{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T04:14:23Z","timestamp":1747196063714,"version":"3.40.5"},"reference-count":82,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2021,6,4]],"date-time":"2021-06-04T00:00:00Z","timestamp":1622764800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Office of the Principal Scientific Advisor (PSA), Govt. of India"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>The genetic influence in epilepsy, characterized by unprovoked and recurrent seizures, is through variants in genes critical to brain development and function. We have carried out variant calling in Mesial Temporal Lobe Epilepsy (MTLE) patients by mapping the RNA-Seq data available at SRA, NCBI, USA onto human genome assembly hg-19. We have identified 1,75,641 SNVs in patient samples. These SNVs are distributed over 14700 genes of which 655 are already known to be associated with epilepsy. Large number of variants occur in the 3\u2019-UTR, which is one of the regions involved in the regulation of protein translation through binding of miRNAs and RNA-binding proteins (RBP). We have focused on studying the structure-function relationship of the 3\u2019-UTR SNVs that are common to at-least 10 of the 35 patient samples. For the first time we find SNVs exclusively in the 3\u2019-UTR of <jats:italic>FGF12<\/jats:italic>, <jats:italic>FAR1<\/jats:italic>, <jats:italic>NAPB<\/jats:italic>, <jats:italic>SLC1A3<\/jats:italic>, <jats:italic>SLC12A6<\/jats:italic>, <jats:italic>GRIN2A<\/jats:italic>, <jats:italic>CACNB4<\/jats:italic> and <jats:italic>FBXO28<\/jats:italic> genes. Structural modelling reveals that the variant 3\u2019-UTR segments possess altered secondary and tertiary structures which could affect mRNA stability and binding of RBPs to form proper ribonucleoprotein (RNP) complexes. Secondly, these SNVs have either created or destroyed miRNA-binding sites, and molecular modeling reveals that, where binding sites are created, the additional miRNAs bind strongly to 3\u2019-UTR of only variant mRNAs. These two factors affect protein production thereby creating an imbalance in the amounts of select proteins in the cell. We suggest that in the absence of missense and nonsense variants, protein-activity imbalances associated with MTLE patients can be caused through 3\u2019-UTR variants in relevant genes by the mechanisms mentioned above. 3\u2019-UTR SNV has already been identified as causative variant in the neurological disorder, Tourette syndrome. Inhibition of these miRNA-mRNA bindings could be a novel way of treating drug-resistant MTLE patients. We also suggest that joint occurrence of these SNVs could serve as markers for MTLE. We find, in the present study, SNV-mediated destruction of miRNA binding site in the 3\u2019-UTR of the gene encoding glutamate receptor subunit, and, interestingly, overexpression of one of this receptor subunit is also associated with Febrile Seizures.<\/jats:p>","DOI":"10.1371\/journal.pone.0252475","type":"journal-article","created":{"date-parts":[[2021,6,4]],"date-time":"2021-06-04T18:32:56Z","timestamp":1622831576000},"page":"e0252475","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Identification of 3\u2019-UTR single nucleotide variants and prediction of select protein imbalance in mesial temporal lobe epilepsy patients"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1200-4853","authenticated-orcid":true,"given":"Tanusree","family":"Chaudhuri","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5046-2885","authenticated-orcid":true,"given":"Janaki","family":"Chintalapati","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1012-0906","authenticated-orcid":true,"given":"Madhusoodan Vijayacharya","family":"Hosur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,6,4]]},"reference":[{"key":"pone.0252475.ref001","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1097\/00019052-200304000-00008","article-title":"The epidemiology of epilepsy revisited","volume":"16","author":"JW Sander","year":"2003","journal-title":"Curr Opin Neurol"},{"key":"pone.0252475.ref002","first-page":"1","article-title":"Novel and de novo mutations in pediatric refractory epilepsy","volume":"11","author":"J Liu","year":"2018","journal-title":"Mol Brain"},{"key":"pone.0252475.ref003","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/S0920-1211(01)00196-6","article-title":"Genetic and environmental factors in epilepsy: A population-based study of 11 900 Danish twin pairs","volume":"44","author":"MJ Kjeldsen","year":"2001","journal-title":"Epilepsy Res"},{"key":"pone.0252475.ref004","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1001\/jamaneurol.2015.3480","article-title":"Genetic correlation between schizophrenia and epilepsy","author":"FW Vonberg","year":"2016","journal-title":"JAMA Neurology."},{"key":"pone.0252475.ref005","first-page":"1","article-title":"Epilepsy","author":"O Devinsky","year":"2018","journal-title":"Nature Reviews Disease Primers."},{"key":"pone.0252475.ref006","first-page":"11","author":"J Wang","year":"2017","journal-title":"Epilepsy-associated genes."},{"key":"pone.0252475.ref007","doi-asserted-by":"crossref","first-page":"352","DOI":"10.3389\/fncel.2019.00352","article-title":"Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development","author":"E Perenthaler","year":"2019","journal-title":"Frontiers in Cellular Neuroscience. 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