
pubmed: 27783953
Int J Epidemiol. 2016 Apr;45(2):382-8
pubmed: 27063603
Gene Expr Patterns. 2012 May-Jun;12(5-6):196-203
pubmed: 22476030
Endocrinology. 2020 Jun 1;161(6):
pubmed: 32335672
Stem Cell Res Ther. 2019 Jun 14;10(1):177
pubmed: 31200769
J R Stat Soc Series B Stat Methodol. 2020 Dec;82(5):1273-1300
pubmed: 37220626
J Stat Softw. 2011 May 1;40(12):1-32
pubmed: 22523482
Proteomics. 2011 Feb;11(4):794-804
pubmed: 21229588
Cell Rep. 2015 Mar 3;10(8):1398-409
pubmed: 25732829
PLoS Biol. 2011 Apr;9(4):e1001046
pubmed: 21526222
Tohoku J Exp Med. 2017;242(2):83-91
pubmed: 28566565
Reprod Biomed Online. 2006 Oct;13(4):591-9
pubmed: 17007686
F1000Res. 2015 Nov 20;4:1310
pubmed: 26835000
Nat Methods. 2017 Apr;14(4):417-419
pubmed: 28263959
J Biol Chem. 2011 Jun 3;286(22):19860-71
pubmed: 21471197
Mol Cell Endocrinol. 2008 Nov 25;295(1-2):32-8
pubmed: 18775765
Nat Methods. 2011 Dec 04;9(2):179-81
pubmed: 22138821
Science. 2011 Feb 18;331(6019):912-6
pubmed: 21330545
PLoS One. 2013 Apr 16;8(4):e61781
pubmed: 23613933
J Immunol Methods. 1990 Sep 14;132(2):181-9
pubmed: 2145368