Underlying causes for prevalent false positives and false negatives in STARR-seq data.
Journal
NAR genomics and bioinformatics
ISSN: 2631-9268
Titre abrégé: NAR Genom Bioinform
Pays: England
ID NLM: 101756213
Informations de publication
Date de publication:
Sep 2023
Sep 2023
Historique:
received:
07
02
2023
revised:
23
08
2023
accepted:
12
09
2023
medline:
25
9
2023
pubmed:
25
9
2023
entrez:
25
9
2023
Statut:
epublish
Résumé
Self-transcribing active regulatory region sequencing (STARR-seq) and its variants have been widely used to characterize enhancers. However, it has been reported that up to 87% of STARR-seq peaks are located in repressive chromatin and are not functional in the tested cells. While some of the STARR-seq peaks in repressive chromatin might be active in other cell/tissue types, some others might be false positives. Meanwhile, many active enhancers may not be identified by the current STARR-seq methods. Although methods have been proposed to mitigate systematic errors caused by the use of plasmid vectors, the artifacts due to the intrinsic limitations of current STARR-seq methods are still prevalent and the underlying causes are not fully understood. Based on predicted
Identifiants
pubmed: 37745976
doi: 10.1093/nargab/lqad085
pii: lqad085
pmc: PMC10516709
doi:
Types de publication
Journal Article
Langues
eng
Pagination
lqad085Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
Références
Nat Rev Genet. 2007 Mar;8(3):206-16
pubmed: 17304246
Nucleic Acids Res. 2017 Feb 28;45(4):1714-1730
pubmed: 27899590
Science. 1975 Apr 11;188(4184):107-16
pubmed: 1090005
Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7
pubmed: 19474294
Nature. 2015 Feb 19;518(7539):317-30
pubmed: 25693563
Cardiovasc Res. 2018 Jul 15;114(9):1226-1240
pubmed: 29554300
BMC Genomics. 2018 Apr 4;19(1):234
pubmed: 29618320
Transcription. 2018;9(5):307-314
pubmed: 29889606
Nat Rev Genet. 2015 Apr;16(4):197-212
pubmed: 25707927
Science. 2013 Mar 1;339(6123):1074-7
pubmed: 23328393
Nat Methods. 2015 Mar;12(3):265-72, 7 p following 272
pubmed: 25240437
Nat Genet. 2017 Jul;49(7):1073-1081
pubmed: 28581502
PLoS Genet. 2018 Nov 14;14(11):e1007793
pubmed: 30427832
Genome Biol. 2020 Jan 22;21(1):17
pubmed: 31969180
Genome Biol. 2020 Sep 10;21(1):243
pubmed: 32912294
Nat Biotechnol. 2012 Nov;30(11):1095-106
pubmed: 23138309
Nat Genet. 2014 Jul;46(7):685-92
pubmed: 24908250
Nucleic Acids Res. 2023 Jan 6;51(D1):D1188-D1195
pubmed: 36420891
Trends Cardiovasc Med. 2017 Aug;27(6):397-404
pubmed: 28456354
Science. 2016 Nov 11;354(6313):769-773
pubmed: 27708057
NAR Genom Bioinform. 2020 Jun;2(2):lqaa036
pubmed: 32500120
Nucleic Acids Res. 2019 Jul 26;47(13):6753-6768
pubmed: 31334813
Nat Rev Genet. 2020 May;21(5):292-310
pubmed: 31988385
Database (Oxford). 2022 Apr 22;2022:
pubmed: 35452518
BMC Biol. 2017 Oct 2;15(1):89
pubmed: 28969617
NAR Genom Bioinform. 2021 Jun 17;3(2):lqab052
pubmed: 34159315
Nat Commun. 2018 May 22;9(1):2022
pubmed: 29789573
Genome Biol. 2020 Dec 8;21(1):298
pubmed: 33292397
Nat Commun. 2018 Dec 19;9(1):5380
pubmed: 30568279
Nat Commun. 2015 Apr 15;6:6905
pubmed: 25872643
Am J Hum Genet. 2018 May 3;102(5):717-730
pubmed: 29727686
Eur J Hum Genet. 2014 Jan;22(1):144-7
pubmed: 23695286
Cell Stem Cell. 2018 Aug 02;23(2):276-288.e8
pubmed: 30033119
J Biol Chem. 2012 Sep 7;287(37):30932-40
pubmed: 22952232
Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92
pubmed: 17130149
Genome Res. 2017 Jan;27(1):38-52
pubmed: 27831498
Cell. 2019 Mar 21;177(1):162-183
pubmed: 30901538
Nat Methods. 2018 Feb;15(2):141-149
pubmed: 29256496
Nucleic Acids Res. 2019 Jan 8;47(D1):D1005-D1012
pubmed: 30445434
Mol Psychiatry. 2019 Mar;24(3):378-389
pubmed: 29942042
Front Cardiovasc Med. 2018 Jun 01;5:60
pubmed: 29911105
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Nucleic Acids Res. 2019 Jan 8;47(D1):D729-D735
pubmed: 30462313
Genome Biol. 2017 Nov 20;18(1):219
pubmed: 29151363
Nucleic Acids Res. 2021 Jan 8;49(D1):D221-D228
pubmed: 33045745
Nat Methods. 2020 Nov;17(11):1083-1091
pubmed: 33046894
BMC Biol. 2022 Oct 5;20(1):221
pubmed: 36199141
Nat Rev Genet. 2015 Apr;16(4):213-23
pubmed: 25732611
F1000Res. 2017 Jun 19;6:939
pubmed: 28690838
Nat Rev Genet. 2018 Mar;19(3):148-159
pubmed: 29335645