Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human
computational biology
developmental biology
enhancers
human
machine learning
mouse
orofacial cleft
periderm
systems biology
zebrafish
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
07 02 2020
07 02 2020
Historique:
received:
25
08
2019
accepted:
06
02
2020
pubmed:
8
2
2020
medline:
4
5
2021
entrez:
8
2
2020
Statut:
epublish
Résumé
Genome-wide association studies for non-syndromic orofacial clefting (OFC) have identified single nucleotide polymorphisms (SNPs) at loci where the presumed risk-relevant gene is expressed in oral periderm. The functional subsets of such SNPs are difficult to predict because the sequence underpinnings of periderm enhancers are unknown. We applied ATAC-seq to models of human palate periderm, including zebrafish periderm, mouse embryonic palate epithelia, and a human oral epithelium cell line, and to complementary mesenchymal cell types. We identified sets of enhancers specific to the epithelial cells and trained gapped-kmer support-vector-machine classifiers on these sets. We used the classifiers to predict the effects of 14 OFC-associated SNPs at 12q13 near
Identifiants
pubmed: 32031521
doi: 10.7554/eLife.51325
pii: 51325
pmc: PMC7039683
doi:
pii:
Substances chimiques
KRT18 protein, human
0
KRT8 protein, human
0
Keratin-18
0
Keratin-8
0
Green Fluorescent Proteins
147336-22-9
Banques de données
GEO
['GSE140241', 'GSE139945', 'GSE139809', 'GSE32483', 'GSE82727']
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 : NIDCR NIH HHS
ID : R01 DE028599
Pays : United States
Organisme : National Natural Science Foundation of China
ID : 81771057
Organisme : NCI NIH HHS
ID : P30 CA086862
Pays : United States
Organisme : NIDCR NIH HHS
ID : R01 DE023575
Pays : United States
Organisme : Natural Science Foundation of Hubei Province
ID : 2017CFB515
Organisme : NIDCR NIH HHS
ID : R01 DE027362
Pays : United States
Organisme : NIDCR NIH HHS
ID : R56 DE023575
Pays : United States
Organisme : National Natural Science Foundation of China
ID : 81400477
Organisme : NIDCR NIH HHS
ID : U01 DE024427
Pays : United States
Organisme : NIDCR NIH HHS
ID : K99 DE025060
Pays : United States
Organisme : NIDCR NIH HHS
ID : R00 DE025060
Pays : United States
Informations de copyright
© 2020, Liu et al.
Déclaration de conflit d'intérêts
HL, KD, AH, PK, CM, YX, JC, FD, AV, EL, PB, AE, RC No competing interests declared
Références
Genome Res. 2012 Nov;22(11):2290-301
pubmed: 23019145
PLoS Genet. 2010 Aug 19;6(8):e1001065
pubmed: 20808887
PLoS Comput Biol. 2014 Jul 17;10(7):e1003711
pubmed: 25033408
Development. 2019 Jun 17;146(12):
pubmed: 31118233
PLoS One. 2014 Jan 06;9(1):e84858
pubmed: 24400120
Dev Cell. 2015 Mar 23;32(6):661-2
pubmed: 25805131
Nat Commun. 2017 Mar 13;8:14759
pubmed: 28287101
Sci Rep. 2019 Jun 21;9(1):9060
pubmed: 31227770
Cell Rep. 2018 May 1;23(5):1581-1597
pubmed: 29719267
Nat Genet. 2017 Oct;49(10):1522-1528
pubmed: 28805829
J Clin Invest. 2014 Sep;124(9):3891-900
pubmed: 25133425
BMC Syst Biol. 2017 Mar 14;11(Suppl 2):7
pubmed: 28361702
Dev Biol. 2009 Feb 15;326(2):431-43
pubmed: 19073166
Int J Oral Maxillofac Surg. 2006 Jul;35(7):653-7
pubmed: 16513324
Am J Hum Genet. 2016 Apr 7;98(4):744-54
pubmed: 27018472
J Cell Sci. 2010 Oct 15;123(Pt 20):3566-75
pubmed: 20930145
Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6
pubmed: 21106759
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
G3 (Bethesda). 2019 Oct 7;9(10):3439-3452
pubmed: 31431477
Nat Methods. 2017 Jul;14(7):687-690
pubmed: 28581496
Heliyon. 2019 Dec 13;5(12):e03019
pubmed: 31886431
Science. 2018 Jun 1;360(6392):
pubmed: 29700225
Nature. 2012 Jan 04;481(7381):389-93
pubmed: 22217937
Nat Commun. 2017 Feb 24;8:14364
pubmed: 28232668
Dev Biol. 2009 Jan 1;325(1):249-62
pubmed: 19013452
Genome Res. 2012 Oct;22(10):2043-53
pubmed: 22593555
Nat Genet. 2006 Nov;38(11):1335-40
pubmed: 17041601
Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 2000 Sep;90(3):340-7
pubmed: 10982956
PLoS Comput Biol. 2018 Oct 4;14(10):e1006484
pubmed: 30286077
