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An PWI- and RRM Motif-Containing Protein Is Critical for Pre-mRNA Splicing and ABA Responses in Arabidopsis

ABSTRACT: We used RNA-seq platform to determine role of a splicing factor RBM25 in regulation of gene expression and pre-mRNA splicing. We found that a loss-of-function allele of RBM25, rbm25-1, causes up- and down-regulation of a large number of genes. We further found that the rbm25-1 mutation results in defects in altenative splicing of transcripts of many genes including signal transduction components in stress responses.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE66737 | GEO | 2015/10/28

SECONDARY ACCESSION(S): PRJNA277840

REPOSITORIES: GEO

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An PWI- and RRM Motif-Containing Protein Is Critical for Pre-mRNA Splicing and ABA Responses in Arabidopsis

Project description:We used RNA-seq platform to determine role of a splicing factor RBM25 in regulation of gene expression and pre-mRNA splicing. We found that a loss-of-function allele of RBM25, rbm25-1, causes up- and down-regulation of a large number of genes. We further found that the rbm25-1 mutation results in defects in altenative splicing of transcripts of many genes including signal transduction components in stress responses. Examination of mRNA levels in bulked individual wild type and rbm25-1 mutant seedlings before and after ABA treatment.

2015-10-28 | E-GEOD-66737 | biostudies-arrayexpress

An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses.

Project description: Not available

| S-EPMC5514415 | biostudies-literature

The splicing factor RBM25 controls MYC activity in Acute Myeloid Leukemia

Project description:Cancer sequencing studies have implicated regulators of pre-mRNA splicing as important disease determinants in Acute Myeloid Leukemia (AML), but the underlying mechanisms have remained elusive. We hypothesized that “non-mutated” splicing regulators may also play a role in AML biology and therefore conducted an in vivo shRNA screen in a mouse model of CEBPA mutant AML. This led to the identification of the splicing regulator RBM25 as a novel tumor suppressor, and down-regulation of RBM25 increased proliferation and decreased apoptosis in human leukemic cell lines. Mechanistically, we could show that RBM25 controlled the splicing of key genes, including those encoding the apoptotic regulator BCL-x and the MYC inhibitor BIN1. Specifically, we demonstrated that RBM25 acts as a regulator of MYC activity and sensitizes cells to increased MYC levels. This mechanism also appears to be operative in human AML patients where RBM25 levels correlative inversely with MYC activity and clinical outcome.

2018-12-07 | GSE114027 | GEO

SlEAD1, an EAR motif-containing ABA down-regulated novel transcription repressor regulates ABA response in tomato.

Project description: Not available

| S-EPMC7518750 | biostudies-literature

RBM25 affects the immune and inflammatory progress by binding to and modulating alternative splicing levels of associated genes in rat H9C2 cells [ABL2020-10020-ABF_H9C2_RBM25_iRIP]

Project description:Alternative splicing (AS) enables genes to be translated into a vast diversity of proteins while aberrant AS predisposes cells to abnormal biological processes. As is closely associated with AS, RNA binding proteins (RBPs) are gradually gaining attention. RBM 25 was reported to participate in the cardiac pathophysiological process via AS regulation. Nonetheless, gaps still existed in whether RBM 25 functions in heart failure by its splicing factor role. H9C2 cells with excessively expressed RBM25 were used to filtrate different expression genes (DEGs) and analyze for RBM25-regulated AS by RNA-seq. Next, iRIP-seq was performed to examine its binding targets. For genes screened, further RT-qPCR-based validation was conducted. RBM25 overexpression caused expressive alteration in 80 genes mainly involved in the inflammatory response and virus response. Notably, RBM25 partially modulated AS of differential genes enriched in the apoptotic process and bound to genes clustered at inflammation response. Further, qRT-PCR verified Slc38a9, IL-17RC, Csf1, and Coro6 as targets of RBM25 being bound to and AS-regulated.

