PXD005223-2

PXD005223 is an original dataset announced via ProteomeXchange.

Title	Transcriptomic and proteomic analysis of alternative splicing in Physcomitrella patens moss
Description	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 lncRNA–mRNA and lncRNA–pre-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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:33:39.118.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD005223
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Georgij Arapidi
SpeciesList	scientific name: Physcomitrella patens subsp. patens (Moss); NCBI TaxID: 3218;
ModificationList	Ammonia-loss; Dehydrated; Acetyl; Carbamidomethyl
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-10-25 05:24:50	ID requested
1	2018-01-15 05:15:49	announced
⏵ 2	2024-10-22 04:33:44	announced	2024-10-22: Updated project metadata.

10.6019/PXD005223;

10.1038/s41598-017-02970-z;

Fesenko I, Khazigaleeva R, Kirov I, Kniazev A, Glushenko O, Babalyan K, Arapidi G, Shashkova T, Butenko I, Zgoda V, Anufrieva K, Seredina A, Filippova A, Govorun V, Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens. Sci Rep, 7(1):2698(2017) [pubmed]

curator keyword: Biological

submitter keyword: alternative splicing, Physcomitrella patens moss, long non-coding RNAs, proteome

Georgij Arapidi
contact affiliation	Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences
contact email	arapidi@gmail.com
lab head
Georgij Arapidi
contact affiliation	Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
contact email	arapidi@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005223
     1. Label: PRIDE project
     2. Name: Transcriptomic and proteomic analysis of alternative splicing in Physcomitrella patens moss