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Bioinformatic analysis of regulation of natural antisense transcripts by transposable elements in human mRNA

Jung, Jaeeun, Lee, Sugi, Cho, Hyun-Soo, Park, Kunhyang, Ryu, Jea-Woon, Jung, Minah, Kim, Jeongkil, Kim, HyeRan, Kim, Dae-Soo
Genomics 2019 v.111 no.2 pp. 159-166
DNA, bioinformatics, databases, gene expression, genes, humans, messenger RNA, non-coding RNA, transcription (genetics), transposons
Non-coding RNA is no longer considered to be “junk” DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletely understood. It is well-known that the insertion of transposable elements (TEs) can affect gene transcription. Using a bioinformatics approach, we identified NATs using human mRNA sequences from the UCSC Genome Browser Database. Our in silico analysis identified 1079 NATs and 700 sense-antisense gene pairs. We identified 179 NATs that showed evidence of having been affected by TEs during cellular gene expression. These findings may provide an understanding of the complex regulation mechanisms of NATs. If our understanding of NATs as modulators of gene expression is further enhanced, we can develop ways to control gene expression.