A novel variant in the 3' UTR of human SCN1A gene from a patient with Dravet syndrome decreases mRNA stability mediated by GAPDH's binding.
Mutations in the SCN1A gene-encoding voltage-gated sodium channel α-I subunit (Nav1.1) cause various spectrum of epilepsies including Dravet syndrome (DS), a severe and intractable form. A large number of SCN1A mutations identified from the DS patients lead to the loss of function or truncation of Nav1.1 that result in a haploinsufficiency effects, indicating that the exact expression level of SCN1A should be essential to maintain normal brain function. In this study, we have identified five variants c.*1025T>C, c.*1031A>T, c.*1739C>T, c.*1794C>T and c.*1961C>T in the SCN1A 3' UTR in the patients with DS. The c.*1025T>C, c.*1031A>T and c.*1794C>T are conserved among different species. Of all the five variants, only c.*1794C>T is a novel variant and alters the predicted secondary structure of the 3' UTR. We also show that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) only binds to the 3' UTR sequence containing the mutation allele 1794U but not the wild-type allele 1794C, indicating that the mutation allele forms a new GAPDH-binding site. Functional analyses show that the variant negatively regulates the reporter gene expression by affecting the mRNA stability that is mediated by GAPDH's binding, and this phenomenon could be reversed by shRNA-induced GAPDH knockdown. These findings suggest that GAPDH and the 3'-UTR variant are involved in regulating SCN1A expression at post-transcriptional level, which may provide an important clue for further investigating on the relationship between 3'-UTR variants and SCN1A-related diseases.
Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
Tao
T
Zeng
Zhao-Fei
ZF
Dong
Shu-Jing
SJ
Liu
Rui-Ping
RP
Wan
Ling-Jia
LJ
Tang
Ting
T
Liu
Qi-Hua
QH
Zhao
Yi-Wu
YW
Shi
Yong-Hong
YH
Yi
Wei-Ping
WP
Liao
Yue-Sheng
YS
Long
D020413:3' Untranslated Regions; D000483:Alleles; D001483:Base Sequence; D001665:Binding Sites; D002648:Child; D004831:Epilepsies, Myoclonic / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D005260:Female; D005786:Gene Expression Regulation; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D057895:Haploinsufficiency; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D062550:NAV1.1 Voltage-Gated Sodium Channel / Q000235:genetics* / Q000378:metabolism; D010375:Pedigree; D011485:Protein Binding; D020871:RNA Stability; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism
D020413:3' Untranslated Regions; D062550:NAV1.1 Voltage-Gated Sodium Channel; D034741:RNA, Small Interfering; C568242:SCN1A protein, human; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases