A novel quantitative targeted analysis of X-chromosome inactivation (XCI) using nanopore sequencing.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
08 08 2023
08 08 2023
Historique:
received:
12
04
2022
accepted:
29
04
2023
medline:
10
8
2023
pubmed:
9
8
2023
entrez:
8
8
2023
Statut:
epublish
Résumé
X-chromosome inactivation (XCI) analyses often assist in diagnostics of X-linked traits, however accurate assessment remains challenging with current methods. We developed a novel strategy using amplification-free Cas9 enrichment and Oxford nanopore technologies sequencing called XCI-ONT, to investigate and rigorously quantify XCI in human androgen receptor gene (AR) and human X-linked retinitis pigmentosa 2 gene (RP2). XCI-ONT measures methylation over 116 CpGs in AR and 58 CpGs in RP2, and separate parental X-chromosomes without PCR bias. We show the usefulness of the XCI-ONT strategy over the PCR-based golden standard XCI technique that only investigates one or two CpGs per gene. The results highlight the limitations of using the golden standard technique when the XCI pattern is partially skewed and the advantages of XCI-ONT to rigorously quantify XCI. This study provides a universal XCI-method on DNA, which is highly valuable in clinical and research framework of X-linked traits.
Identifiants
pubmed: 37553382
doi: 10.1038/s41598-023-34413-3
pii: 10.1038/s41598-023-34413-3
pmc: PMC10409790
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
12856Informations de copyright
© 2023. Springer Nature Limited.
Références
Clin Epigenetics. 2015 Oct 16;7:113
pubmed: 26478754
Nat Biotechnol. 2020 Apr;38(4):433-438
pubmed: 32042167
Eur J Hum Genet. 2019 Mar;27(3):455-465
pubmed: 30552425
Mol Neurobiol. 2020 Sep;57(9):3671-3684
pubmed: 32564284
Hum Genome Var. 2016 Oct 13;3:16033
pubmed: 27790374
Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E668-E675
pubmed: 29282321
Am J Hum Genet. 2002 Jul;71(1):168-73
pubmed: 12068376
Science. 1981 Jan 23;211(4480):393-6
pubmed: 6164095
PLoS One. 2014 Jul 31;9(7):e103714
pubmed: 25078280
Am J Hum Genet. 1992 Dec;51(6):1229-39
pubmed: 1281384
Nat Methods. 2012 Jul;9(7):671-5
pubmed: 22930834
Eur J Hum Genet. 2021 Feb;29(2):241-249
pubmed: 33082527
Cell. 2008 Feb 8;132(3):410-21
pubmed: 18267073
Science. 2022 Apr;376(6588):eabj5089
pubmed: 35357915
J Hum Genet. 2018 May;63(5):589-595
pubmed: 29459630
Front Genet. 2021 Dec 17;12:782629
pubmed: 34976017
Eur J Hum Genet. 2007 Jun;15(6):628-37
pubmed: 17342157
Cytogenet Genome Res. 2007;116(1-2):24-8
pubmed: 17268174
Nat Rev Mol Cell Biol. 2022 Apr;23(4):231-249
pubmed: 35013589
Cytogenet Cell Genet. 1998;80(1-4):142-8
pubmed: 9678349
Blood. 2001 Mar 1;97(5):1274-81
pubmed: 11222370
Blood. 1996 Jul 1;88(1):59-65
pubmed: 8704202
Cell. 1987 Jan 16;48(1):39-46
pubmed: 3791414
Nat Biotechnol. 2019 Dec;37(12):1478-1481
pubmed: 31740840
Biol Sex Differ. 2020 Jul 17;11(1):39
pubmed: 32680558
J Cell Biol. 2001 May 14;153(4):773-84
pubmed: 11352938
Nucleic Acids Res. 1995 Apr 25;23(8):1411-8
pubmed: 7753634
Ophthalmol Retina. 2020 May;4(5):510-520
pubmed: 31953110
Proc Natl Acad Sci U S A. 1984 May;81(9):2806-10
pubmed: 6585829
Genome Res. 2011 Oct;21(10):1592-600
pubmed: 21862626
Nature. 2022 Apr;604(7904):160-166
pubmed: 35355011
Clin Genet. 2011 Nov;80(5):466-71
pubmed: 20950395
Nature. 1961 Apr 22;190:372-3
pubmed: 13764598
Sci Rep. 2019 Jul 24;9(1):10730
pubmed: 31341187
Neurology. 2008 Apr 15;70(16 Pt 2):1397-402
pubmed: 18057320
BMC Genomics. 2015 May 06;16:350
pubmed: 25943404
Eur J Hum Genet. 1995;3(6):333-43
pubmed: 8825575
Nephrol Dial Transplant. 2010 Mar;25(3):764-9
pubmed: 19854849
Nat Methods. 2020 Dec;17(12):1191-1199
pubmed: 33230324
Hum Mol Genet. 1997 Nov;6(12):2005-10
pubmed: 9328463
Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3704-9
pubmed: 20133578
Brain Sci. 2021 Jul 09;11(7):
pubmed: 34356138
Nat Commun. 2021 Jun 11;12(1):3586
pubmed: 34117247
Nat Commun. 2019 Nov 25;10(1):5339
pubmed: 31767861
Front Genet. 2021 Sep 20;12:724625
pubmed: 34616429
Plant Methods. 2020 Sep 01;16:121
pubmed: 32884578
Biol Rev Camb Philos Soc. 1972 Jan;47(1):1-35
pubmed: 4554151
Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):8185-8190
pubmed: 30038001
Hum Genet. 2014 Nov;133(11):1359-67
pubmed: 25037250
Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12591-8
pubmed: 25136103
Nat Methods. 2017 Apr;14(4):407-410
pubmed: 28218898
Cells. 2022 Feb 03;11(3):
pubmed: 35159344
Neurol Genet. 2016 Feb 03;2(1):e45
pubmed: 27066582
Orphanet J Rare Dis. 2012 Oct 23;7:82
pubmed: 23092449
Am J Hum Genet. 2006 Sep;79(3):493-9
pubmed: 16909387
Eur J Hum Genet. 2005 May;13(5):599-606
pubmed: 15756296
Proc Natl Acad Sci U S A. 1982 Apr;79(7):2352-4
pubmed: 6179098
Development. 2020 Jan 3;147(1):
pubmed: 31900287
Nucleic Acids Res. 2019 Jul 2;47(W1):W171-W174
pubmed: 31106371
Eur J Med Genet. 2019 Apr;62(4):243-247
pubmed: 30048822
Am J Hum Genet. 2007 Jun;80(6):1138-49
pubmed: 17503331
Hum Mutat. 2018 Sep;39(9):1262-1272
pubmed: 29932473
Hum Mutat. 2016 Aug;37(8):804-11
pubmed: 27159028
Mol Cell Biol. 1986 Nov;6(11):4122-5
pubmed: 3025634
Ann Neurol. 2005 Jan;57(1):144-7
pubmed: 15622531