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PXD048160

PXD048160 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHuman SMN C2A-2B-3-4 OE (LC-MS/MS)
DescriptionSpinal muscular atrophy (SMA) genes SMN1/SMN2 produce multiplecircular RNAs (circRNAs), including C2A-2B-3-4that encompassesearly exons 2A, 2B, 3 and 4. Here we report the transcriptome-and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysisrevealedaltered expression of ~15% genes (4,172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/SMN2.These findings underscore theuniquerole of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high numberof upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/SMN2transcripts, C2A-2B-3-4 and L2A-2B-3-4upregulated and downregulatedSMN1/SMN2mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect ofC2A-2B-3-4on expression ofgenesassociated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferationand neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, a universally expressed circRNA produced by SMN1/SMN2.
HostingRepositoryPRIDE
AnnounceDate2024-05-23
AnnouncementXMLSubmission_2024-05-22_23:40:56.349.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterEric Ottesen
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-12-28 11:03:36ID requested
12024-05-22 23:40:57announced
Publication List
Luo D, Ottesen EW, Lee JH, Singh RN, Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. Sci Rep, 14(1):10442(2024) [pubmed]
10.1038/s41598-024-60593-7;
Keyword List
submitter keyword: Human,LC-MS/MS, C2A-2B-3-4, HEK293 derived inducible cells (T-REx), circular RNA, overexpression, SMN
Contact List
Ravindra Singh
contact affiliationIowa State University
contact emailsinghr@iastate.edu
lab head
Eric Ottesen
contact affiliationIowa State University
contact emaileottesen@iastate.edu
dataset submitter
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Dataset FTP location
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