Nucleic Acids Res. 2011 Mar;39(6):e35
pubmed: 21177645
Development. 2007 May;134(9):1789-97
pubmed: 17376812
J Cell Biol. 1985 Oct;101(4):1257-69
pubmed: 2413039
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Methods Cell Biol. 2019;151:115-126
pubmed: 30948003
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
J Comp Neurol. 2012 Mar 1;520(4):816-31
pubmed: 22020759
Dev Dyn. 2002 Mar;223(2):204-15
pubmed: 11836785
Genes Dev. 2014 Sep 15;28(18):2013-26
pubmed: 25228645
PLoS Biol. 2011 Jan 18;9(1):e1000582
pubmed: 21267068
J Clin Invest. 2014 Dec;124(12):5205-18
pubmed: 25347468
Nat Biotechnol. 2018 Oct;36(9):888-893
pubmed: 29969439
Nucleic Acids Res. 2020 Jan 8;48(D1):D87-D92
pubmed: 31701148
Curr Opin Genet Dev. 2009 Dec;19(6):535-40
pubmed: 19913405
Sci Rep. 2017 Dec 14;7(1):17607
pubmed: 29242584
Development. 2013 Sep;140(18):3777-86
pubmed: 23924630
Bioinformatics. 2016 Jul 15;32(14):2205-7
pubmed: 27153639
Clin Exp Rheumatol. 2015 Jul-Aug;33(4 Suppl 92):S44-9
pubmed: 26458100
Science. 2006 Apr 14;312(5771):276-9
pubmed: 16556802
Differentiation. 1998 Sep;63(5):273-84
pubmed: 9810706
Nat Genet. 1999 Aug;22(4):356-60
pubmed: 10431239
Cell. 2014 Sep 11;158(6):1431-1443
pubmed: 25215497
Mol Cell. 2016 Apr 7;62(1):79-91
pubmed: 27058788
Nature. 2015 Feb 19;518(7539):317-30
pubmed: 25693563
Cancer Med. 2017 Nov;6(11):2686-2696
pubmed: 28960866
Curr Protoc Mol Biol. 2015 Jan 05;109:21.29.1-21.29.9
pubmed: 25559105
Eur J Oral Sci. 2010 Jun;118(3):221-36
pubmed: 20572855
Differentiation. 1982;23(2):170-8
pubmed: 6187618
Science. 2018 Jun 1;360(6392):981-987
pubmed: 29700229
Nature. 2019 Dec;576(7785):149-157
pubmed: 31634902
PLoS Genet. 2017 Sep 25;13(9):e1007009
pubmed: 28945736
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Development. 1990 Apr;108(4):581-94
pubmed: 2387237
J Cell Biol. 1998 Oct 19;143(2):469-86
pubmed: 9786956
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
Nat Genet. 2008 Nov;40(11):1341-7
pubmed: 18836445
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Oral Dis. 2018 Oct;24(7):1303-1309
pubmed: 29873870
Genesis. 2012 Mar;50(3):192-206
pubmed: 22139962
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Protoc. 2006;1(3):1297-305
pubmed: 17406414
J Dent Res. 2005 Jan;84(1):69-72
pubmed: 15615879
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Hum Genet. 2017 Mar;136(3):275-286
pubmed: 28054174
Biol Open. 2013 Dec 15;2(12):1336-45
pubmed: 24337118
Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13710-5
pubmed: 21807998
Genome Res. 2011 Mar;21(3):447-55
pubmed: 21106904
Genome Res. 2019 Mar;29(3):449-463
pubmed: 30696696
Nat Genet. 2008 Feb;40(2):158-60
pubmed: 18176564
Nat Biotechnol. 2010 May;28(5):495-501
pubmed: 20436461
Dev Dyn. 2012 Feb;241(2):340-9
pubmed: 22113860
Nat Genet. 2015 Aug;47(8):955-61
pubmed: 26075791
J Invest Dermatol. 2013 Jan;133(1):68-77
pubmed: 22931925
J Cell Biol. 2007 Dec 31;179(7):1599-612
pubmed: 18166659
Exp Ther Med. 2017 Oct;14(4):3393-3398
pubmed: 29042924
Development. 2002 May;129(9):2233-46
pubmed: 11959831
PLoS Genet. 2017 Jun 12;13(6):e1006828
pubmed: 28604778
Nature. 2015 May 14;521(7551):217-221
pubmed: 25778702
Proc Natl Acad Sci U S A. 2011 May 10;108(19):7902-7
pubmed: 21464299
Hum Mol Genet. 2015 Jul 15;24(14):3895-907
pubmed: 25652407
Hum Mol Genet. 2016 Feb 15;25(4):766-76
pubmed: 26692521
Semin Perinatol. 1986 Jan;10(1):50-64
pubmed: 3532342
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Dev Biol. 2010 Oct 15;346(2):272-83
pubmed: 20692251
Cell Rep. 2017 Jul 18;20(3):709-720
pubmed: 28723572
Hum Mol Genet. 2014 May 15;23(10):2711-20
pubmed: 24442519
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Am J Respir Cell Mol Biol. 2012 Oct;47(4):454-63
pubmed: 22652201
Proc Natl Acad Sci U S A. 1991 Sep 15;88(18):7948-52
pubmed: 1716766
Cell Host Microbe. 2015 Dec 9;18(6):723-35
pubmed: 26651948
Development. 2016 May 15;143(10):1674-87
pubmed: 26989177
Tissue Cell. 2006 Oct;38(5):293-301
pubmed: 16973199
Dev Biol. 2007 Oct 1;310(1):10-22
pubmed: 17719025
Am J Hum Genet. 2014 Jan 2;94(1):23-32
pubmed: 24360809