PXD048160 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Human SMN C2A-2B-3-4 OE (LC-MS/MS) |
Description | Spinal 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. |
HostingRepository | PRIDE |
AnnounceDate | 2024-05-23 |
AnnouncementXML | Submission_2024-05-22_23:40:56.349.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Eric Ottesen |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-12-28 11:03:36 | ID requested | |
⏵ 1 | 2024-05-22 23:40:57 | announced | |
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 affiliation | Iowa State University |
contact email | singhr@iastate.edu |
lab head | |
Eric Ottesen |
contact affiliation | Iowa State University |
contact email | eottesen@iastate.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/05/PXD048160 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD048160
- Label: PRIDE project
- Name: Human SMN C2A-2B-3-4 OE (LC-MS/MS)