Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens

Abstract Alternative splicing (AS) can significantly impact the transcriptome and proteome of a eukaryotic cell. Here, using transcriptome and proteome profiling data, we analyzed AS in two life forms of the model moss Physcomitrella patens, namely protonemata and gametophores, as well as in protopl...

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Autores principales:	Igor Fesenko, Regina Khazigaleeva, Ilya Kirov, Andrey Kniazev, Oksana Glushenko, Konstantin Babalyan, Georgij Arapidi, Tatyana Shashkova, Ivan Butenko, Victor Zgoda, Ksenia Anufrieva, Anna Seredina, Anna Filippova, Vadim Govorun
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/acfca1a4ac874a9a8cdbcaa3a18fa28a
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spelling	oai:doaj.org-article:acfca1a4ac874a9a8cdbcaa3a18fa28a2021-12-02T15:05:09ZAlternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens10.1038/s41598-017-02970-z2045-2322https://doaj.org/article/acfca1a4ac874a9a8cdbcaa3a18fa28a2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02970-zhttps://doaj.org/toc/2045-2322Abstract Alternative splicing (AS) can significantly impact the transcriptome and proteome of a eukaryotic cell. Here, using transcriptome and proteome profiling data, we analyzed AS in two life forms of the model moss Physcomitrella patens, namely protonemata and gametophores, as well as in protoplasts. We identified 12 043 genes subject to alternative splicing and analyzed the extent to which AS contributes to proteome diversity. We could distinguish a few examples that unambiguously indicated the presence of two or more splice isoforms from the same locus at the proteomic level. Our results indicate that alternative isoforms have a small effect on proteome diversity. We also revealed that mRNAs and pre-mRNAs have thousands of complementary binding sites for long non-coding RNAs (lncRNAs) that may lead to potential interactions in transcriptome. This finding points to an additional level of gene expression and AS regulation by non-coding transcripts in Physcomitrella patens. Among the differentially expressed and spliced genes we found serine/arginine-rich (SR) genes, which are known to regulate AS in cells. We found that treatment with abscisic (ABA) and methyl jasmonic acids (MeJA) led to an isoform-specific response and suggested that ABA in gametophores and MeJA in protoplasts regulate AS and the transcription of SR genes.Igor FesenkoRegina KhazigaleevaIlya KirovAndrey KniazevOksana GlushenkoKonstantin BabalyanGeorgij ArapidiTatyana ShashkovaIvan ButenkoVictor ZgodaKsenia AnufrievaAnna SeredinaAnna FilippovaVadim GovorunNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Igor Fesenko Regina Khazigaleeva Ilya Kirov Andrey Kniazev Oksana Glushenko Konstantin Babalyan Georgij Arapidi Tatyana Shashkova Ivan Butenko Victor Zgoda Ksenia Anufrieva Anna Seredina Anna Filippova Vadim Govorun Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens
description	Abstract Alternative splicing (AS) can significantly impact the transcriptome and proteome of a eukaryotic cell. Here, using transcriptome and proteome profiling data, we analyzed AS in two life forms of the model moss Physcomitrella patens, namely protonemata and gametophores, as well as in protoplasts. We identified 12 043 genes subject to alternative splicing and analyzed the extent to which AS contributes to proteome diversity. We could distinguish a few examples that unambiguously indicated the presence of two or more splice isoforms from the same locus at the proteomic level. Our results indicate that alternative isoforms have a small effect on proteome diversity. We also revealed that mRNAs and pre-mRNAs have thousands of complementary binding sites for long non-coding RNAs (lncRNAs) that may lead to potential interactions in transcriptome. This finding points to an additional level of gene expression and AS regulation by non-coding transcripts in Physcomitrella patens. Among the differentially expressed and spliced genes we found serine/arginine-rich (SR) genes, which are known to regulate AS in cells. We found that treatment with abscisic (ABA) and methyl jasmonic acids (MeJA) led to an isoform-specific response and suggested that ABA in gametophores and MeJA in protoplasts regulate AS and the transcription of SR genes.
format	article
author	Igor Fesenko Regina Khazigaleeva Ilya Kirov Andrey Kniazev Oksana Glushenko Konstantin Babalyan Georgij Arapidi Tatyana Shashkova Ivan Butenko Victor Zgoda Ksenia Anufrieva Anna Seredina Anna Filippova Vadim Govorun
author_facet	Igor Fesenko Regina Khazigaleeva Ilya Kirov Andrey Kniazev Oksana Glushenko Konstantin Babalyan Georgij Arapidi Tatyana Shashkova Ivan Butenko Victor Zgoda Ksenia Anufrieva Anna Seredina Anna Filippova Vadim Govorun
author_sort	Igor Fesenko
title	Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens
title_short	Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens
title_full	Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens
title_fullStr	Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens
title_full_unstemmed	Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens
title_sort	alternative splicing shapes transcriptome but not proteome diversity in physcomitrella patens
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/acfca1a4ac874a9a8cdbcaa3a18fa28a
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Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens

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