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Uncovering human DCP1 is essential for mRNA decapping process and paralog-specific functions in gene regulation

ABSTRACT: Uncovering human DCP1 is essential for mRNA decapping process and paralog-specific functions in gene regulation

PROVIDER: PRJNA962829 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24333900_1.fastq.gz	Fastqsanger.gz
	SRR24333900_2.fastq.gz	Fastqsanger.gz
	SRR24333901_1.fastq.gz	Fastqsanger.gz
	SRR24333901_2.fastq.gz	Fastqsanger.gz
	SRR24333902_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Uncovering human DCP1 is essential for mRNA decapping process and paralog-specific functions in gene regulation

Project description:The decapping complex is crucial in regulating gene expression by removing the mRNA cap structure. While DCP2 serves as the catalytic subunit in this complex, DCP1 is recognized as its major activator. In humans, there exist two distinct paralogs of DCP1, DCP1a and DCP1b, which each form separate decapping complexes. However, the endogenous mRNA targets of these DCP1 paralogs are largely unknown. To address the role of human DCP1 paralogs, we generated multiple DCP1-knockout cell lines and evaluated the importance of human DCP1 in mRNA decapping. Surprisingly, our results revealed that human DCP1 is essential for decapping process. We also discovered that the EVH1 domain of DCP1 is indispensable for the decapping activity of DCP2, as it enhances the mRNA-binding affinity of DCP2. Additionally, the knock-out of DCP1 paralogs led to the significant activation of several pathways associated with cancer and mRNA processing, as well as the downregulation of DCP1a in various cancer types. Moreover, the knock-out cell lines of the two paralogs also exhibited distinct metabolome profiles. Overall, our findings highlight the crucial role of human DCP1 in mRNA decapping and shed light on the distinct functions of its two paralogs.

2024-10-26 | GSE230847 | GEO

WGD paralog evolution

Project description:WGD paralog evolution

| PRJNA743682 | ENA

Human DCP1 is crucial for mRNA decapping and possesses paralog-specific gene regulating functions.

Project description: Not available

| S-EPMC11530239 | biostudies-literature

Nudt3 is a mRNA Decapping Enzyme That Modulates Cell Migration

Project description:The Dcp2 and Nudt16 Nudix hydrolases, are mRNA decapping enzymes that preferentially modulate stability of a subset of mRNAs. Here we report Nudt3 is a third Nudix protein that possess mRNA decapping activity in cells and is a modulator of cell migration in MCF-7 breast cancer cells. Genome-wide analysis of Nudt3 compromised cells identified increases in mRNAs involved in cell motility including integrin Î²6, lipocalin-2 and fibronectin. The increase in mRNA levels was dependent on Nudt3 decapping activity where integrin Î²6 and lipocalin-2 were modulated directly through mRNA stability, while fibronectin was indirectly controlled. Moreover, increased cell migration observed in Nudt3 depleted cells was mediated through the extracellular integrin Î²6 and fibronectin protein nexus. We conclude, Nudt3 is an mRNA decapping enzyme that orchestrates expression of a subset of mRNAs to modulate cell migration and further substantiates the existence of multiple decapping enzymes functioning in distinct cellular pathways in mammals. Stably transformed MCF-7 cell lines constitutively expressing either a short hairpin RNA (shRNA) directed against Nudt3 (Nudt3KD) or a non-targeted control shRNA (ConKD) were used, with three replicate cultures used per group (n=3).

2016-07-21 | E-GEOD-75146 | biostudies-arrayexpress

Drosophila importin alpha1 performs paralog-specific functions essential for gametogenesis.

Project description: Not available

| S-EPMC2248332 | biostudies-literature

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

WGD paralog evolution

Project description:Studying the evolution of binding preferences for 30 paralog TF pairs in S.cerevisiae

2022-01-21 | GSE179430 | GEO

Nudt3 is a mRNA Decapping Enzyme That Modulates Cell Migration

Project description:The Dcp2 and Nudt16 Nudix hydrolases, are mRNA decapping enzymes that preferentially modulate stability of a subset of mRNAs. Here we report Nudt3 is a third Nudix protein that possess mRNA decapping activity in cells and is a modulator of cell migration in MCF-7 breast cancer cells. Genome-wide analysis of Nudt3 compromised cells identified increases in mRNAs involved in cell motility including integrin β6, lipocalin-2 and fibronectin. The increase in mRNA levels was dependent on Nudt3 decapping activity where integrin β6 and lipocalin-2 were modulated directly through mRNA stability, while fibronectin was indirectly controlled. Moreover, increased cell migration observed in Nudt3 depleted cells was mediated through the extracellular integrin β6 and fibronectin protein nexus. We conclude, Nudt3 is an mRNA decapping enzyme that orchestrates expression of a subset of mRNAs to modulate cell migration and further substantiates the existence of multiple decapping enzymes functioning in distinct cellular pathways in mammals.

2016-07-21 | GSE75146 | 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 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

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