| Title |
The genetic variants in 3’ untranslated region of voltage-gated sodium channel alpha 1 subunit gene affect the mRNA-microRNA interactions and associate with epilepsy
|
|---|---|
| Published in |
BMC Genomic Data, July 2016
|
| DOI | 10.1186/s12863-016-0417-y |
| Pubmed ID | |
| Authors |
Tian Li, Yaoyun Kuang, Bin Li |
| Abstract |
mRNA expression in a cell or subcellular organelle is precisely regulated for the purpose of gene function regulation. The 3' untranslated region (3'UTR) of mRNA is the binding target of microRNA and RNA binding proteins. Their interactions regulate mRNA level in specific subcellular regions and determine the intensity of gene repression. The mutations in the coding region of voltage-gated sodium channel alpha 1 subunit gene, SCN1A, were identified in epileptic patients and confirmed as causative factors of epilepsy. We investigated if there were genetic variants in 3'UTR of SCN1A, affecting the microRNA-mRNA 3'UTR interaction and SCN1A gene repression, potentially associated with epilepsy. In this case-control study, we identified twelve variants, NM_001202435.1:n.6277A > G, n.6568_6571del, n.6761C > T, n.6874A > T, n.6907 T > C, n.6978A > G, n.7065_7066insG, n.7282 T > C, n.7338_7344del, n.7385 T > A, n.7996C > T, and n.8212C > T in 3'UTR of SCN1A gene. We found that the variant of n.6978A > G in all our samples was completely mutated (G/G). In male group, T allele in n.7282 T > C was associated with epilepsy, while C allele was significantly less frequent in epileptic patients than in normal males (OR 0.424). Consequently, the haplotype "CTTACATGACGA" / "CTCTA" was significantly less frequent in male epileptic patients (0.173) than in normal males (0.305). The frequency of haplotype block found in females, "TTTAACA", "TTCAACA", and "CTTAACA" was 0.499, 0.254 and 0.234 respectively. Within STarMir model analysis, the "CTCTA" haplotype showed significantly higher site accessibility to microRNA targeting and higher downstream sequence accessibility for nonconserved binding than that of other haplotypes. Overall, the male genotypes have the higher accessibility of the downstream 30nt block of nonconserved site than the female genotypes. NM_001202435.1:n.7282 T > C is the genetic variant associated with epilepsy in males, and the related haplotype "CTTACATGACGA" / "CTCTA" in the region of chr2: 165991297-165989081, which has high site accessibility for microRNA binding, is the genetic protective factor against epilepsy in males. In female subset, the frequencies of haplotype block "TTTAACA", "TTCAACA", and "CTTAACA" were 0.499,0.254 and 0.234 respectively. Alleles and haplotypes distribution did not differ in female cases in comparison to female controls. |
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 33% |
| Unknown | 2 | 67% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 2 | 67% |
| Scientists | 1 | 33% |
Mendeley readers
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Chile | 1 | 6% |
| Unknown | 17 | 94% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 7 | 39% |
| Other | 2 | 11% |
| Student > Doctoral Student | 2 | 11% |
| Student > Ph. D. Student | 2 | 11% |
| Student > Bachelor | 1 | 6% |
| Other | 2 | 11% |
| Unknown | 2 | 11% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 5 | 28% |
| Medicine and Dentistry | 4 | 22% |
| Agricultural and Biological Sciences | 2 | 11% |
| Neuroscience | 2 | 11% |
| Unspecified | 1 | 6% |
| Other | 0 | 0% |
| Unknown | 4 | 22% |
Attention Score in Context
This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 31 July 2016.
All research outputs
#16,047,334
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Outputs from BMC Genomic Data
#548
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Outputs of similar age
#229,542
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Outputs of similar age from BMC Genomic Data
#15
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