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Tristetraprolin specifically binds to intron regions and regulates alternative splicing of immune response genes in HeLa cells

ABSTRACT: Tristetraprolin specifically binds to intron regions and regulates alternative splicing of immune response genes in HeLa cells

PROVIDER: PRJNA533642 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8929420_1.fastq.gz	Fastqsanger.gz
	SRR8929420_2.fastq.gz	Fastqsanger.gz
	SRR8929417_1.fastq.gz	Fastqsanger.gz
	SRR8929417_2.fastq.gz	Fastqsanger.gz
	SRR8929418_1.fastq.gz	Fastqsanger.gz

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Tristetraprolin specifically binds to intron regions and regulates alternative splicing of immune response genes in HeLa cells

Project description:Tristetraprolin (TTP) regulates inflammatory and immune responses by destabilizing target mRNAs via binding to their 3’-UTR AREs. However, we first found that TTP can regulate gene expression and alternative splicing of inflammatory and immune responses genes in the absence of stimulation. In order to find the regulatory mechanisms, we performed iRIP-seq experiments in HeLa cells. iRIP-seq study revealed that TTP binding sites are enriched in the CDS and intronic RNA regions. We also found that the TTP-targets genes were enriched in positive regulation of I-kappaB kinase/NF-kappaB cascade and positive regulation of NF-kappaB transcription factor activity pathway, such as STAT4, EGR3, RELB, TRIM22, RNF25, and TRAF1. Furthermore, we found that alternative splicing of the innate immune response genes were globally regulated by TTP in HeLa cells. Genome-wide mapping of TTP-RNA interactions now reveal that dominant TTP binding near a competing constitutive splice site, whereas prevalent binding close to an alternative site often causes intron retention. This positional effect was further demonstrated by disrupting a TTP-binding site on minigene constructs and detecting their AS events. These findings suggest a mechanism for TTP to modulate splice site competition to produce opposite functional consequences in HeLa cells.

2020-03-12 | GSE130053 | GEO

Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in Hela cells

Project description:Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in Hela cells

| PRJNA470575 | ENA

Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in Hela cells

Project description:we cloned and overexpressed human TTP-encoding gene ZFP36 in HeLa cell in the absence of inflammatory stimuli. The transcriptomes of the control and ZFP36-overexpression cells were sequenced and subjected to analysis and validation. Upon ZFP36 overexpression, expression of genes in innate immunity, including those in type I interferon signaling pathway and viral response, were specifically up-regulated, implying a transcriptional regulatory mechanism associated with the predicted DNA binding activity of TTP. TTP preferentially regulates the alternative splicing of genes involved in positive regulation of I-B/NF-B cascade and TRIF-dependent toll-like receptor signaling pathway, MAPK signaling pathway, TNF signaling pathway and T cell receptor signaling pathways.Our study indicates that TTP may regulates immune response via alternative splicing regulation and possibly by transcriptional regulation as well, which greatly expands the current understanding of the central role of TTP in regulating immune response and tumorigenesis.

2019-03-24 | GSE114216 | GEO

Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells.

Project description:BackgroundTristetraprolin (TTP) is an RNA binding protein that plays a critical role in regulating proinflammatory immune responses by destabilizing target mRNAs via binding to their AU-rich elements (AREs) in the 3'-UTRs of mRNAs. A recent CLIP-seq study revealed that TTP-binding sites are enriched in the intronic regions of RNA. TTP is also a nuclear protein that exhibits putative DNA-binding activity. These features suggested that TTP might regulate gene transcription and/or alternative splicing of pre-mRNAs in the absence of stimulation.ResultsTo elucidate the regulatory pattern of TTP, we cloned and overexpressed the human TTP-encoding gene, ZFP36, in HeLa cells in the absence of inflammatory stimuli. The transcriptomes of the control and ZFP36-overexpressing cells were sequenced and subjected to analysis and validation. Upon ZFP36 overexpression, the expression of genes associated with innate immunity, including those in the type I interferon signaling pathway and viral response, were specifically upregulated, implying a transcriptional regulatory mechanism associated with the predicted DNA binding activity of TTP. TTP preferentially regulated the alternative splicing of genes involved in the positive regulation of the I-κB/NF-κB cascade and the TRIF-dependent toll-like receptor, MAPK, TNF, and T cell receptor signaling pathways.ConclusionsOur findings indicated that TTP may regulate the immune response via the regulation of alternative splicing and potentially transcription, which greatly expands the current understanding of the mechanisms of TTP-mediated gene regulation.

