Dataset Information

Transcriptomic and proteomic analysis of alternative splicing in Physcomitrella patens moss

ABSTRACT: Alternative splicing (AS) has a significant potential to impact on the eukaryotic cell transcriptome and proteome. However, the extent of this influence as well as mechanisms, providing the tissue-specific pattern of AS are poorly studied. Here, we analyzed the AS of two life forms, protonema and gametophores, as well as the protoplasts, of a model organism, the Physcomitrella patens moss, using the data of transcriptome and proteome profiling. Altogether, 12,043 genes subjected to alternative splicing were identified. The alternative splicing patterns of 302 genes involved in stress response, growth, and development are changed considerably in the process of the gametophore development, whereas AS of 276 genes involved in transcription regulation, development, cell interactions, and cell response to biotic and abiotic stresses altered upon protoplastitation. Using mass spectrometry analysis, we studied the extent to which AS contributes to proteome diversity and identified 117 isoform-specific peptides for 36 genes with AS events. Our results indicate that AS event have a little impact on the proteome diversity and mostly result in the addition of extra amino acids rather than editing of existing proteins sequences. Among differentially expressed and spliced genes we found serine/arginine-rich (SR) genes, which are known to regulate AS in cells. We identified new isoforms of these genes and data evidencing their translation were obtained at transcriptome and proteome level. We also found that treatment with abscisic and jasmonic acids led to the isoform-specific response in protonema. Besides, we revealed the potential lncRNAmRNA and lncRNApre-mRNA interactions that can influence both the expression and alternative splicing of genes. It can point at an additional level of gene expression and AS regulation by non-coding transcripts in the Physcomitrella patens moss.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Physcomitrella Patens Subsp. Patens (moss)

TISSUE(S): Whole Body

DISEASE(S): Disease Free

SUBMITTER: Georgij Arapidi

LAB HEAD: Georgij Arapidi

PROVIDER: PXD005223 | Pride | 2018-01-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	F043_gametophores-4_MGFPeaklist.dat	Other
	F043_gametophores-4_MGFPeaklist.mgf	Mgf
	F043_gametophores-4_MGFPeaklist.mzid.gz	Mzid
	F043_gametophores-4_MGFPeaklist.mzid_F043_gametophores-4_MGFPeaklist.MGF	Mzid
	F043_gametophores-4_MGFPeaklist.xml	Xml

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Publications

Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens.

Fesenko Igor I Khazigaleeva Regina R Kirov Ilya I Kniazev Andrey A Glushenko Oksana O Babalyan Konstantin K Arapidi Georgij G Shashkova Tatyana T Butenko Ivan I Zgoda Victor V Anufrieva Ksenia K Seredina Anna A Filippova Anna A Govorun Vadim V

Scientific reports 20170602 1

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 pres ...[more]

PMID: 28578384

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