Similar Datasets
Project description:FLAG-tagged hnRNPM iCLIP in AGS cells
| PRJNA737793 | ENA
Project description:Cancer cells are differentially dependent on the splicing machinery compared to normal untransformed cells. The splicing machinery thus presents a potential therapeutic target in cancer. To identify splicing factors important for prostate cancer cell (PCa) growth, we performed an unbiased pooled shRNA screen in in vitro passaged cells and in vivo xenografted PCa tumors. Our screen revealed HNRNPM as a potential regulator of PCa cell growth. RNA- and eCLIP- sequencing data suggest that HNRNPM is bound to key homeostatic genes, and that loss of HNRNPM binding in a subset of these genes results in aberrant exon inclusion and exon back-splicing events in target transcripts. In mis-spliced transcripts, HNRNPM appears to preferentially bind to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM dependent splicing events using antisense oligonucleotides was sufficient to inhibit cell growth in HNRNPM expressing cells, suggesting that inhibition of cell growth in HNRNPM deficient cells likely has a multi-genic component. Taken together, our data reveal a role for HNRNPM in regulating PCa cell growth, and also as a potential therapeutic target in PCa.
2019-12-25 | GSE113782 | GEO
Project description:Cancer cells are differentially dependent on the splicing machinery compared to normal untransformed cells. The splicing machinery thus presents a potential therapeutic target in cancer. To identify splicing factors important for prostate cancer cell (PCa) growth, we performed an unbiased pooled shRNA screen in in vitro passaged cells and in vivo xenografted PCa tumors. Our screen revealed HNRNPM as a potential regulator of PCa cell growth. RNA- and eCLIP- sequencing data suggest that HNRNPM is bound to key homeostatic genes, and that loss of HNRNPM binding in a subset of these genes results in aberrant exon inclusion and exon back-splicing events in target transcripts. In mis-spliced transcripts, HNRNPM appears to preferentially bind to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM dependent splicing events using antisense oligonucleotides was sufficient to inhibit cell growth in HNRNPM expressing cells, suggesting that inhibition of cell growth in HNRNPM deficient cells likely has a multi-genic component. Taken together, our data reveal a role for HNRNPM in regulating PCa cell growth, and also as a potential therapeutic target in PCa.
2019-12-25 | GSE113783 | GEO
Project description:Tumor metastasis remains the major cause of cancer-related death, but its molecular basis is still not well understood. Here we uncovered a splicing-mediated pathway that is essential for breast cancer metastasis. We show that the RNA-binding protein hnRNPM promotes breast cancer metastasis by activating the switch of alternative splicing that occurs during epithelial-mesenchymal transition (EMT). Genome-wide deep sequencing analysis suggests that hnRNPM potentiates TGFb signaling and identifies CD44 as a key downstream target of hnRNPM. hnRNPM ablation prevents TGFb-induced EMT and inhibits breast cancer metastasis in mice, whereas enforced expression of the specific CD44s splice isoform overrides the loss of hnRNPM and permits EMT and metastasis. Mechanistically, we demonstrate that the ubiquitously expressed hnRNPM acts in a mesenchymal-specific manner to precisely control CD44 splice isoform switching during EMT. This restricted cell-type activity of hnRNPM is achieved by competition with ESRP1, an epithelial-splicing regulator that binds to the same cis-regulatory RNA elements and is repressed during EMT. Importantly, hnRNPM is associated with aggressive breast cancer and correlates with increased CD44s in patient specimens. These findings demonstrate a novel molecular mechanism through which tumor metastasis is endowed by the hnRNPM-mediated splicing program. RNAseq for control, hnRNPM siRNA treated lung metastatic LM2 clonal line, derived from the mesenchymal MDA-MB-231 cells
2014-06-03 | E-GEOD-57243 | biostudies-arrayexpress
Project description:Understanding the roles of splicing factors and splicing events during tumorigenesis would open new avenues for targeted therapies. Here we identify an oncofetal splicing factor, heterogeneous nuclear ribonucleoprotein M (HNRNPM), which promotes tumorigenesis and predicts poor prognosis of hepatocellular carcinoma (HCC) patients. HNRNPM knockdown almost completely abolishes HCC tumorigenesis. Transcriptomic analysis combined with RNA-immunoprecipatation sequencing revealed that HNRNPM induces lncRNA-TRIM7-AS exon 2 inclusion. The transcript containing exon 2 binds to coding sequences of TRIM7 mRNA, causes dissociation of translation elongation factors from TRIM7 mRNA, and thereby inhibits TRIM7 mRNA translation. In contrast, the transcript including exon 3 preferentially binds to the 3’ untranslated region of TRIM7 mRNA, protects TRIM7 mRNA from microRNA-145-5p induced degradation, and thereby increases TRIM7 expression. Through inducing exon 2 inclusion, HNRNPM downregulates TRIM7 protein expression, which mediates the pro-tumorigenic roles of HNRNPM. Collectively, these data demonstrate detailed mechanistic links between an oncofetal splicing factor, a splicing event and tumorigenesis, and establish splicing factors and splicing events as potential therapeutic targets.
