Dynamic enhancer landscapes in human craniofacial development.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
06 Mar 2024
06 Mar 2024
Historique:
received:
29
06
2023
accepted:
25
02
2024
medline:
8
3
2024
pubmed:
7
3
2024
entrez:
6
3
2024
Statut:
epublish
Résumé
The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
Identifiants
pubmed: 38448444
doi: 10.1038/s41467-024-46396-4
pii: 10.1038/s41467-024-46396-4
pmc: PMC10917818
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2030Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIDCR NIH HHS
ID : R01 DE028599
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG003988
Pays : United States
Organisme : NIDCR NIH HHS
ID : U01 DE024427
Pays : United States
Informations de copyright
© 2024. The Author(s).
Références
Development. 2019 Jun 17;146(12):
pubmed: 31118233
Clin Genet. 2017 Jul;92(1):91-98
pubmed: 28067412
J Clin Invest. 2011 Apr;121(4):1585-95
pubmed: 21364285
J Dent Res. 2022 Oct;101(11):1289-1298
pubmed: 35912790
Genome Biol. 2020 Feb 7;21(1):31
pubmed: 32033589
Connect Tissue Res. 2002;43(2-3):153-60
pubmed: 12489152
Wiley Interdiscip Rev Dev Biol. 2014 Nov-Dec;3(6):403-18
pubmed: 25176500
Front Cell Dev Biol. 2020 Dec 18;8:620735
pubmed: 33392208
Biomed Res Int. 2016;2016:3054578
pubmed: 28053980
Hum Mol Genet. 2016 Oct 1;25(R2):R190-R197
pubmed: 27402881
Pigment Cell Melanoma Res. 2008 Dec;21(6):627-45
pubmed: 18983540
Cell Rep. 2018 May 1;23(5):1581-1597
pubmed: 29719267
Front Bioinform. 2023 Feb 24;3:1092853
pubmed: 36909938
Front Cell Dev Biol. 2020 Oct 26;8:587699
pubmed: 33195244
Cell. 2013 Dec 19;155(7):1521-31
pubmed: 24360275
Nucleic Acids Res. 2023 Jan 6;51(D1):D1188-D1195
pubmed: 36420891
Genomics. 2015 Sep;106(3):159-164
pubmed: 26072433
Nat Commun. 2020 Sep 23;11(1):4816
pubmed: 32968047
Nat Commun. 2022 Jan 10;13(1):13
pubmed: 35013168
PLoS Genet. 2014 May 29;10(5):e1004360
pubmed: 24875170
Nat Commun. 2023 Aug 2;14(1):4623
pubmed: 37532691
Nucleic Acids Res. 2002 Jan 1;30(1):207-10
pubmed: 11752295
Neuron. 2004 Feb 5;41(3):337-50
pubmed: 14766174
Nature. 2015 Oct 1;526(7571):75-81
pubmed: 26432246
Nat Neurosci. 2018 Mar;21(3):432-439
pubmed: 29434377
Nature. 2020 Jul;583(7818):744-751
pubmed: 32728240
Am J Hum Genet. 2013 Feb 7;92(2):265-70
pubmed: 23312594
Nat Commun. 2020 May 13;11(1):2389
pubmed: 32404924
Nat Rev Genet. 2001 Jun;2(6):458-68
pubmed: 11389462
Blood. 1999 Jan 1;93(1):165-75
pubmed: 9864158
Front Genet. 2018 Oct 16;9:462
pubmed: 30386375
Nucleic Acids Res. 2015 Jan;43(Database issue):D789-98
pubmed: 25428349
Genome Biol. 2015 Jan 05;16:22
pubmed: 25723102
