MYC dependent mRNA translation shapes gene expression and cell biology
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE79864 | GEO | 2019/04/30
REPOSITORIES: GEO
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Project description:Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a genome-wide 5’UTR CRISPRi screen in PDAC cells, we identified activators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, RBM42 was our top hit, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5’UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.
2024-11-29 | GSE279023 | GEO
Project description:Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a genome-wide 5’UTR CRISPRi screen in PDAC cells, we identified activators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, RBM42 was our top hit, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5’UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.
2024-11-29 | GSE255740 | GEO
Project description:Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a genome-wide 5’UTR CRISPRi screen in PDAC cells, we identified activators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, RBM42 was our top hit, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5’UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.
2024-11-29 | GSE255703 | GEO
Project description:Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a genome-wide 5’UTR CRISPRi screen in PDAC cells, we identified activators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, RBM42 was our top hit, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5’UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.
2024-11-29 | GSE255702 | GEO
Project description:Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a genome-wide 5’UTR CRISPRi screen in PDAC cells, we identified activators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, RBM42 was our top hit, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5’UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.
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Project description:p53-mediated cell cycle arrest during DNA damage is dependent on the induction of p21 protein, encoded by the CDKN1A gene. p21 inhibits cyclin-dependent kinases required for cell cycle progression to guarantee accurate repair of DNA lesions. Hence, fine-tuning of p21 levels is crucial to preserve genomic stability. Currently, the multilayered regulation of p21 levels during DNA damage is not fully understood. Herein, we identified the human RNA binding motif protein 42 (RBM42) as a novel regulator of p21 levels during DNA damage. Genome-wide transcriptome and interactome analysis revealed that RBM42 alters the expression of p53-regulated genes during DNA damage. Specifically, we demonstrated that RBM42 facilitates CDKN1A splicing by counteracting the splicing inhibitory effect of RBM4 protein. Unexpectedly, we also show that RBM42, underpins translation of various splicing targets, including CDKN1A. Concordantly, transcriptome-wide mapping of RBM42-RNA interactions using eCLIP further substantiates the dual function of RBM42 in regulating splicing and translation of its target genes, including CDKN1A. Collectively, our data show that RBM42 couples splicing and translation machineries to fine-tune gene expression during DNA damage response.
2023-11-03 | GSE245744 | GEO
Project description:The SR protein family of splicing factors regulate constitutive and alternative pre-mRNA splicing. A subset of them, including SRSF1, shuttles continuously between the nucleus and cytoplasm affecting post-splicing processes. We have previously identified a role for SRSF1 in promoting the translation of specific mRNA transcripts, particularly those encoding centrosomal proteins. Here, we used CRISPR/Cas9 editing to knock-in a nuclear retention signal (NRS) in Srsf1 resulting in a non-shuttling SRSF1 mouse model (Srsf1NRS). Srsf1NRS/NRS mice displayed small body size, hydrocephaly and male infertility, all associated with ciliary defects. We observed reduced translation of thousands of mRNAs, in particular of ciliary components, in cells derived from this model. Consistently, we found that the lack of cytoplasmic SRSF1 led to decreased abundance of proteins involved in multiciliogenesis and affected ciliary structure and motility in multiciliated cells. Altogether, these results highlight the physiological relevance of the activity of a splicing factor in the cytoplasm.
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Project description:Maintenance of high-turnover tissues such as the epidermis requires a tight balance between stem and progenitor cell proliferation and differentiation. The molecular mechanisms governing this process are an area of active investigation. Here we show that HNRNPK, a multifunctional protein, is necessary to prevent premature differentiation and sustains the proliferative capacity of epidermal stem and progenitor cells. To prevent premature differentiation of progenitor cells, HNRNPK recruits DDX6 to a subset of mRNAs that code for transcription factors that induce differentiation. Upon binding, these mRNAs such as GRHL3, KLF4, and ZNF750 are degraded which prevents premature differentiation. To sustain the proliferative capacity of the epidermis, HNRNPK recruits RNA polymerase II to genomic sites of proliferation genes such as MYC, FGFBP1, PTHLH, ITGB4 to promote their expressions. Our study establishes a prominent role for HNRNPK in maintaining adult tissue homeostasis through both transcriptional and post-transcriptional mechanisms.
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Project description:RNA binding motif protein 42 (RBM42) is an understudied gene mapped to 19q13.12 region and codes for a protein that consists of 480 amino acids, containing one RNA recognition motif (RRM) at its C-terminal region. We mapped the RBM42 interactome using ascorbate peroxidase (APEX2)-based proximity labelling combined with mass spectrometry. We utilized CRISPR-Cas9 methodology for biallelic knock-in APEX2 at the C-terminus of the endogenous RBM42 coding sequence (CDS) and established an HCT116 cell line expressing RBM42-APEX2 fusion. RBM42 interactome mapping was performed by using Control and and HCT116 expressing RBM42-APEX2 cells that were treated with DMSO or Etoposide (VP-16) that induce DNA repair and incubated in media containing biotin phenol, followed by H2O2 treatment, to activate APEX2 peroxidase activity. Pathway enrichment analysis revealed that the majority of proteins that appeared in proximity to RBM42 are implicated in mRNA splicing and processing. Furthermore, we observed a significant enrichment of proteins involved in cell cycle checkpoints and regulation, further highlighting the role of RBM42 in DNA damage response. Together, RBM42 interactome analysis substantiates its function as a splicing regulator and implicates it in additional cellular pathways related to mRNA metabolism and DNA damage response.
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