Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH.
Adaptor Proteins, Signal Transducing
/ genetics
Bayes Theorem
Clustered Regularly Interspaced Short Palindromic Repeats
Delta-5 Fatty Acid Desaturase
Deoxyribonuclease I
/ genetics
Fatty Acid Desaturases
/ genetics
Flow Cytometry
GATA1 Transcription Factor
/ genetics
Humans
In Situ Hybridization, Fluorescence
/ methods
K562 Cells
LIM Domain Proteins
/ genetics
Models, Genetic
Polymorphism, Single Nucleotide
Proto-Oncogene Proteins
/ genetics
Quantitative Trait Loci
RNA, Guide, Kinetoplastida
Regulatory Sequences, Nucleic Acid
Journal
Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904
Informations de publication
Date de publication:
08 2021
08 2021
Historique:
received:
27
05
2020
accepted:
23
06
2021
pubmed:
31
7
2021
medline:
11
9
2021
entrez:
30
7
2021
Statut:
ppublish
Résumé
Effective interpretation of genome function and genetic variation requires a shift from epigenetic mapping of cis-regulatory elements (CREs) to characterization of endogenous function. We developed hybridization chain reaction fluorescence in situ hybridization coupled with flow cytometry (HCR-FlowFISH), a broadly applicable approach to characterize CRISPR-perturbed CREs via accurate quantification of native transcripts, alongside CRISPR activity screen analysis (CASA), a hierarchical Bayesian model to quantify CRE activity. Across >325,000 perturbations, we provide evidence that CREs can regulate multiple genes, skip over the nearest gene and display activating and/or silencing effects. At the cholesterol-level-associated FADS locus, we combine endogenous screens with reporter assays to exhaustively characterize multiple genome-wide association signals, functionally nominate causal variants and, importantly, identify their target genes.
Identifiants
pubmed: 34326544
doi: 10.1038/s41588-021-00900-4
pii: 10.1038/s41588-021-00900-4
pmc: PMC8925018
mid: NIHMS1723995
doi:
Substances chimiques
Adaptor Proteins, Signal Transducing
0
Delta-5 Fatty Acid Desaturase
0
GATA1 Transcription Factor
0
GATA1 protein, human
0
LIM Domain Proteins
0
LMO2 protein, human
0
Proto-Oncogene Proteins
0
RNA, Guide
0
Fatty Acid Desaturases
EC 1.14.19.-
Deoxyribonuclease I
EC 3.1.21.1
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
1166-1176Subventions
Organisme : NHGRI NIH HHS
ID : R00 HG008179
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007226
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NHGRI NIH HHS
ID : R00 HG010669
Pays : United States
Organisme : NHGRI NIH HHS
ID : K99 HG008179
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009435
Pays : United States
Organisme : NHGRI NIH HHS
ID : F32 HG009226
Pays : United States
Organisme : NHGRI NIH HHS
ID : K99 HG010669
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI151051
Pays : United States
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
PLoS One. 2012;7(12):e52880
pubmed: 23285212
Science. 2016 Nov 11;354(6313):769-773
pubmed: 27708057
Nat Biotechnol. 2016 Feb;34(2):184-191
pubmed: 26780180
Nat Biotechnol. 2013 Sep;31(9):827-32
