 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 07, 2023 |
| Title |
SRSF2 plays an unexpected role as reader of m5C on mRNA, linking epitranscriptomics to cancer |
| Organism |
Homo sapiens |
| Experiment type |
Other
Methylation profiling by high throughput sequencing
|
| Summary |
A common mRNA modification is 5-methylcytosine (m5C), whose role in gene-transcript processing and cancer remains unclear. Here we identify Serine/arginine-Rich Splicing Factor 2 (SRSF2) as a reader of m5C, and impaired SRSF2 m5C binding as a potential contributor to leukemogenesis. Structurally, we identify residues involved in m5C recognition and in the impact of the prevalent leukemia-associated mutation SRSF2P95H. We show that SRSF2 binding and m5C colocalize within transcripts. Furthermore, knocking down the m5C writer NSUN2 decreases mRNA m5C, reduces SRSF2 binding, and alters RNA splicing. We also show that the SRSF2P95H mutation impairs the ability of the protein to read m5C-marked mRNA, notably reducing its binding to key leukemia-related transcripts in leukemic cells. In leukemia patients, low NSUN2 expression leads to mRNA m5C hypomethylation and, combined with SRSF2P95H, predicts poor outcomes. Altogether, we highlight an unrecognized mechanistic link between epitranscriptomics and a key oncogenesis driver.
|
| |
|
| Overall design |
SRSF2 PAR-CLIP Seq in HeLa and K562 cells.
Bulk RNA-seq in HeLa and K562 cells (wild-type, NSUN2 knockdown, SRSF2 knockdown, and SRSF2P95H mutant).
RNA m5C MeRIP-seq in wild-type and NSUN2 knockdown HeLa cells.
RNA bisulfite sequencing of peripheral blood mononuclear cell RNA from CMML patients.
|
| Web link |
https://doi.org/10.1016/j. molcel.2023.11.003
|
| |
|
| Contributor(s) |
Ma HL, Bizet M, Soares Da Costa C, Murisier F, de Bony EJ, Wang MK, Yoshimi A, Lin KT, Riching KM, Wang X, Beckman JI, Arya S, Droin N, Calonne E, Hassabi B, Zhang QY, Li A, Putmans P, Malbec L, Hubert C, Lan J, Mies F, Yang Y, Solary E, Daniels DL, Gupta YK, Deplus R, Abdel-Wahab O, Yang YG, Fuks F |
| Citation(s) |
38065062 |
| |
| Submission date |
Jul 07, 2022 |
| Last update date |
Dec 11, 2023 |
| Contact name |
Haili Ma |
| Organization name |
ULB
|
| Street address |
route de lennik 808
|
| City |
anderlecht |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
| |
|
| Platforms (4)
|
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL20795 |
HiSeq X Ten (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (38)
|
| GSM6304265 |
SRSF2 PAR-CLIP Seq in siCtrl HeLa cell rep1 |
| GSM6304266 |
SRSF2 PAR-CLIP Seq in siCtrl HeLa cell rep2 |
| GSM6304267 |
SRSF2 PAR-CLIP Seq in siNSUN2 HeLa cell rep1 |
| GSM6304268 |
SRSF2 PAR-CLIP Seq in siNSUN2 HeLa cell rep2 |
| GSM6304269 |
SRSF2 PAR-CLIP Seq in Ctrl K562 cell rep1 |
| GSM6304270 |
SRSF2 PAR-CLIP Seq in Ctrl K562 cell rep2 |
| GSM6304271 |
SRSF2 PAR-CLIP Seq in shNSUN2 K562 cell rep1 |
| GSM6304272 |
SRSF2 PAR-CLIP Seq in shNSUN2 K562 cell rep2 |
| GSM6304273 |
SRSF2 PAR-CLIP Seq in SRSF2(P95H) K562 cell rep1 |
| GSM6304274 |
SRSF2 PAR-CLIP Seq in SRSF2(P95H) K562 cell rep2 |
| GSM6620512 |
HeLa cells, siCtrl, rep1 |
| GSM6620513 |
HeLa cells, siCtrl, rep2 |
| GSM6620514 |
HeLa cells, siNSUN2, rep1 |
| GSM6620515 |
HeLa cells, siNSUN2, rep2 |
| GSM6620516 |
HeLa cells, siSRSF2, rep1 |
| GSM6620517 |
HeLa cells, siSRSF2, rep2 |
| GSM6620518 |
K562 cells, Ctrl, rep1 |
| GSM6620519 |
K562 cells, Ctrl, rep2 |
| GSM6620520 |
K562 cells, shNSUN2, rep1 |
| GSM6620521 |
K562 cells, shNSUN2, rep2 |
| GSM6620522 |
K562 cells, SRSF2P95H, rep1 |
| GSM6620523 |
K562 cells, SRSF2P95H, rep2 |
| GSM7709752 |
Biopsy 1954 |
| GSM7709753 |
Biopsy 1633 |
| GSM7709754 |
Biopsy 2042 |
| GSM7709755 |
Biopsy 2146 |
| GSM7709756 |
Biopsy 1925 |
| GSM7709757 |
Biopsy 1504 |
| GSM7709758 |
Biopsy 1745 |
| GSM7709759 |
Biopsy 1555 |
| GSM7709760 |
HeLa-siNSUN2-1-m5C |
| GSM7709761 |
HeLa-siCTRL-1-m5C |
| GSM7709762 |
HeLa-siNSUN2-2-m5C |
| GSM7709763 |
HeLa-siCTRL-2-m5C |
| GSM7709764 |
HeLa-siNSUN2-1-INP |
| GSM7709765 |
HeLa-siCTRL-1-INP |
| GSM7709766 |
HeLa-siNSUN2-2-INP |
| GSM7709767 |
HeLa-siCTRL-2-INP |
|
| Relations |
| BioProject |
PRJNA856509 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE207643_RAW.tar |
1.0 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, TSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...