Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants.
CRISPR/Cas9
Sonic hedgehog
ZRS
cis-regulatory element
enhancer
genome editing
limb development
mutation
polydactyly
rare non-coding variant
Journal
Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066
Informations de publication
Date de publication:
19 03 2020
19 03 2020
Historique:
received:
12
11
2019
revised:
13
01
2020
accepted:
12
02
2020
pubmed:
15
3
2020
medline:
21
10
2020
entrez:
15
3
2020
Statut:
ppublish
Résumé
Establishing causal links between non-coding variants and human phenotypes is an increasing challenge. Here, we introduce a high-throughput mouse reporter assay for assessing the pathogenic potential of human enhancer variants in vivo and examine nearly a thousand variants in an enhancer repeatedly linked to polydactyly. We show that 71% of all rare non-coding variants previously proposed as causal lead to reporter gene expression in a pattern consistent with their pathogenic role. Variants observed to alter enhancer activity were further confirmed to cause polydactyly in knockin mice. We also used combinatorial and single-nucleotide mutagenesis to evaluate the in vivo impact of mutations affecting all positions of the enhancer and identified additional functional substitutions, including potentially pathogenic variants hitherto not observed in humans. Our results uncover the functional consequences of hundreds of mutations in a phenotype-associated enhancer and establish a widely applicable strategy for systematic in vivo evaluation of human enhancer variants.
Identifiants
pubmed: 32169219
pii: S0092-8674(20)30208-7
doi: 10.1016/j.cell.2020.02.031
pmc: PMC7179509
mid: NIHMS1568780
pii:
doi:
Substances chimiques
Hedgehog Proteins
0
RNA, Untranslated
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1262-1271.e15Subventions
Organisme : NHGRI NIH HHS
ID : K99 HG009682
Pays : United States
Organisme : NIAMS NIH HHS
ID : R01 AR067715
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG003988
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
Published by Elsevier Inc.
Déclaration de conflit d'intérêts
Declaration of Interests The authors declare no competing interests.
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