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Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability

ABSTRACT: Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, and as a translational repressor, but their functions in cells are incompletely understood. We have analyzed these questions by a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE216831 | GEO | 2023/02/07

REPOSITORIES: GEO

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Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability II

Project description:Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, and as a translational repressor, but their functions in cells are incompletely understood. We have analyzed these questions by a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs.

2023-02-07 | GSE220578 | GEO

RNAi knock down of mRNA decapping co-activators in Drosophila S2 cells

Project description:We analyzed mRNA expression profiles in Drosophila melanogaster S2 cells that had been depleted of proteins known as mRNA decapping co-activators. mRNA decapping is catalyzed by DCP2, and DCP2 activity is stimulated by decapping co-activators. This group of proteins includes DCP1, Hedls (also known as Ge-1), LSm16 (also known as EDC3), rck/p54 (also known as DHH1 or Me31B), Pat1, and the heptameric LSm1-7 complex. We used the RNA interference technology to deplete cultured S2 cells of DCP1 (CG11183), Ge-1 (CG6181), Pat1 (CG5208), LSm16 (CG6311), and LSm1 (CG4279). We used Affymetrix oligonucleotide microarrays to analyze two independent samples for each depletion. We included the following controls: mock RNAi treatment and GFP dsRNA treatment (two profiles each). We also profiled AGO1 (CG6671) depleted cells (3 independent samples). AGO1 is a key protein required for miRNA-mediated gene silencing. We had shown previously that silencing by miRNAs involves decapping of target mRNAs.

2007-09-03 | E-MEXP-1012 | biostudies-arrayexpress

Genome-wilde identification of decapping substrates in the yeast Saccharomyces cervisiae

Project description:To assess the roles of the Dcp2 C-terminal domain and the decapping activators Pat1, Lsm1, and Dhh1 in mRNA decapping, we used RNA-Seq to analyze the expression profiles of yeast cells harboring a truncation of the Dcp2 C-terminal domain, mutations that render Dcp2 catalytically inactive, or deletions of the PAT1, LSM1, and DHH1 genes. Consistent with our recent model for decapping regulation, we found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation and that loss of these control functions causes significant deregulation of mRNA decapping; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap and, as expected, are targeted to decapping-dependent decay.

2017-12-09 | GSE107841 | GEO

Expression data from mid-aged decapping mutant C. elegans nematodes

Project description:Removal of the 5’ cap of mRNAs (decapping) is mainly catalyzed by a conserved holoenzyme, composed of the catalytic subunit DCP2 and its essential cofactor DCP1. Studies in C. elegans have shown that ageing is characterized by the accumulation of decapping factors in P-Bodies, and loss of DCAP-1/DCP1 or DCAP-2/DCP2 significantly shortens lifespan. However, the relationship between mRNA decapping and ageing remains elusive. Here we present a comparative microarray study that aims to uncover this link by identifying differentially expressed genes between wild type mid-aged worms (9 days old) and age-matched animals with reduced function of DCAP-1/DCP1.

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Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo

Project description:We have identified mRNAs whose abundance or translational efficiency is regulated in nutrient-rich medium by the Scd6 or Dhh1 protein in either wild-type cells or dcp2∆ cells lacking the decapping enzyme

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Regulation of transcript abundance and translationny decapping activators Pat1 and Dhh1

Project description:We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors. Although the Environmental Stress Response (ESR) is activated in dhh1 and pat1 mutants, hundreds of non-ESR transcripts are elevated in a manner indicating cumulative repression by Pat1 and Dhh1 in WT. These mRNAs show reduced decapping and diminished transcription in the mutants, indicating that impaired mRNA turnover drives transcript derepression in cells lacking Dhh1 or Pat1. mRNA degradation stimulated by Dhh1/Pat1 is not dictated by poor translation nor enrichment for suboptimal codons. Pat1 and Dhh1 also collaborate to reduce translation and protein production from many mRNAs. Transcripts showing concerted translational repression by Pat1/Dhh1 include mRNAs involved in cell adhesion or utilization of the poor nitrogen source allantoin. Pat1/Dhh1 also repress numerous transcripts involved in respiration, catabolism of non-preferred carbon or nitrogen sources, or autophagy; and we obtained evidence for elevated respiration and autophagy in the mutants. Thus, Pat1 and Dhh1 function as post-transcriptional repressors of multiple pathways normally activated only during nutrient limitation.

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Identification of proteins associated with the decapping complex and the endonuclease DNE1 in Arabidopsis

Project description:In this work, we used an unbiased approach coupling immunoprecipitations (IPs) and mass spectrometry to define the interactome of the decapping activator DCP1 and the decapping enzyme DCP2. In addition we unravel the interactome of the endonuclease DNE1 harboring an endoribonuclease domain of the NYN family.

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mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability

2023-10-24 | PXD042828 | Pride

Genome-wilde expression profiling analysis of yeast cells lacking the decapping activator Scd6

Project description:To assess the role of the decapping activator Scd6 in mRNA decay, we used RNA-Seq to analyze the expression profile of yeast cells harboring a deletion of the SCD6 gene. Consistent with our recent model for decapping regulation, we found that Scd6 targets a small number of specific mRNAs in yeast cells. Interestingly, degradation of Scd6-targeted transcripts also requires the functions of the decapping activators Pat1, Lsm1, and Dhh1, suggesting that Scd6 functions together with Pat1, Lsm1, and Dhh1 in promoting mRNA decapping.

2018-05-15 | GSE114428 | GEO

Effects of Dcp1a and Dcp2 knockdown during mouse oocyte maturation

Project description:Oocyte maturation is accompanied by a transition from mRNA stability to instability. We investigated the role of DCP1A and DCP2, proteins responsible for mRNA decapping, in mRNA destabilization during mouse oocyte maturation. siRNA-mediated knockdown of both Dcp1a and Dcp2 transcripts prior to initiation of maturation inhibited the maturation-associated increase of DCP1A and DCP2, stabilized a set of maternal mRNAs that are normally degraded during maturation, and inhibited development beyond the 2-cell stage, likely a consequence of failure to activate fully the zygotic genome. Total RNA from 30 MII eggs was used in each sample. Three independent biological replicates were analyzed for each condition.

2013-02-06 | E-GEOD-27049 | biostudies-arrayexpress

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