Elife. 2019 May 29;8:
pubmed: 31140974
Nat Commun. 2021 Feb 26;12(1):1337
pubmed: 33637727
Development. 2016 Jul 15;143(14):2677-88
pubmed: 27287806
Nucleic Acids Res. 2021 Jan 8;49(D1):D981-D987
pubmed: 33231642
Cell. 2020 Mar 19;180(6):1262-1271.e15
pubmed: 32169219
Science. 2021 Feb 5;371(6529):
pubmed: 33542111
Nat Rev Genet. 2021 May;22(5):324-336
pubmed: 33442000
J Med Genet. 2017 Aug 9;54(10):698-704
pubmed: 28794130
Nat Commun. 2021 Aug 10;12(1):4797
pubmed: 34376651
Cell. 2021 Jun 24;184(13):3573-3587.e29
pubmed: 34062119
Front Cell Dev Biol. 2021 Apr 01;9:595744
pubmed: 33869166
Cell Tissue Res. 2013 Jul;353(1):99-115
pubmed: 23689684
AJNR Am J Neuroradiol. 2013 Dec;34(12):2233-40
pubmed: 23493891
Development. 2020 Sep 21;147(18):
pubmed: 32958507
FASEB J. 2012 Aug;26(8):3464-72
pubmed: 22581782
Hum Mol Genet. 2013 Aug 15;22(16):3250-8
pubmed: 23591992
Am J Med Genet A. 2016 Sep;170(9):2462-5
pubmed: 27380734
Nature. 2020 Jul;583(7818):699-710
pubmed: 32728249
Hum Mol Genet. 2015 Oct 15;24(R1):R50-9
pubmed: 26085576
Development. 2004 Nov;131(21):5319-26
pubmed: 15456728
Gene. 2016 May 10;582(1):1-13
pubmed: 26774798
Nat Commun. 2023 Sep 14;14(1):5687
pubmed: 37709732
Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5
pubmed: 23193258
BMC Med Genet. 2018 Sep 10;19(1):160
pubmed: 30200890
Nat Methods. 2020 Feb;17(2):137-145
pubmed: 31792435
Dev Biol. 2011 Jul 15;355(2):175-82
pubmed: 21458441
Cell. 2005 Mar 25;120(6):843-56
pubmed: 15797384
Dev Cell. 2015 Apr 6;33(1):56-66
pubmed: 25800090
Nat Biotechnol. 2018 Jun;36(5):411-420
pubmed: 29608179
Methods Mol Biol. 2022;2403:147-186
pubmed: 34913122
Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92
pubmed: 17130149
Sci Adv. 2019 May 01;5(5):eaaw0946
pubmed: 31049400
Bone. 2014 Sep;66:96-104
pubmed: 24929242
Postgrad Med J. 2001 Aug;77(910):489-91
pubmed: 11470926
Nucleic Acids Res. 2019 Jan 8;47(D1):D23-D28
pubmed: 30395293
Am J Med Genet A. 2019 Feb;179(2):312-316
pubmed: 30561111
Nat Methods. 2019 Jul;16(7):619-626
pubmed: 31209384
Front Cell Dev Biol. 2021 May 20;9:644410
pubmed: 34095113
Nucleic Acids Res. 2019 Jan 8;47(D1):D1005-D1012
pubmed: 30445434
F1000Res. 2016 Aug 31;5:2122
pubmed: 27909575
Nat Rev Genet. 2019 May;20(5):257-272
pubmed: 30696980
Hum Genet. 2020 Oct;139(10):1261-1272
pubmed: 32318854
Hum Genet. 2000 Mar;106(3):345-50
pubmed: 10798365
Eur J Hum Genet. 2014 Mar;22(3):419-22
pubmed: 23881059
Nat Commun. 2021 Dec 8;12(1):7132
pubmed: 34880220
Elife. 2021 Aug 16;10:
pubmed: 34397384
Science. 2013 Oct 25;342(6157):1241006
pubmed: 24159046
Cell. 2004 Nov 12;119(4):567-78
