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RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE145458 | GEO | 2020/10/20

REPOSITORIES: GEO

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RNA polymerase II CTD S2P is dispensable for embryogenesis but mediates exit from developmental diapause in C. elegans.

Project description:Serine 2 phosphorylation (S2P) within the CTD of RNA polymerase II is considered a Cdk9/Cdk12-dependent mark required for 3'-end processing. However, the relevance of CTD S2P in metazoan development is unknown. We show that cdk-12 lesions or a full-length CTD S2A substitution results in an identical phenotype in Caenorhabditis elegans Embryogenesis occurs in the complete absence of S2P, but the hatched larvae arrest development, mimicking the diapause induced when hatching occurs in the absence of food. Genome-wide analyses indicate that when CTD S2P is inhibited, only a subset of growth-related genes is not properly expressed. These genes correspond to SL2 trans-spliced mRNAs located in position 2 and over within operons. We show that CDK-12 is required for maximal occupancy of cleavage stimulatory factor necessary for SL2 trans-splicing. We propose that CTD S2P functions as a gene-specific signaling mark ensuring the nutritional control of the C. elegans developmental program.

| S-EPMC7725455 | biostudies-literature

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [ChIP-seq]

Project description:We show that inactivating CDK-12 or expressing a full-length CTD S2A mutant in Caenorhabditis elegans results in developmental arrest at the L1 stage,which mimicks the diapause induced when hatching occurs in the absence of food. Transcriptomic analyses indicate that when CDK-12 is inhibited, only a subset of growth-related genes is not properly expressed. These genes correspond to SL2 trans-spliced mRNAs located in position 2 and over within operons. We show that CDK-12 is required for maximal occupancy of CstF (cleavage stimulatory factor) required for SL2 trans-splicing. The addition of food to developmentally arrested worms leads to an increase of both CTD S2P and SL2 trans-splicing. We propose that CTD S2P functions as a gene-specific signaling mark ensuring the nutritional control of C. elegans development.

2020-10-20 | GSE145456 | GEO

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [RNA-seq]

2020-10-20 | GSE145457 | GEO

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans

Project description:RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans

| PRJNA607250 | ENA

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [ChIP-seq]

Project description:RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [ChIP-seq]

| PRJNA607254 | ENA

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [RNA-seq]

Project description:RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [RNA-seq]

| PRJNA607253 | ENA

RNA Polymerase II CTD is dispensable for transcription and required for termination in human cells

Project description:The largest subunit of RNA polymerase (Pol) II harbors an evolutionarily conserved C-Terminal-Domain (CTD), composed of heptapeptide repeats, central to the transcriptional process. Here, we analyze the transcriptional phenotypes of a CTD-delta5 mutant that carries a large CTD truncation in human cells. Our data show that this mutant can transcribe genes in living cells but displays a pervasive phenotype with impaired termination, similar to but more severe than previously characterized mutations of CTD tyrosine residues. The CTD-delta5 mutant does not interact with the Mediator and Integrator complexes involved in activation of transcription and processing of RNAs. Examination of long-distance interactions and CTCF binding patterns in CTD-delta5 mutant cells reveals no changes in TAD domains or borders. Our data demonstrate that the CTD is largely dispensable for the act of transcription in living cells. We propose a model in which CTD-depleted Pol II has a lower entry rate onto DNA but becomes pervasive once engaged in transcription, resulting in a defect in termination.

| S-SCDT-10_15252-EMBR_202256150 | biostudies-other

The C. elegans developmental timing protein LIN-42 regulates diapause in response to environmental cues.

Project description:Environmental conditions can have a major impact on developmental progression in animals. For example, when C. elegans larvae encounter harsh conditions they can reversibly halt the passage of developmental time by forming a long-lived dauer larva at the end of the second larval stage. Here, we show that the period homolog lin-42, known to control developmental time, also acts as a component of a switch that mediates dauer entry. Loss of lin-42 function renders animals hypersensitive to dauer formation under stressful conditions, whereas misexpression of lin-42 in the pre-dauer stage inhibits dauer formation, indicating that lin-42 acts as a negative regulator of this life history decision. These phenotypes place LIN-42 in opposition to the ligand-free form of the nuclear receptor DAF-12, which indirectly senses environmental conditions and helps to integrate external cues into developmental decisions. Mutations that impair DAF-12 ligand binding are exquisitely sensitive to the absence of lin-42, whereas overexpression of LIN-42 can suppress the dauer constitutive phenotype of a ligand-insensitive daf-12 mutant, suggesting that LIN-42 and DAF-12 are intimate partners in controlling the decision to become a dauer larva. The functional outputs of Period family proteins and nuclear receptors also converge in other organisms, suggesting that the relationship between lin-42 and daf-12 represents an ancient genetic framework for responding to environmental stimuli.

| S-EPMC2947761 | biostudies-literature

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.

2015-06-01 | GSE67649 | GEO

Structural Motifs for CTD Kinase Specificity on RNA Polymerase II during Eukaryotic Transcription.

Project description:The phosphorylation states of RNA polymerase II coordinate the process of eukaryotic transcription by recruitment of transcription regulators. The individual residues of the repetitive heptad of the C-terminal domain (CTD) of the biggest subunit of RNA polymerase II are phosphorylated temporally at different stages of transcription. Intriguingly, despite similar flanking residues, phosphorylation of Ser2 and Ser5 in CTD heptads play dramatically different roles. The mechanism of how the kinases place phosphorylation on the correct serine is not well understood. In this paper, we use biochemical assays, mass spectrometry, molecular modeling, and structural analysis to understand the structural elements determining which serine of the CTD heptad is subject to phosphorylation. We identified three motifs in the activation/P+1 loops differentiating the intrinsic specificity of CTD in various CTD kinases. We characterized the enzyme specificity of the CTD kinases-CDK7 as Ser5-specific, Erk2 with dual specificity for Ser2 and Ser5, and Dyrk1a as a Ser2-specific kinase. We also show that the specificities of kinases are malleable and can be modified by incorporating mutations in their activation/P+1 loops that alter the interactions of the three motifs. Our results provide an important clue to the understanding of post-translational modification of RNA polymerase II temporally during active transcription.

| S-EPMC8018230 | biostudies-literature

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