| S-EPMC6498542 | biostudies-literature

NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts

Project description:NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts

| PRJNA844354 | ENA

Identification of FUS RNA targets in HeLa cells

Project description:We identified a landscape of FUS-binding RNA targets in HeLa cells. The majority of the FUS binding sites are in introns of pre-mRNAs and less are in exons and untranslated regions. Significant FUS binding in introns flanking cassette exons, long intron (>100kb) containing transcripts and noncoding RNAs were detected in our study. We specifically determined the function of FUS in regulating the alternative splicing of cassette exons. The top FUS-associated cassette exon is exon 7 of the pre-mRNA of FUS itself. We demonstrated that FUS is a repressor of its own exon 7 splicing. FUS autoregulates its own protein levels by exon 7 alternative splicing and nonsense mediated decay. Moreover, Amyotrophic Lateral Sclerosis (ALS) linked FUS mutants are deficient in FUS autoregulation. CLIP-seq of FUS in HeLa cells

2013-12-16 | E-GEOD-50178 | biostudies-arrayexpress

Tristetraprolin is a tumor suppressor that impairs Myc-induced lymphoma and abolishes the malignant state

Project description:This SuperSeries is composed of the following subset Series: GSE33474: Tristetraprolin is a tumor suppressor that impairs Myc-induced lymphoma and abolishes the malignant state [bone marrow B cells]. GSE37790: Tristetraprolin is a tumor suppressor that impairs Myc-induced lymphoma and abolishes the malignant state [Lymphoma]. GSE37791: Tristetraprolin is a tumor suppressor that impairs Myc-induced lymphoma and abolishes the malignant state [retrovirally infected ex vivo lymphoma] Refer to individual Series

2012-08-01 | E-GEOD-37792 | biostudies-arrayexpress

Multivalent Interactions with CCR4-NOT and PABPC1 Determine mRNA Repression Efficiency by Tristetraprolin

Project description:Tristetraprolin family of proteins regulate mRNA stability by binding to specific AU-rich elements in transcripts. This binding promotes the shortening of the mRNA poly(A) tail, or deadenylation, initiating mRNA degradation. The CCR4-NOT complex plays a central role in deadenylation, while the cytoplasmic poly(A)-binding protein PABPC1 typically protects mRNAs from decay. Here, we investigate how tristetraprolin interacts with CCR4-NOT and PABPC1 to control mRNA stability. Using purified proteins and in vitro assays, we find that tristetraprolin engages CCR4-NOT through multiple interaction sites and promotes its activity, emphasizing the importance of multivalent binding for efficient deadenylation. Phosphorylation of tristetraprolin does not affect its interaction with CCR4-NOT or its deadenylation activity, but is essential for tristetraprolin binding to PABPC1. We propose that tristetraprolin promotes the processive deadenylation activity of CCR4-NOT on mRNAs containing AU-rich elements, with phosphorylation-dependent interactions with PABPC1 potentially enhancing deadenylation and promoting regulated mRNA decay.

2025-06-30 | MSV000098386 | MassIVE

NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts [RNA-seq]

Project description:NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts [RNA-seq]

| PRJNA844346 | ENA

NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts [RIP-seq]

Project description:NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts [RIP-seq]

| PRJNA841993 | ENA