pubmed: 15537545
Cell. 2016 Nov 17;167(5):1170-1187
pubmed: 27863239
Development. 2005 Jul;132(13):3127-38
pubmed: 15944192
Nucleic Acids Res. 2021 Jan 8;49(D1):D1207-D1217
pubmed: 33264411
Sci Data. 2017 Aug 29;4:170112
pubmed: 28850106
Development. 1995 Jan;121(1):37-51
pubmed: 7867507
Nat Genet. 2000 Apr;24(4):391-5
pubmed: 10742104
Elife. 2019 Jan 14;8:
pubmed: 30638444
Sci Rep. 2019 Jun 27;9(1):9354
pubmed: 31249361
PLoS Genet. 2011 Mar;7(3):e1002027
pubmed: 21455487
Nat Biotechnol. 2010 May;28(5):495-501
pubmed: 20436461
Brief Funct Genomics. 2018 Jul 1;17(4):283-294
pubmed: 29092000
Commun Biol. 2023 Apr 20;6(1):435
pubmed: 37081156
Bioinformatics. 2023 Jan 1;39(1):
pubmed: 36394265
Mech Dev. 2007 Sep-Oct;124(9-10):729-45
pubmed: 17693062
Development. 2023 Apr 15;150(8):
pubmed: 36971348
Nature. 2019 Feb;566(7745):496-502
pubmed: 30787437
Cell. 2019 Jun 13;177(7):1888-1902.e21
pubmed: 31178118
J Vis Exp. 2018 Jun 28;(136):
pubmed: 30010637
Development. 2021 Nov 15;148(22):
pubmed: 35020873
Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14036-41
pubmed: 14623956
PLoS One. 2013 Sep 16;8(9):e74137
pubmed: 24066106
Development. 2022 Jul 15;149(14):
pubmed: 35781558
Genome Res. 1999 Aug;9(8):677-9
pubmed: 10447503
Am J Orthod. 1985 Jul;88(1):64-76
pubmed: 3860013
Nat Genet. 2019 Dec;51(12):1664-1669
pubmed: 31784727
Brain Res Rev. 2007 Oct;55(2):237-47
pubmed: 17765317
EMBO J. 1998 Oct 1;17(19):5718-33
pubmed: 9755172
Development. 2007 Sep;134(18):3283-95
pubmed: 17699607
J Biol Chem. 1998 Jun 12;273(24):14989-97
pubmed: 9614106
Nat Genet. 2019 Oct;51(10):1442-1449
pubmed: 31501517
Cell. 2015 Sep 24;163(1):68-83
pubmed: 26365491
Sci Adv. 2020 Dec 16;6(51):
pubmed: 33328221
Bioinformatics. 2015 Apr 15;31(8):1334-6
pubmed: 25431330
Genes Dev. 2001 Nov 15;15(22):3039-49
pubmed: 11711438
Science. 2019 Jun 07;364(6444):
pubmed: 31171666
Nat Methods. 2009 May;6(5):343-5
pubmed: 19363495
Nucleic Acids Res. 2019 Jan 8;47(D1):D1038-D1043
pubmed: 30445645
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Am J Hum Genet. 2020 Jul 2;107(1):124-136
pubmed: 32574564
Cell Rep. 2022 Sep 20;40(12):111400
pubmed: 36130500
Elife. 2021 Jan 27;10:
pubmed: 33501917
Elife. 2022 Mar 25;11:
pubmed: 35333176
J Invest Dermatol. 2002 Dec;119(6):1388-93
pubmed: 12485444
J Dent Res. 2017 Oct;96(11):1184-1191
pubmed: 28745929
Nat Genet. 2021 Jan;53(1):45-53
pubmed: 33288918
Elife. 2017 Dec 04;6:
pubmed: 29199959
Dev Biol. 2016 Jul 15;415(2):171-187
pubmed: 26808208
Science. 1981 Jul 31;213(4507):563-5
pubmed: 7017936
Am J Med Genet A. 2019 Jul;179(7):1214-1225
pubmed: 31069901