Proteomics

Dataset Information

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Human SMN C2A-2B-3-4 OE (LC-MS/MS)


ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Early Embryonic Cell

SUBMITTER: Eric Ottesen  

LAB HEAD: Ravindra Singh

PROVIDER: PXD048160 | Pride | 2024-05-23

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
P1145-01_Ctrl_1.msf Msf
P1145-01_Ctrl_1.raw Raw
P1145-02_1ug_Ctrl_2.msf Msf
P1145-02_1ug_Ctrl_2.raw Raw
P1145-03_Ctrl_3.msf Msf
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Publications

Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes.

Luo Diou D   Ottesen Eric W EW   Lee Ji Heon JH   Singh Ravindra N RN  

Scientific reports 20240507 1


Spinal muscular atrophy (SMA) genes, SMN1 and SMN2 (hereinafter referred to as SMN1/2), produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. C2A-2B-3-4 is a universally and abundantly expressed circRNA of SMN1/2. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~ 15% genes (4172 genes) by C2A-2B-3-4. About half of the a  ...[more]

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