pubmed: 23873081
Nat Ecol Evol. 2017 May 26;1:167
pubmed: 29094686
BMC Genomics. 2019 Mar 14;20(1):217
pubmed: 30871473
Hum Mol Genet. 2012 Mar 15;21(6):1444-55
pubmed: 22156771
Cell. 2018 May 31;173(6):1398-1412.e22
pubmed: 29731168
Cell. 2016 Nov 17;167(5):1398-1414.e24
pubmed: 27863251
Nature. 2017 Jul 13;547(7662):173-178
pubmed: 28658209
Bioinformatics. 2016 May 15;32(10):1493-501
pubmed: 26773131
Cell. 2016 Jun 2;165(6):1530-1545
pubmed: 27259154
Nat Biotechnol. 2016 Feb;34(2):192-8
pubmed: 26751173
Proc Natl Acad Sci U S A. 2016 Jun 21;113(25):E3501-8
pubmed: 27274053
Genome Biol. 2009;10(3):R25
pubmed: 19261174
Development. 2018 Jun 26;145(12):
pubmed: 29945988
Nature. 2015 Oct 1;526(7571):75-81
pubmed: 26432246
Nature. 2014 Mar 27;507(7493):455-461
pubmed: 24670763
Nat Commun. 2017 May 05;8:15178
pubmed: 28474669
Nat Biotechnol. 2017 Apr;35(4):347-349
pubmed: 28263296
Nat Genet. 2014 Dec;46(12):1311-20
pubmed: 25383968
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nat Genet. 2018 Jul;50(7):906-908
pubmed: 29892013
Blood. 2009 Jun 4;113(23):5783-92
pubmed: 19171877
Bioinformatics. 2019 Nov 1;35(22):4851-4853
pubmed: 31233103
J Med Genet. 2018 Jul;55(7):459-468
pubmed: 29514873
BMC Genomics. 2018 Aug 23;19(1):633
pubmed: 30139328
Nat Genet. 2013 Nov;45(11):1274-1283
pubmed: 24097068
Nat Genet. 2019 Apr;51(4):683-693
pubmed: 30858613
Nat Genet. 2018 Sep;50(9):1335-1341
pubmed: 30104761
Nucleic Acids Res. 2018 Jan 4;46(D1):D794-D801
pubmed: 29126249
Prostaglandins Leukot Essent Fatty Acids. 2016 Sep;112:12-23
pubmed: 27637336
Cold Spring Harb Protoc. 2016 Mar 01;2016(3):pdb.prot090811
pubmed: 26933250
Oncogene. 2010 Oct 28;29(43):5796-808
pubmed: 20676125
Nat Commun. 2019 Sep 6;10(1):4063
pubmed: 31492858
Nature. 2017 Oct 11;550(7675):204-213
pubmed: 29022597
Nature. 2015 Nov 12;527(7577):192-7
pubmed: 26375006
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92
pubmed: 17130149
Nucleic Acids Res. 2018 Jan 4;46(D1):D252-D259
pubmed: 29140464
Nucleic Acids Res. 2019 Jan 8;47(D1):D1005-D1012
pubmed: 30445434
Science. 2016 Sep 30;353(6307):1545-1549
pubmed: 27708104
Nat Methods. 2017 Jun;14(6):629-635
pubmed: 28417999
Genome Res. 2015 Aug;25(8):1206-14
pubmed: 26084464
Cell. 2016 Jun 2;165(6):1519-1529
pubmed: 27259153
Nat Genet. 2018 Nov;50(11):1505-1513
pubmed: 30297969
Nature. 2015 Dec 24;528(7583):499-503
pubmed: 26595274
Cell. 2013 Jul 18;154(2):442-51
pubmed: 23849981
Nature. 2018 Oct;562(7726):203-209
pubmed: 30305743
Cell. 2019 Jan 10;176(1-2):377-390.e19
pubmed: 30612741
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Nat Biotechnol. 2016 Feb;34(2):167-74
pubmed: 26807528
Science. 2012 Sep 7;337(6099):1190-5
pubmed: 22955828
Nat Genet. 2019 Dec;51(12):1664-1669
pubmed: 31784727
Cell. 2014 Oct 23;159(3):647-61
pubmed: 25307932
Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6
pubmed: 23203885
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Nature. 2012 Sep 6;489(7414):109-13
pubmed: 22955621
Nat Commun. 2020 Mar 6;11(1):1237
pubmed: 32144282
Nat Commun. 2018 Apr 10;9(1):1366
pubmed: 29636450