Expression data from control or CCR4b/CNOT6L-depleted cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE31148 | GEO | 2011/08/03
SECONDARY ACCESSION(S): PRJNA144809
REPOSITORIES: GEO
Similar Datasets
Project description:The stability of mRNA influences the abundance of cellular transcripts and proteins. Deadenylases play critical roles in mRNA turnover and thus are important for the regulation of arious biological events. Here, we report the identification and characterization of CCR4b/CNOT6L, which is homologous to yeast CCR4 mRNA deadenylase. We compared the expression profiles of the cellular genes between control and CCR4b/CNOT6L-depleted cells by microarray analysis Total RNAs were extracted from control or CCR4b-depleted cells. Following the isolation of RNA, all subsequent technical procedures, including quality control of RNA, labeling, hybridization, and scanning of the arrays, were performed in BIO MATRIX Research, Inc., cDNA, and biotinlabeled cRNA was synthesized according to protocols for Affymetrix array analysis. Biotin-labeled cRNAs (15 g) were hybridized to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA). To determine the average differences for each probe set, changes were calculated by a global normalization method using Affymetrix GCOS (GeneChipOperating Software) software.
2011-08-02 | E-GEOD-31148 | biostudies-arrayexpress
Project description:mRNA poly(A) tail plays a key role in post-transcriptional regulation of gene expression, including mRNA decay and translation. Deadenylation is a rate-limiting step in mRNA decay, which is catalyzed by the CCR4-NOT complex. To identify mRNAs associated with the CCR4-NOT complex, we have done RIP-CHIP (RNA-immunoprecipitation followed by DNA microarray) using primary hepatocytes from CNOT6L wild-type and knockout mice.
2019-03-29 | GSE62365 | GEO
Project description:The transmission of the malaria parasite between mosquitoes and mammals requires translational repression to ensure that only the proper proteins are expressed at the right time, while still allowing the parasite to prepare the mRNAs it will need for the next developmental stage. With relatively few known specific transcription factors (ApiAP2 family) that may specifically initiate gene transcription, Plasmodium parasites also regulate the stability and turnover of transcripts to provide more comprehensive gene regulation. The CAF1/CCR4/NOT complex has been shown in model organisms to be important for not only mRNA degradation, but also translational control through its deadenylases CAF1 and CCR4. However, few proteins that impose translational repression in Plasmodium sexual stages are known, and those that are characterized primarily affect female gametocytes. Therefore, we have characterized two deadenylases and have uncovered their roles in transmission. We have identified and characterized CCR4-1, which we show plays a role in activating male gametocytes, stabilizing transcripts in gametocytes, and regulating host-to-vector transmission. We find that when ccr4-1 is genetically deleted, there is a loss in the coordination of male gametocyte activation and a reduction in the ability of the parasite to productively infect the mosquito, which is independent of its effect upon male activation. Comparative RNA-seq shows that the deletion of ccr4-1 affects many transcripts that are translationally repressed in females, are related to male gamete function, and/or are important for early mosquito stage development. In contrast, we found that genetic deletion of the major deadenylase Caf1 is lethal. However, we observed that expression of only the N-terminal Caf1 domain is permissive, yet prevents proper complex assembly and phenocopies the ccr4-1 deletion. We therefore conclude that the general and transmission-specialized deadenylases of the CAF1/CCR4/NOT complex play critical and intertwined roles in parasite growth and transmission.