2023-10-05 | GSE209941 | GEO

RBM25 affects the immune and inflammatory progress by binding to and modulating alternative splicing levels of associated genes in rat H9C2 cells [ABL2020-10020-ABF_RBM25_OE]

2023-10-05 | GSE209940 | GEO

The dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons [seCLIP-Seq]

Project description:Precise coordination of molecular programs and neuronal growth govern the formation, maintenance, and adaptation of neuronal circuits. RNA metabolism has emerged as a key regulatory node of neural development and nervous system pathologies. To uncover novel cell-type-specific RNA regulators, we systematically investigated expression of RNA recognition motif-containing proteins in the mouse neocortex. Surprisingly, we found RBM20, an alternative splicing regulator associated with dilated cardiomyopathy, to be expressed in cortical parvalbumin interneurons and mitral cells of the olfactory bulb. Genome-wide mapping of RBM20 target mRNAs revealed that neuronal RBM20 binds distal intronic regions. Loss of neuronal RBM20 has only modest impact on alternative splice isoforms but results in a significant reduction in an array of mature mRNAs in the neuronal cytoplasm. This phenotype is particularly pronounced for genes with long introns that encode synaptic proteins. We hypothesize that RBM20 ensures fidelity of pre-mRNA splicing by suppressing non-productive splicing events in long neuronal genes. This work highlights a common requirement of two excitable cell types, cardiomyocytes and neurons, for RBM20-dependent transcriptome regulation.

2023-12-16 | GSE250098 | GEO

SKIP regulates ABA-mediated alternative splicing and its signaling in Arabidopsis

Project description:Abscisic acid (ABA) plays a key role in plant development and responses to abiotic stress. A wide number of regulatory mechanisms on ABA perception and signaling are known, including transcriptional regulation and post-translational regulations; however, less to know about the post-transcriptional regulations. In this work, we have found that SKIP, a splicing factor in spliceosome, positively regulates ABA signal transduction. Mutation of SKIP, skip-1, confers ABA insensitive phenotype in seed germination, root growth, and ABA-responsive gene expression. Transformation of SKIP genomic DNA to skip-1 is able to recover its defects. SKIP binds to the pre-mRNA of genes in ABA signaling, such as PYL8, to regulate their splicing. The alternative splicing of PYL7, PYL8, ABF2, and ABI5 in ABA pathway is disrupted by skip-1, reducing the mRNA levels of them. The abnormal splicing of PP2Cs activates their transcription by skip-1, suggesting there is a feedback regulation for PP2Cs caused by skip-1. The down-regulation of PYL ABA receptors, ABF2 and ABI5 ABA response transcription factors, and the up-regulation of PP2Cs through alternative splicing reduce the plant responses to ABA in skip-1. SKIP is required for ABA-mediated genome-wide alternative splicing. ABA treatment enhances the novel splicing events in WT genome-widely. The novel alternative splicing events are increased by skip-1 in the absence and present of ABA. Our results first reveal a principle on how a splicing factor affects the ABA signaling.

2023-02-02 | GSE144823 | GEO

An ancient testis-specific IQ motif containing H gene regulates specific isoform expression during spermatogenesis

Project description:Spermatogenic cells express more alternatively spliced RNAs than most whole tissues; however, the regulation of these events remains unclear. Here we characterize the function of a testis-specific IQ motif containing H gene (Iqch), whose expression has been confirmed to be testis specific in all mammalian species analyzed yet its role remains elusive. Using a mutant mouse model, we found that Iqch is essential for the specific expression of RNA isoforms during spermatogenesis. Through immunohistochemistry of adult mouse testis, we noted that Iqch was localized in somatic and germ cells, including spermatogonia, spermatocytes and round spermatids. Further, Iqch was expressed mainly in the nucleus at the stages spermatocyte and spermatid, where IQCH appeared juxtaposed with SRRM2 and ERSP1, suggesting that interactions among these proteins regulate alternative splicing (AS). By RNA-seq, we noted that mutant Iqch produces alterations in gene expression, including the clear downregulation of testis-specific lncRNAs and protein coding genes at the spermatid stage, and AS modifications, principally increased intron retention, resulting in complete male infertility. Interestingly, the presence of WT Iqch allowed us to identify novel spliced transcripts, while mutant Iqch modified the expression and use of hundreds of RNA isoforms, favoring the expression of the canonical form. This suggests that Iqch is part of a splicing control mechanism, essential in germ cell biology. Our findings reveal the role of Iqch in spermatogenesis and provide clues to the molecular mechanisms controlling the expression of RNA isoforms, mainly in the last stages of spermatogenesis

2023-03-22 | GSE214201 | GEO

The dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons [Ribo-TRAP RNA-seq]

2023-12-16 | GSE250096 | GEO

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