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PAF1 N-terminal extension-generated PAF1c-SKIP-CDKB module regulates plant-specific cell cycle in the plant kingdom

ABSTRACT: Through systematic biochemical analyses, we identified a novel protein-protein interaction between PAF1 and SKIP in Chlamydomonas reinhardtii. To investigate the functional significance of this interaction, we generated targeted mutants using CRISPR-Cas9 genome editing technology. Phenotypic characterization revealed that both PAF1 and SKIP mutants exhibit coordinated regulation of the cell cycle progression. To elucidate the molecular mechanism underlying PAF1-SKIP mediated cell cycle regulation, we employed an integrated multi-omics approach. RNA sequencing (RNA-seq) analysis was performed to identify differentially expressed genes, while chromatin immunoprecipitation sequencing (ChIP-seq) was utilized to map the genomic loci directly bound by the PAF1-SKIP protein complex. This comprehensive strategy enabled us to delineate the transcriptional network governed by the PAF1-SKIP regulatory module.

ORGANISM(S): Chlamydomonas reinhardtii

PROVIDER: GSE300409 | GEO | 2025/06/25

REPOSITORIES: GEO

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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.

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SKIP Is a Component of the Spliceosome Linking Alternative Splicing and the Circadian Clock in Arabidopsis

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2012-12-13 | E-GEOD-32216 | biostudies-arrayexpress

SKIP Confers Salt Tolerance through Controlling Gene Alternative Splicing in Arabidopsis

Project description:A better understanding of the mechanisms for plant in response to abiotic stresses is key for the improvement of plant to resistant to the stresses. Much has been known for the regulation of gene expression in response to salt stress at transcriptional level, however, little is known at posttranscriptional level for this response. Recently, we identified that SKIP is a component of spliceosome and is necessary for the regulation of alternative splicing and mRNA maturation of clock genes. In this study, we observed that skip-1 is hypersensitive to salt stress. SKIP is necessary for the alternative splicing and mRNA maturation of several salt tolerance genes, e.g. NHX1, CBL1, P5CS1, RCI2A, and PAT10. Genome-wide analysis reveals that SKIP mediates the alternative splicing of many genes under salt stress condition, most of the new alternative splicing events in skip-1 is intron retention, which leads to the premature termination codon in their mRNA. SKIP also controls the alternative splicing by modulating the recognition or cleavage of 5' and 3' splice donor and acceptor sites under salt stress condition. Therefore, this study addresses a fundamental question on how the mRNA splicing machinery contributes to salt response at a posttranscriptional level. Totally six samples, two treatments and two genotypes, and each have two replicats.

2015-04-01 | E-GEOD-55632 | biostudies-arrayexpress

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SKIP Confers Salt Tolerance through Controlling Gene Alternative Splicing in Arabidopsis

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2015-10-01 | GSE73632 | GEO

SKIP Is a Component of the Spliceosome Linking Alternative Splicing and the Circadian Clock in Arabidopsis

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RNA expression profiling for Paf1 complex mutant strains [miRNA]

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