SCN1A: bioinformatically informed revised boundaries for promoter and enhancer regions.
Journal
Human molecular genetics
ISSN: 1460-2083
Titre abrégé: Hum Mol Genet
Pays: England
ID NLM: 9208958
Informations de publication
Date de publication:
05 05 2023
05 05 2023
Historique:
received:
07
10
2022
revised:
06
01
2023
accepted:
24
01
2023
medline:
8
5
2023
pubmed:
31
1
2023
entrez:
30
1
2023
Statut:
ppublish
Résumé
Pathogenic variations in the sodium voltage-gated channel alpha subunit 1 (SCN1A) gene are responsible for multiple epilepsy phenotypes, including Dravet syndrome, febrile seizures (FS) and genetic epilepsy with FS plus. Phenotypic heterogeneity is a hallmark of SCN1A-related epilepsies, the causes of which are yet to be clarified. Genetic variation in the non-coding regulatory regions of SCN1A could be one potential causal factor. However, a comprehensive understanding of the SCN1A regulatory landscape is currently lacking. Here, we summarized the current state of knowledge of SCN1A regulation, providing details on its promoter and enhancer regions. We then integrated currently available data on SCN1A promoters by extracting information related to the SCN1A locus from genome-wide repositories and clearly defined the promoter and enhancer regions of SCN1A. Further, we explored the cellular specificity of differential SCN1A promoter usage. We also reviewed and integrated the available human brain-derived enhancer databases and mouse-derived data to provide a comprehensive computationally developed summary of SCN1A brain-active enhancers. By querying genome-wide data repositories, extracting SCN1A-specific data and integrating the different types of independent evidence, we created a comprehensive catalogue that better defines the regulatory landscape of SCN1A, which could be used to explore the role of SCN1A regulatory regions in disease.
Identifiants
pubmed: 36715146
pii: 7008867
doi: 10.1093/hmg/ddad015
pmc: PMC10162429
doi:
Substances chimiques
NAV1.1 Voltage-Gated Sodium Channel
0
SCN1A protein, human
0
Scn1a protein, mouse
0
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
1753-1763Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : U41 HG007234
Pays : United States
Organisme : Wellcome Trust
ID : 108749/Z/15/Z
Pays : United Kingdom
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
Références
Nature. 2014 Mar 27;507(7493):455-461
pubmed: 24670763
Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923
pubmed: 33270111
Eur J Med Genet. 2020 Jan;63(1):103628
pubmed: 30771507
Epilepsia. 2017 Feb;58(2):282-290
pubmed: 28012175
Cureus. 2019 Jun 26;11(6):e5006
pubmed: 31497436
Nature. 2016 May 5;533(7601):95-9
pubmed: 27096366
Genome Med. 2021 Apr 26;13(1):69
pubmed: 33910599
Nature. 1982 Apr 15;296(5858):627-31
pubmed: 6280057
Genome Res. 2013 Jan;23(1):169-80
pubmed: 22936248
Nat Neurosci. 2020 Dec;23(12):1629-1636
pubmed: 32807948
Seizure. 2020 Feb;75:1-6
pubmed: 31864146
Epilepsia. 2018 Mar;59(3):690-703
pubmed: 29460957
Nat Genet. 2018 Mar;50(3):333-337
pubmed: 29483654
Nat Cell Biol. 2020 Mar;22(3):282-288
pubmed: 32066906
Nature. 2014 Mar 27;507(7493):462-70
pubmed: 24670764
Science. 2013 Feb 22;339(6122):957-9
pubmed: 23348506
Hum Mutat. 2010 Jul;31(7):820-9
pubmed: 20506560
Genomics. 2007 Aug;90(2):225-35
pubmed: 17544618
Epilepsia. 2021 Sep;62(9):2205-2217
pubmed: 34338318
Mol Neurobiol. 2014 Oct;50(2):438-48
pubmed: 24436055
N Engl J Med. 2017 Jan 5;376(1):21-31
pubmed: 27959697
Nature. 2020 Jul;583(7818):699-710
pubmed: 32728249
Sci Data. 2017 Aug 29;4:170107
pubmed: 28850105
Nature. 2022 Apr;604(7905):310-315
pubmed: 35388217
Epilepsia. 2019 Dec;60 Suppl 3:S17-S24
pubmed: 31904117
Nucleic Acids Res. 2013 Jan;41(Database issue):D110-7
pubmed: 23161672
Neuropathol Appl Neurobiol. 2022 Apr;48(3):e12775
pubmed: 34820881
Science. 2018 Dec 14;362(6420):
pubmed: 30545857
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Cell Res. 2016 Dec;26(12):1345-1348
pubmed: 27886167
Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995
pubmed: 34791404
Front Neurol. 2020 Nov 26;11:591690
pubmed: 33324329
Mol Genet Genomic Med. 2019 Jul;7(7):e00727
pubmed: 31144463
Annu Rev Physiol. 2010;72:335-55
pubmed: 20148679
J Neurosci Res. 2008 Nov 15;86(15):3375-81
pubmed: 18655196
Science. 2019 Nov 29;366(6469):1134-1139
pubmed: 31727856