2022-06-01 | GSE169223 | GEO
Project description:The epithelial-mesenchymal transition (EMT) is a fundamental developmental process that is abnormally activated in cancer metastasis. Dynamic changes in alternative splicing occur during EMT. ESRP1 and hnRNPM are splicing regulators that promote an epithelial splicing program and a mesenchymal splicing program, respectively. The functional relationships between these splicing factors in the genome-scale remain elusive. Comparing alternative splicing targets of hnRNPM and ESRP1 revealed that they co-regulate a set of cassette exon events, with the majority showing discordant splicing regulation. hnRNPM discordantly regulated splicing events show a positive correlation with splicing during EMT while concordant splicing events do not, highlighting the antagonistic role of hnRNPM and ESRP1 during EMT. Motif enrichment analysis near co-regulated exons identifies guanine-uridine rich motifs downstream of hnRNPM-repressed and ESRP1-enhanced exons, supporting a model of competitive binding to these cis-elements to antagonize alternative splicing. The set of co-regulated exons are enriched in genes associated with cell-migration and cytoskeletal reorganization, which are pathways associated with EMT. Splicing levels of co-regulated exons are associated with breast cancer patient survival and correlate with gene sets involved in EMT and breast cancer subtypes. In conclusion, hnRNPM and ESRP1 co-regulate antagonistically a set of alternative splicing events that occur during EMT. This regulation is likely mediated through competition for the same intronic binding sites downstream of variable exons. hnRNPM and ESRP1 regulated splicing events are associated with breast cancer survival.
2018-08-01 | GSE112516 | GEO
Project description:Tumor metastasis remains the major cause of cancer-related death, but its molecular basis is still not well understood. Here we uncovered a splicing-mediated pathway that is essential for breast cancer metastasis. We show that the RNA-binding protein hnRNPM promotes breast cancer metastasis by activating the switch of alternative splicing that occurs during epithelial-mesenchymal transition (EMT). Genome-wide deep sequencing analysis suggests that hnRNPM potentiates TGFb signaling and identifies CD44 as a key downstream target of hnRNPM. hnRNPM ablation prevents TGFb-induced EMT and inhibits breast cancer metastasis in mice, whereas enforced expression of the specific CD44s splice isoform overrides the loss of hnRNPM and permits EMT and metastasis. Mechanistically, we demonstrate that the ubiquitously expressed hnRNPM acts in a mesenchymal-specific manner to precisely control CD44 splice isoform switching during EMT. This restricted cell-type activity of hnRNPM is achieved by competition with ESRP1, an epithelial-splicing regulator that binds to the same cis-regulatory RNA elements and is repressed during EMT. Importantly, hnRNPM is associated with aggressive breast cancer and correlates with increased CD44s in patient specimens. These findings demonstrate a novel molecular mechanism through which tumor metastasis is endowed by the hnRNPM-mediated splicing program.
2014-06-03 | GSE57243 | GEO
Project description:These are the results of the iCLIP experiment for p62/SQSTM1 in Human Huh-7 cells treated with DMSO. We used iCLIP method to identify the RNA targets of p62 and nucleotide positions of the p62 interaction on RNA. We used 2 replicates and 2 different antibodies against endogenous p62 to enrich protein/RNA complexes. cDNAs were tagged with iCLIP composite barcodes (e.g. NNNTTGTNN) which contain 4 sample-encoding bases (e.g. TTGT) and and 5 random bases (noted with N in NNNTTGTNN example) which serve as unique molecular identifiers to post-filter PCR duplicates. These composite barcodes are found in the read headers (after last colon ':' character) of submitted fastq files.
2018-03-31 | E-MTAB-4894 | biostudies-arrayexpress
Project description:A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) for genome-wide determining the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7. We have established iCLIP for plants to identify target transcripts of the RNA-binding protein AtGRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues.
2017-09-28 | GSE99427 | GEO
Project description:Our ChIP resuls suggested that coilin association with U3, snRNA and histone genes might be dependent on coilin-RNA interaction. We used iCLIP of coilin-GFP expressed in HeLa and P19 cell lines at endogenous levels to identify coilin RNA targets and investigate RNA-binding specificity. P19 cells expressing GFP fused to a nuclear localization signal (GFP-NLS) was used as a negative control. iCLIP results revealed that coilin binds several classes of ncRNA including snRNAs, U3 snoRNA and scaRNAs. Interestlignly the majority of coilin targets were intronic snoRNAs, suggesting a novel role of CBs in snoRNA biogenesis.
2014-11-06 | GSE58448 | GEO