{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T00:50:32Z","timestamp":1777942232385,"version":"3.51.4"},"reference-count":162,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2023,9,14]],"date-time":"2023-09-14T00:00:00Z","timestamp":1694649600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Huntington\u2019s disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor\/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes\/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD.<\/jats:p>","DOI":"10.3390\/genes14091801","type":"journal-article","created":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T02:54:13Z","timestamp":1694746453000},"page":"1801","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Investigating Neuron Degeneration in Huntington\u2019s Disease Using RNA-Seq Based Transcriptome Study"],"prefix":"10.3390","volume":"14","author":[{"given":"Nela Pragathi","family":"Sneha","sequence":"first","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S. Akila Parvathy","family":"Dharshini","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0867-8986","authenticated-orcid":false,"given":"Y.-h.","family":"Taguchi","sequence":"additional","affiliation":[{"name":"Department of Physics, Chuo University, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1776-4096","authenticated-orcid":false,"given":"M. Michael","family":"Gromiha","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,9,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"15005","DOI":"10.1038\/nrdp.2015.5","article-title":"Huntington disease","volume":"1","author":"Bates","year":"2015","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"91","DOI":"10.31887\/DCNS.2016.18.1\/pnopoulos","article-title":"Huntington disease: A single-gene degenerative disorder of the striatum","volume":"18","author":"Nopoulos","year":"2022","journal-title":"Dialogues Clin. 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