文章基本信息

标题：Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation
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作者：Hyeon-Mu Cho ; Se-Hee Choe ; Young-Hyun Kim 等
期刊名称：Scientific Reports
电子版ISSN：2045-2322
出版年度：2021
卷号：11
期号：1
页码：3665
DOI：10.1038/s41598-021-83360-4
出版社：Springer Nature
摘要：Abstract Transposable elements cause alternative splicing (AS) in different ways, contributing to transcript diversification. Alternative polyadenylation (APA), one of the AS events, is related to the generation of mRNA isoforms in 70% of human genes. In this study, we tried to investigate Alu YRa1s located at the terminal region of cynomolgus monkey genes, utilizing both computational analysis and molecular experimentation. We found that ten genes had Alu YRa1 at their 3′ end, and nine of these Alu YRa1s were sense-oriented. Furthermore, in seven genes , Alu YRa1s were expected to have a similar consensus sequence for polyadenylation cleavage. Additional computational analysis using the annotation files from the UCSC database showed that Alu YRa1 was more involved in polyadenylation than in open reading frame exon splicing. To examine the extent of Alu YRa1 involvement in polyadenylation, RNA-seq data from 30 normal cynomolgus monkeys were analyzed using TAPAS, a recently devised software that detects all the promising polyadenylation sites including APA sites. We observed that approximately 74% of possible polyadenylation sites in the analyzed genes were provided by sense-oriented Alu YRa1. In conclusion, Alu YRa1 is an Old-World monkey-specific TE, and its sense-oriented insertion at the 3′UTR region tends to provide a favorable environment for polyadenylation, diversifying gene transcripts.
其他摘要：Abstract Transposable elements cause alternative splicing (AS) in different ways, contributing to transcript diversification. Alternative polyadenylation (APA), one of the AS events, is related to the generation of mRNA isoforms in 70% of human genes. In this study, we tried to investigate Alu YRa1s located at the terminal region of cynomolgus monkey genes, utilizing both computational analysis and molecular experimentation. We found that ten genes had Alu YRa1 at their 3′ end, and nine of these Alu YRa1s were sense-oriented. Furthermore, in seven genes , Alu YRa1s were expected to have a similar consensus sequence for polyadenylation cleavage. Additional computational analysis using the annotation files from the UCSC database showed that Alu YRa1 was more involved in polyadenylation than in open reading frame exon splicing. To examine the extent of Alu YRa1 involvement in polyadenylation, RNA-seq data from 30 normal cynomolgus monkeys were analyzed using TAPAS, a recently devised software that detects all the promising polyadenylation sites including APA sites. We observed that approximately 74% of possible polyadenylation sites in the analyzed genes were provided by sense-oriented Alu YRa1. In conclusion, Alu YRa1 is an Old-World monkey-specific TE, and its sense-oriented insertion at the 3′UTR region tends to provide a favorable environment for polyadenylation, diversifying gene transcripts.