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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Hyeon-Mu Cho, Se-Hee Choe, Young-Hyun Kim, Hye-Ri Park, Hee-Eun Lee, Ja-Rang Lee, Sang-Je Park, Jae-Won Huh
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0b8e9df5dd3e4c8da179b4056626899f
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:0b8e9df5dd3e4c8da179b4056626899f
record_format	dspace
spelling	oai:doaj.org-article:0b8e9df5dd3e4c8da179b4056626899f2021-12-02T14:27:01ZSense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation10.1038/s41598-021-83360-42045-2322https://doaj.org/article/0b8e9df5dd3e4c8da179b4056626899f2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83360-4https://doaj.org/toc/2045-2322Abstract 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.Hyeon-Mu ChoSe-Hee ChoeYoung-Hyun KimHye-Ri ParkHee-Eun LeeJa-Rang LeeSang-Je ParkJae-Won HuhNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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
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.
format	article
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
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 Portfolio
publishDate	2021
url	https://doaj.org/article/0b8e9df5dd3e4c8da179b4056626899f
work_keys_str_mv	AT hyeonmucho senseorientedaluyra1elementsprovidealineagespecifictranscriptionenvironmentforpolyadenylation AT seheechoe senseorientedaluyra1elementsprovidealineagespecifictranscriptionenvironmentforpolyadenylation AT younghyunkim senseorientedaluyra1elementsprovidealineagespecifictranscriptionenvironmentforpolyadenylation AT hyeripark senseorientedaluyra1elementsprovidealineagespecifictranscriptionenvironmentforpolyadenylation AT heeeunlee senseorientedaluyra1elementsprovidealineagespecifictranscriptionenvironmentforpolyadenylation AT jaranglee senseorientedaluyra1elementsprovidealineagespecifictranscriptionenvironmentforpolyadenylation AT sangjepark senseorientedaluyra1elementsprovidealineagespecifictranscriptionenvironmentforpolyadenylation AT jaewonhuh senseorientedaluyra1elementsprovidealineagespecifictranscriptionenvironmentforpolyadenylation
_version_	1718391292291973120

Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation

Ejemplares similares