Project description:RNA splicing plays a critical role in post-transcriptional gene regulation. Exponential expansion of intron length poses a challenge for accurate splicing. Little is known about how cells prevent inadvertent and often deleterious expression of intronic elements due to cryptic splicing. In this study, we identify hnRNPM as an essential RNA binding protein that suppresses cryptic splicing through binding to deep introns, preserving transcriptome integrity. Long interspersed nuclear elements (LINEs) harbor large amounts of pseudo splice sites in introns. hnRNPM preferentially binds at intronic LINEs and represses LINE-containing pseudo splice site usage for cryptic splicing. Remarkably, a subgroup of the cryptic exons can form long dsRNAs through base-pairing of inverted Alu transposable elements scattered in between LINEs and trigger interferon immune response, a well-known antiviral defense mechanism. Notably, these interferon-associated pathways are found to be upregulated in hnRNPM-deficient tumors, which also exhibit elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity. Targeting hnRNPM in tumors may be used to trigger an inflammatory immune response thereby boosting cancer surveillance.
Project description:RNA splicing plays a critical role in post-transcriptional gene regulation. Exponential expansion of intron length poses a challenge for accurate splicing. Little is known about how cells prevent inadvertent and often deleterious expression of intronic elements due to cryptic splicing. In this study, we identify hnRNPM as an essential RNA binding protein that suppresses cryptic splicing through binding to deep introns, preserving transcriptome integrity. Long interspersed nuclear elements (LINEs) harbor large amounts of pseudo splice sites in introns. hnRNPM preferentially binds at intronic LINEs and represses LINE-containing pseudo splice site usage for cryptic splicing. Remarkably, a subgroup of the cryptic exons can form long dsRNAs through base-pairing of inverted Alu transposable elements scattered in between LINEs and trigger interferon immune response, a well-known antiviral defense mechanism. Notably, these interferon-associated pathways are found to be upregulated in hnRNPM-deficient tumors, which also exhibit elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity. Targeting hnRNPM in tumors may be used to trigger an inflammatory immune response thereby boosting cancer surveillance.
Project description:Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG-I was responsible for such tumor-inhibitory effect. Interestingly, repression of HNRNPC resulted in accumulation of endogenous double-stranded RNA (dsRNA), the binding ligand of RIG-I. These up-regulated dsRNA species were highly enriched by Alu sequences and mostly originated from pre-mRNA introns that harbor the known HNRNPC binding sites. Such source of dsRNA is different than the recently well-characterized endogenous retroviruses that encode dsRNA. In summary, essentialness of HNRNPC in the breast cancer cells was attributed to its function in controlling the endogenous dsRNA and the down-stream interferon response. This is a novel extension from the previous understandings about HNRNPC in binding with introns and regulating RNA splicing.
Project description:In this study, we employed a combination of RIP-seq and short- and long-wave iCLIP technologies to identify transcripts associated with cytoplasmic RNPs containing the RNA-binding protein Drosophila Imp. We also made a Imp knockdown vs luciferase control experiment. Two biological iCLIP-seq, as well as two mRNAseq made on cells harvested on the same day. Two biological PAR-iCLIP-seq. Two biological RIP-seq, as well as two mRNAseq made on cells harvested on the same day. Three biological mRNAseq of imp dsRNA treated cells as well as three control mRNAseq of cells treated with Luciferase dsRNA.
Project description:The interferon (IFN) is a major effector of the innate immunity which mediates an adaptive immune response against broad spectrum pathogens. The aim of this work has been to investigate the differences of the virus mimic dsRNA (Poly I:C)-inducted in vivo transcriptomic alteration between pigs with high (HIGH) and low (LOW) serum interferon-alpha production. The pigs with extreme yield of induced interferon-alpha from a F2 resource population were selected for whole blood gene expression analysis using the porcine Affymetrix microarray
Project description:The goal of this study was to investigate DNA methylation and gene expression changes in a zebrafish model of ICF Syndrome which were generated by mutation of ICF-gene zbtb24. Comparison of gene expression changes between wildtype and zbtb24 homozygous mutants revealed upregulation of interferon response genes following zbtb24 deletion. Upregulation of interferon response genes was blocked by mutation of the dsRNA helicase Mda5.
Project description:Transactive response DNA-binding protein 43 (TDP-43) is a key factor in maintaining the fidelity of neuronal RNA splicing, and its dysfunction is observed in amyotrophic lateral sclerosis (ALS) and Alzheimer’s disease (AD) with TDP-43 pathology. Although loss of TDP-43 can activate multiple cryptic splicing events, whether specific cryptic exons generate stable and toxic peptides remains unclear. Here, we identify a TDP-43–dependent cryptic splicing event (PKN1-5a1) in the serine/threonine kinase gene PKN1: in transcriptomes of ALS patient brains it is markedly activated, inserting a 127-bp unannotated exon and introducing multiple premature termination codons. We further show that this aberrant transcript can partially escape nonsense-mediated mRNA decay (NMD) and is translated into a truncated peptide, N207; in AD brains with TDP-43 pathology, N207 is also detected by a specific antibody. Functional studies indicate that N207 overexpression impairs cognitive behaviors and weakens synaptic plasticity. These results indicate that cryptic splicing resulting from dysregulated TDP-43 not only causes loss of protein function but can also generate truncated toxic peptides that evade NMD, providing a new molecular-level explanation for the pathogenesis of TDP-43–related proteinopathies.