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The SSUP-72/PINN-1 module is required for efficient 3’end processing and coordinates developmental gene expression during exit from diapause in C. elegans [RNAseq-SSUP72]

ABSTRACT: During the exit from the developmental diapause of Caenorhabditis elegans (C. elegans), a network of growth and developmental genes is activated. These genes are organized into operons, where transcriptional termination is uncoupled from mRNA 3’-end processing. Although the Pol II CTD-S2P mark deposited by CDK-12 is unnecessary during embryogenesis, it plays a critical role in the timely expression of most operonic genes by enhancing SL2 trans-splicing at position 2 and above. This process protects mRNA from degradation and prevents termination. Here, a genetic screen has identified the SSUP-72/PINN-1 module as an effective suppressor of CDK-12-induced defects. Our data show that the SSUP-72/PINN-1 module regulates intra-operon termination and affects 3’ pausing genome-wide, coordinating growth and developmental gene expression during post-embryonic development in C. elegans.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE263771 | GEO | 2025/02/08

REPOSITORIES: GEO

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The SSUP-72/PINN-1 module is required for efficient 3’end processing and coordinates developmental gene expression during exit from diapause in C. elegans [RNAseq-suppression]

Project description:During the exit from the developmental diapause of Caenorhabditis elegans (C. elegans), a network of growth and developmental genes is activated. These genes are organized into operons, where transcriptional termination is uncoupled from mRNA 3’-end processing. Although the Pol II CTD-S2P mark deposited by CDK-12 is unnecessary during embryogenesis, it plays a critical role in the timely expression of most operonic genes by enhancing SL2 trans-splicing at position 2 and above. This process protects mRNA from degradation and prevents termination. Here, a genetic screen has identified the SSUP-72/PINN-1 module as an effective suppressor of CDK-12-induced defects. Our data show that the SSUP-72/PINN-1 module regulates intra-operon termination and affects 3’ pausing genome-wide, coordinating growth and developmental gene expression during post-embryonic development in C. elegans.

2025-02-08 | GSE263774 | GEO

The SSUP-72/PINN-1 module is required for efficient 3’end processing and coordinates developmental gene expression during exit from diapause in C. elegans [GROseq]

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The RNA polymerase II CTD phosphatase SSUP-72 regulates alternative polyadenylation in C. elegans neurons.

Project description:Alternative polyadenylation (APA) plays important roles in generating transcriptomediversity. In the nervous system widespread APA are observed in development and activity-mediated neural plasticity. However, the underlying molecular mechanisms are largely unknown. Through systematic genetic studies and genome-wide survey of transcriptional landscape, here, we report a mechanism controlling APA of two neuronal genes, UNC-44/Ankyrin and DLK-1/MAPKK, during development of C. elegans nervous system. We show that SSUP-72, a Ser5 phosphatase for RNA polymerase II (Pol II) Carboxyl-Terminal Domain (CTD), differentially affects the usage of poly(A) sites (PASs) in the coding regions of unc-44 and dlk-1. A novel nuclear protein SYDN-1 interacts with both SSUP-72 and RNA pol II, and inhibits the function of SSUP-72 and nuclear polyadenylation factors. This regulatory pathway dampens the usage of a strong internal PAS of unc-44 for the production of neuron-specific ankyrin, and promotes the usage of a weak PAS of dlk-1 to control its activity. Deregulation of unc-44 and dlk-1 mRNA isoforms impairs neuronal development. Our data illustrate the high degree selectivity of APA regulation in complex nervous systems.

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2015-11-01 | E-GEOD-68203 | biostudies-arrayexpress

The SSUP-72/PINN-1 module is required for efficient 3’end processing and coordinates developmental gene expression during exit from diapause in C. elegans [GROseq]

Project description:The SSUP-72/PINN-1 module is required for efficient 3’end processing and coordinates developmental gene expression during exit from diapause in C. elegans [GROseq]

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Genome wide expression analysis of Caenorhabditis elegans cdk-8(tm1238) null mutants (vs. WT N2 worms)

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