Epigenetic patterns in a complete human genome.
Journal
Science (New York, N.Y.)
ISSN: 1095-9203
Titre abrégé: Science
Pays: United States
ID NLM: 0404511
Informations de publication
Date de publication:
04 2022
04 2022
Historique:
entrez:
31
3
2022
pubmed:
1
4
2022
medline:
6
4
2022
Statut:
ppublish
Résumé
The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.
Identifiants
pubmed: 35357915
doi: 10.1126/science.abj5089
pmc: PMC9170183
mid: NIHMS1804273
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
eabj5089Subventions
Organisme : NHGRI NIH HHS
ID : U24 HG010263
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007445
Pays : United States
Organisme : NIGMS NIH HHS
ID : F32 GM134558
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA253481
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG011274
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG010971
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM123312
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG002385
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG009190
Pays : United States
Organisme : NIDDK NIH HHS
ID : R24 DK106766
Pays : United States
Commentaires et corrections
Type : CommentIn
Références
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
Annu Rev Cell Dev Biol. 2018 Oct 6;34:265-288
pubmed: 30044650
Eur Rev Med Pharmacol Sci. 2020 Feb;24(4):1807-1814
pubmed: 32141549
Nucleic Acids Res. 2018 Mar 16;46(5):2252-2264
pubmed: 29365171
Bioinformatics. 2017 Sep 01;33(17):2759-2761
pubmed: 28472236
Cancers (Basel). 2020 Dec 09;12(12):
pubmed: 33316946
Nature. 2021 May;593(7857):101-107
pubmed: 33828295
Genome Res. 2016 Oct;26(10):1301-1311
pubmed: 27510565
Nat Rev Genet. 2020 Oct;21(10):597-614
pubmed: 32504078
Science. 2011 Feb 4;331(6017):593-6
pubmed: 21233348
Genes Chromosomes Cancer. 2006 Apr;45(4):392-400
pubmed: 16382448
Nature. 2017 Sep 13;549(7671):219-226
pubmed: 28905911
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Annu Rev Genomics Hum Genet. 2009;10:355-86
pubmed: 19630567
Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):E4504-12
pubmed: 27432957
Elife. 2019 Jun 25;8:
pubmed: 31237235
Nat Genet. 2007 Nov;39(11):1361-8
pubmed: 17922013
Genome Res. 2011 Jun;21(6):908-14
pubmed: 21518739
Genes (Basel). 2019 May 08;10(5):
pubmed: 31072070
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Cell Rep. 2018 Dec 4;25(10):2891-2903.e5
pubmed: 30517874
Bioinformatics. 2008 Dec 15;24(24):2818-24
pubmed: 18952627
PLoS Comput Biol. 2019 Apr 8;15(4):e1006650
pubmed: 30958812
Genome Biol. 2012 Oct 03;13(10):R83
pubmed: 23034175
Cell Discov. 2018 Aug 7;4:41
pubmed: 30109120
EMBO J. 2012 Nov 5;31(21):4165-78
pubmed: 23010778
Bioinformatics. 2021 May 5;37(6):744-749
pubmed: 33107913
Nature. 2006 Feb 23;439(7079):973-7
pubmed: 16341202
Cell. 2018 May 31;173(6):1370-1384.e16
pubmed: 29856955
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Cell. 2018 May 31;173(6):1356-1369.e22
pubmed: 29856954
Annu Rev Genomics Hum Genet. 2021 Aug 31;22:81-102
pubmed: 33929893
