Long-read single-molecule maps of the functional methylome.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
14
06
2018
accepted:
25
02
2019
pubmed:
9
3
2019
medline:
14
6
2019
entrez:
9
3
2019
Statut:
ppublish
Résumé
We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spanning hundreds of kilobase pairs. The method provides kilobase pair-scale genomic methylation patterns comparable to whole-genome bisulfite sequencing (WGBS) along genes and regulatory elements. These long single-molecule reads allow for methylation variation calling and analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell second-generation sequencing. The method is applied here to study facioscapulohumeral muscular dystrophy (FSHD), simultaneously recording the haplotype, copy number, and methylation status of the disease-associated, highly repetitive locus on Chromosome 4q.
Identifiants
pubmed: 30846530
pii: gr.240739.118
doi: 10.1101/gr.240739.118
pmc: PMC6442387
doi:
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
Pagination
646-656Subventions
Organisme : European Research Council
ID : 337830
Pays : International
Organisme : NIMH NIH HHS
ID : U01 MH106884
Pays : United States
Organisme : NICHD NIH HHS
ID : U54 HD060848
Pays : United States
Organisme : NICHD NIH HHS
ID : U54 HD090257
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2019 Sharim et al.; Published by Cold Spring Harbor Laboratory Press.
Références
Cell. 1975 Nov;6(3):345-58
pubmed: 1052772
Am J Hum Genet. 2000 Jan;66(1):26-35
pubmed: 10631134
Hum Mol Genet. 2000 Apr 12;9(6):901-8
pubmed: 10767313
Genes Dev. 2002 Jan 1;16(1):6-21
pubmed: 11782440
Nat Rev Genet. 2002 May;3(5):370-9
pubmed: 11988762
Genome Res. 2002 Jun;12(6):996-1006
pubmed: 12045153
Oncogene. 2002 Aug 12;21(35):5427-40
pubmed: 12154405
Nucleic Acids Res. 1992 May 11;20 Suppl:2145-57
pubmed: 1317957
Gene. 2004 May 26;333:143-9
pubmed: 15177689
Nat Chem Biol. 2006 Jan;2(1):31-2
pubmed: 16408089
Trends Biotechnol. 2007 Mar;25(3):99-104
pubmed: 17254657
Genomics. 1992 Feb;12(2):241-53
pubmed: 1740333
Nature. 2007 Jun 14;447(7146):799-816
pubmed: 17571346
Genome Res. 2008 Jan;18(1):19-29
pubmed: 18032725
Nature. 2008 Mar 13;452(7184):215-9
pubmed: 18278030
Cell. 2008 May 2;133(3):523-36
pubmed: 18423832
Int J Cancer. 2009 Aug 1;125(3):723-9
pubmed: 19437537
Genome Res. 2009 Sep;19(9):1586-92
pubmed: 19657104
Nucleic Acids Res. 2010 Oct;38(18):e177
pubmed: 20699272
J Gerontol A Biol Sci Med Sci. 2011 Feb;66(2):202-13
pubmed: 21030466
J Cell Biol. 2010 Dec 13;191(6):1049-60
pubmed: 21149563
Nat Protoc. 2011 Apr;6(4):468-81
pubmed: 21412275
Nat Genet. 2011 Jun 26;43(8):768-75
pubmed: 21706001
Eur J Hum Genet. 2012 Feb;20(2):185-91
pubmed: 21811308
Nat Rev Genet. 2011 Nov 29;13(1):36-46
pubmed: 22124482
Nat Rev Genet. 2012 May 29;13(7):484-92
pubmed: 22641018
PLoS One. 2012;7(7):e41361
pubmed: 22848472
Nat Biotechnol. 2012 Aug;30(8):762-3
pubmed: 22871713
Nat Genet. 2012 Dec;44(12):1370-4
pubmed: 23143600
BMC Med Genet. 2013 Jan 29;14:18
pubmed: 23356558
Curr Opin Biotechnol. 2013 Aug;24(4):690-8
pubmed: 23428595
Chem Commun (Camb). 2013 Oct 7;49(77):8599-601
pubmed: 23756466
Nat Rev Cancer. 2013 Jul;13(7):497-510
pubmed: 23760024
Nat Commun. 2013;4:2190
pubmed: 23877302
Nature. 2013 Oct 3;502(7469):59-64
pubmed: 24067610
Am J Hum Genet. 2013 Oct 3;93(4):744-51
pubmed: 24075187
Genome Res. 2013 Dec;23(12):2126-35
pubmed: 24179143
ACS Nano. 2014 Jan 28;8(1):14-26
pubmed: 24328256
Nucleic Acids Res. 2014 Apr;42(7):e50
pubmed: 24452797
J Am Chem Soc. 2014 May 28;136(21):7771-6
pubmed: 24802414
Nucleic Acids Res. 2014 Sep;42(15):e118
pubmed: 25013180
Neurology. 2014 Aug 19;83(8):733-42
pubmed: 25031281
J Vis Exp. 2014 Nov 22;(93):e52014
pubmed: 25490674
PLoS One. 2014 Dec 29;9(12):e115278
pubmed: 25545674
Gigascience. 2014 Dec 30;3(1):34
pubmed: 25671094
BMC Genomics. 2015 May 06;16:350
pubmed: 25943404
Nucleic Acids Res. 2015 Oct 15;43(18):e117
pubmed: 26019180
Nat Methods. 2015 Aug;12(8):780-6
pubmed: 26121404
Chembiochem. 2015 Sep 7;16(13):1857-1860
pubmed: 26147952
PLoS One. 2016 Mar 22;11(3):e0151963
pubmed: 27002334
Nat Methods. 2016 Jul;13(7):587-90
pubmed: 27159086
Bioinformatics. 2016 Oct 1;32(19):2911-9
pubmed: 27318202
ACS Nano. 2016 Sep 27;10(9):8861-70
pubmed: 27580095
ACS Nano. 2016 Nov 22;10(11):9823-9830
pubmed: 27646634
BMC Genomics. 2016 Dec 6;17(1):997
pubmed: 27919246
Nat Methods. 2017 Apr;14(4):411-413
pubmed: 28218897
Nat Methods. 2017 Apr;14(4):407-410
pubmed: 28218898
Front Genet. 2017 Jun 07;8:76
pubmed: 28638402
Bioinformatics. 2018 Jan 1;34(1):134-136
pubmed: 29036307
Nat Genet. 2018 Oct;50(10):1388-1398
pubmed: 30202056
Nat Genet. 1995 Apr;9(4):432-8
pubmed: 7795651
Nucleic Acids Res. 1994 Aug 11;22(15):3181-6
pubmed: 8065934
Mol Cell Biol. 1993 Dec;13(12):7334-48
pubmed: 8246954
Nat Genet. 1993 Aug;4(4):387-92
pubmed: 8401587