Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation
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 AluYRa1s...
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doaj-0b8e9df5dd3e4c8da179b4056626899f2021-02-14T12:32:34ZengNature Publishing GroupScientific Reports2045-23222021-02-0111111110.1038/s41598-021-83360-4Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylationHyeon-Mu Cho0Se-Hee Choe1Young-Hyun Kim2Hye-Ri Park3Hee-Eun Lee4Ja-Rang Lee5Sang-Je Park6Jae-Won Huh7National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)Primate Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)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 AluYRa1s located at the terminal region of cynomolgus monkey genes, utilizing both computational analysis and molecular experimentation. We found that ten genes had AluYRa1 at their 3′ end, and nine of these AluYRa1s were sense-oriented. Furthermore, in seven genes, AluYRa1s were expected to have a similar consensus sequence for polyadenylation cleavage. Additional computational analysis using the annotation files from the UCSC database showed that AluYRa1 was more involved in polyadenylation than in open reading frame exon splicing. To examine the extent of AluYRa1 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 AluYRa1. In conclusion, AluYRa1 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.https://doi.org/10.1038/s41598-021-83360-4 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hyeon-Mu Cho Se-Hee Choe Young-Hyun Kim Hye-Ri Park Hee-Eun Lee Ja-Rang Lee Sang-Je Park Jae-Won Huh |
spellingShingle |
Hyeon-Mu Cho Se-Hee Choe Young-Hyun Kim Hye-Ri Park Hee-Eun Lee Ja-Rang Lee Sang-Je Park Jae-Won Huh Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation Scientific Reports |
author_facet |
Hyeon-Mu Cho Se-Hee Choe Young-Hyun Kim Hye-Ri Park Hee-Eun Lee Ja-Rang Lee Sang-Je Park Jae-Won Huh |
author_sort |
Hyeon-Mu Cho |
title |
Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation |
title_short |
Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation |
title_full |
Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation |
title_fullStr |
Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation |
title_full_unstemmed |
Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation |
title_sort |
sense-oriented aluyra1 elements provide a lineage-specific transcription environment for polyadenylation |
publisher |
Nature Publishing Group |
series |
Scientific Reports |
issn |
2045-2322 |
publishDate |
2021-02-01 |
description |
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 AluYRa1s located at the terminal region of cynomolgus monkey genes, utilizing both computational analysis and molecular experimentation. We found that ten genes had AluYRa1 at their 3′ end, and nine of these AluYRa1s were sense-oriented. Furthermore, in seven genes, AluYRa1s were expected to have a similar consensus sequence for polyadenylation cleavage. Additional computational analysis using the annotation files from the UCSC database showed that AluYRa1 was more involved in polyadenylation than in open reading frame exon splicing. To examine the extent of AluYRa1 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 AluYRa1. In conclusion, AluYRa1 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. |
url |
https://doi.org/10.1038/s41598-021-83360-4 |
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