Nature. 2004 Jul 22;430(6998):471-6
pubmed: 15269773
Cancer Res. 2010 Apr 1;70(7):2718-27
pubmed: 20233874
Genom Data. 2015 Sep 1;5:139-146
pubmed: 26167452
Chromosome Res. 2017 Mar;25(1):77-87
pubmed: 28078514
Nature. 2020 Sep;585(7823):79-84
pubmed: 32663838
Genes Dev. 2019 Dec 1;33(23-24):1688-1701
pubmed: 31727772
J Cell Sci. 2001 Oct;114(Pt 19):3529-42
pubmed: 11682612
Nucleic Acids Res. 2018 Jan 4;46(D1):D794-D801
pubmed: 29126249
Nature. 2014 Jul 31;511(7511):606-10
pubmed: 25079557
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Nature. 2004 Sep 16;431(7006):268-74
pubmed: 15372022
Science. 2016 Oct 28;354(6311):477-481
pubmed: 27789843
Hum Mol Genet. 2018 Oct 15;27(20):3488-3497
pubmed: 30281091
Genome Biol. 2007;8(7):R151
pubmed: 17663781
Psychiatr Genet. 2009 Apr;19(2):64-71
pubmed: 19672138
Nature. 2015 Feb 19;518(7539):317-30
pubmed: 25693563
Genet Med. 2010 Mar;12(3):145-52
pubmed: 20057317
Science. 2022 Apr;376(6588):eabl4178
pubmed: 35357911
Science. 2007 Feb 23;315(5815):1141-3
pubmed: 17322062
Science. 1971 Dec 17;174(4015):1200-9
pubmed: 4943851
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Nat Biotechnol. 2020 Sep;38(9):1044-1053
pubmed: 32686750
Hum Mol Genet. 2009 Jan 15;18(2):304-17
pubmed: 18971205
Genomics. 1999 Dec 15;62(3):508-18
pubmed: 10644450
Genome Res. 2008 Aug;18(8):1259-69
pubmed: 18456864
PLoS Genet. 2019 Mar 27;15(3):e1008075
pubmed: 30917130
Nature. 2016 Feb 11;530(7589):177-83
pubmed: 26814963
Nat Methods. 2020 Dec;17(12):1191-1199
pubmed: 33230324
Int J Gynecol Pathol. 2021 Jul 1;40(4):333-341
pubmed: 33021557
Nat Genet. 1992 May;1(2):137-43
pubmed: 1302007
Science. 2022 Apr;376(6588):eabj6965
pubmed: 35357917
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
FEBS J. 2005 Jan;272(1):282-9
pubmed: 15634350
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Cancer Sci. 2006 Dec;97(12):1374-80
pubmed: 16995877
Genome Biol. 2019 Dec 16;20(1):278
pubmed: 31842956
Science. 2012 Nov 9;338(6108):758-67
pubmed: 23145453
Science. 2022 Apr;376(6588):eabk3112
pubmed: 35357925
Carcinogenesis. 1997 Jun;18(6):1215-23
pubmed: 9214605
Front Cell Dev Biol. 2020 Jan 21;7:328
pubmed: 32076600
Nat Rev Genet. 2008 Dec;9(12):923-37
pubmed: 19002142
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Science. 2020 Jun 26;368(6498):1449-1454
pubmed: 32587015
Nucleic Acids Res. 2018 Nov 16;46(20):e120
pubmed: 30169659
Hum Mol Genet. 2015 Mar 15;24(6):1528-39
pubmed: 25381334
Hum Genet. 2001 Oct;109(4):452-62
pubmed: 11702227
Genes Dev. 2018 Jan 1;32(1):20-25
pubmed: 29386331
Bioinformatics. 2011 Jun 1;27(11):1571-2
pubmed: 21493656
Nat Methods. 2017 Apr;14(4):407-410
pubmed: 28218898
Science. 2010 Oct 29;330(6004):641-6
pubmed: 21030649
Cell. 2002 Aug 9;110(3):339-48
pubmed: 12176321
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
J Physiol. 2014 Jun 1;592(11):2251-60
pubmed: 24882810
Am J Hum Genet. 2019 Nov 7;105(5):947-958
pubmed: 31668704
Nat Commun. 2017 Nov 28;8(1):1833
pubmed: 29184138
Genes Chromosomes Cancer. 1996 Dec;17(4):234-44
pubmed: 8946205