Alternative splicing level related to intron size and organism complexity

Abstract Background Alternative splicing is the process of selecting different combinations of splice sites to produce variably spliced mRNAs. However, the relationships between alternative splicing prevalence and level (ASP/L) and variations of intron size and organism complexity (OC) remain vague....

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Autores principales:	Pengcheng Yang, Depin Wang, Le Kang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	RNA-Seq Protein disorder Intron density Splicing factor Conservation Gene family Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/eec82f8d9d8e4e009f32e2e935e5d09f
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spelling	oai:doaj.org-article:eec82f8d9d8e4e009f32e2e935e5d09f2021-11-28T12:23:06ZAlternative splicing level related to intron size and organism complexity10.1186/s12864-021-08172-21471-2164https://doaj.org/article/eec82f8d9d8e4e009f32e2e935e5d09f2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08172-2https://doaj.org/toc/1471-2164Abstract Background Alternative splicing is the process of selecting different combinations of splice sites to produce variably spliced mRNAs. However, the relationships between alternative splicing prevalence and level (ASP/L) and variations of intron size and organism complexity (OC) remain vague. Here, we developed a robust protocol to analyze the relationships between ASP/L and variations of intron size and OC. Approximately 8 Tb raw RNA-Seq data from 37 eumetazoan species were divided into three sets of species based on variations in intron size and OC. Results We found a strong positive correlation between ASP/L and OC, but no correlation between ASP/L and intron size across species. Surprisingly, ASP/L displayed a positive correlation with mean intron size of genes within individual genomes. Moreover, our results revealed that four ASP/L-related pathways contributed to the differences in ASP/L that were associated with OC. In particular, the spliceosome pathway displayed distinct genomic features, such as the highest gene expression level, conservation level, and fraction of disordered regions. Interestingly, lower or no obvious correlations were observed among these genomic features. Conclusions The positive correlation between ASP/L and OC ubiquitously exists in eukaryotes, and this correlation is not affected by the mean intron size of these species. ASP/L-related splicing factors may play an important role in the evolution of OC.Pengcheng YangDepin WangLe KangBMCarticleRNA-SeqProtein disorderIntron densitySplicing factorConservationGene familyBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	RNA-Seq Protein disorder Intron density Splicing factor Conservation Gene family Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	RNA-Seq Protein disorder Intron density Splicing factor Conservation Gene family Biotechnology TP248.13-248.65 Genetics QH426-470 Pengcheng Yang Depin Wang Le Kang Alternative splicing level related to intron size and organism complexity
description	Abstract Background Alternative splicing is the process of selecting different combinations of splice sites to produce variably spliced mRNAs. However, the relationships between alternative splicing prevalence and level (ASP/L) and variations of intron size and organism complexity (OC) remain vague. Here, we developed a robust protocol to analyze the relationships between ASP/L and variations of intron size and OC. Approximately 8 Tb raw RNA-Seq data from 37 eumetazoan species were divided into three sets of species based on variations in intron size and OC. Results We found a strong positive correlation between ASP/L and OC, but no correlation between ASP/L and intron size across species. Surprisingly, ASP/L displayed a positive correlation with mean intron size of genes within individual genomes. Moreover, our results revealed that four ASP/L-related pathways contributed to the differences in ASP/L that were associated with OC. In particular, the spliceosome pathway displayed distinct genomic features, such as the highest gene expression level, conservation level, and fraction of disordered regions. Interestingly, lower or no obvious correlations were observed among these genomic features. Conclusions The positive correlation between ASP/L and OC ubiquitously exists in eukaryotes, and this correlation is not affected by the mean intron size of these species. ASP/L-related splicing factors may play an important role in the evolution of OC.
format	article
author	Pengcheng Yang Depin Wang Le Kang
author_facet	Pengcheng Yang Depin Wang Le Kang
author_sort	Pengcheng Yang
title	Alternative splicing level related to intron size and organism complexity
title_short	Alternative splicing level related to intron size and organism complexity
title_full	Alternative splicing level related to intron size and organism complexity
title_fullStr	Alternative splicing level related to intron size and organism complexity
title_full_unstemmed	Alternative splicing level related to intron size and organism complexity
title_sort	alternative splicing level related to intron size and organism complexity
publisher	BMC
publishDate	2021
url	https://doaj.org/article/eec82f8d9d8e4e009f32e2e935e5d09f
work_keys_str_mv	AT pengchengyang alternativesplicinglevelrelatedtointronsizeandorganismcomplexity AT depinwang alternativesplicinglevelrelatedtointronsizeandorganismcomplexity AT lekang alternativesplicinglevelrelatedtointronsizeandorganismcomplexity
_version_	1718408053032747008

Alternative splicing level related to intron size and organism complexity

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