Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans

• Published in: Genome research 2023-03, Vol.33 (3), p.435-447
• Main Authors: Hamanaka, Kohei, Yamauchi, Daisuke, Koshimizu, Eriko, Watase, Kei, Mogushi, Kaoru, Ishikawa, Kinya, Mizusawa, Hidehiro, Tsuchida, Naomi, Uchiyama, Yuri, Fujita, Atsushi, Misawa, Kazuharu, Mizuguchi, Takeshi, Miyatake, Satoko, Matsumoto, Naomichi
• Format: Article
• Language: English
• Subjects: Gene polymorphism; Gene regulation; Genetic disorders; Genetic Engineering; Genomes; Humans; Polymorphism, Genetic; Regression analysis; Resources; RNA Splicing; Spinocerebellar ataxia; Splicing; Tandem Repeat Sequences
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.277335.122

Tandem repeats (TRs) are one of the largest sources of polymorphism, and their length is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in (spl-TRs), no large-scale study has been conducted. In this study, we established a genome-wide catalog of 9537 spl-TRs with a total of 58,290 significant TR-splicing associations across 49 tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci for repeat expansion diseases, spinocerebellar ataxia 6 (SCA6) and 12 (SCA12). Splicing alterations by these spl-TRs were compatible with those observed in SCA6 and SCA12. Thus, our comprehensive spl-TR catalog may help elucidate the pathomechanism of genetic diseases.