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LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity [iCLIP]

ABSTRACT: LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity [iCLIP]

PROVIDER: PRJNA942961 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23783153.fastq.gz	Fastqsanger.gz
	SRR23783154.fastq.gz	Fastqsanger.gz

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LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity [iCLIP]

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.

2024-05-29 | GSE227048 | GEO

LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity

Project description:LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity

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LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity [RNA-seq]

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LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity [RNA-seq]

Project description:LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity [RNA-seq]

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LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-05-29 | GSE227050 | GEO

Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response

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.

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Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation

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.

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A neurotoxic cryptic peptide arising from TDP-43-dependent cryptic splicing of PKN1

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.

| PXD069368 |

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