2019-01-07 | PXD007042 | Pride
Project description:CCR4-NOT deadenylase is a major regulator of mRNA turnover in eukaryotes. It contains 2 heterogeneous catalytic subunits encoded by Cnot7/8 and Cnot6/6l genes in vertebrates, respectively. The physiological function of each catalytic subunit was unclear due to potential gene redundancy in vivo. In this study Cnot6/6l double knockout mice were generated. These mice were viable and generally healthy, but females were infertile with irregular estrus cycle and poor ovarian responses to gonadotropins. Follicle-stimulating hormone (FSH) stimulated transcription and translation of mRNAs encoding CNOT6 and CNOT6L in ovarian granulosa cells through the activity of phosphoinositide 3-kinase signaling pathway. Results of transcriptome analyses indicated that FSH downregulated a large number of transcripts in granulosa cells during the transition from pre-antral to antral follicles in a CNOT6/6L-dependent manner. These two deadenylases functioned as key effectors of FSH in altering the developmental programs in granulosa cells and triggered clearance of specific transcripts in growing follicles, particularly those encoding repressing factors of granulosa cell proliferation and steroidogenesis. These results demonstrated that FSH modulates granulosa cells function by stimulating selective translational activation and degradation of existed mRNAs, in additional to inducing de novo gene transcription. Meanwhile, this study provides in vivo evidence that CCR4-NOTCNOT6/6L-mediated mRNA deadenylation is dispensable in most somatic cell types, but is essential for the female reproductive endocrine regulation.
2021-11-04 | GSE158773 | GEO
Project description:We profiled transcriptomes from Cnot6l deadenylase knock-out mouse GV oocytes, MII eggs and 1-cell zygotes in order to analyse its function during the oocyte-to-embryo (OET) transition. Transcriptome of wild-type golden hamster GV oocytes was also profiled.
2018-07-10 | GSE116771 | GEO
Project description:The transmission of the malaria parasite between mosquitoes and mammals requires translational repression to ensure that only the proper proteins are expressed at the right time, while still allowing the parasite to prepare the mRNAs it will need for the next developmental stage. With relatively few known specific transcription factors (ApiAP2 family) that may specifically initiate gene transcription, Plasmodium parasites also regulate the stability and turnover of transcripts to provide more comprehensive gene regulation. The CAF1/CCR4/NOT complex has been shown in model organisms to be important for not only mRNA degradation, but also translational control through its deadenylases CAF1 and CCR4. However, few proteins that impose translational repression in Plasmodium sexual stages are known, and those that are characterized primarily affect female gametocytes. Therefore, we have characterized two deadenylases and have uncovered their roles in transmission. We have identified and characterized CCR4-1, which we show plays a role in activating male gametocytes, stabilizing transcripts in gametocytes, and regulating host-to-vector transmission. We find that when ccr4-1 is genetically deleted, there is a loss in the coordination of male gametocyte activation and a reduction in the ability of the parasite to productively infect the mosquito, which is independent of its effect upon male activation. Comparative RNA-seq shows that the deletion of ccr4-1 affects many transcripts that are translationally repressed in females, are related to male gamete function, and/or are important for early mosquito stage development. In contrast, we found that genetic deletion of the major deadenylase Caf1 is lethal. However, we observed that expression of only the N-terminal Caf1 domain is permissive, yet prevents proper complex assembly and phenocopies the ccr4-1 deletion. We therefore conclude that the general and transmission-specialized deadenylases of the CAF1/CCR4/NOT complex play critical and intertwined roles in parasite growth and transmission.
2019-01-02 | GSE101484 | GEO
Project description:The first and rate-limiting step in eukaryotic mRNA decay is the shortening of the poly(A) tail catalyzed by a family of enzymes known as deadenylases. In humans, several deadenylases have been recognized so far, yet it is not clear what the advantage is to have many enzymes catalyzing the same reaction. It is hypothesized that specific deadenylases may target unique subsets of mRNAs, or multiple deadenylases can act on the same mRNA, with discrete but overlapping functions. To understand the biological significance of the diversity of these enzymes we silenced the expression of several deadenylases, including PARN, NOC, CNOT6, CNOT6L, and CNOT7, in human cells of cancer origin (NCI-H520; squamous lung cancer), and analyze the impact on gene expression with microarrays.
2015-10-01 | GSE67598 | GEO
Project description:we transiently transfected LHCN cells (human skeletal myoblasts) with a CNOT6L-targeting siRNA or with an irrelevant siRNA as control. Cells were then placed under differentiation conditions for 2 days and total mRNA used for microarray analysis
2015-12-04 | E-MTAB-3472 | biostudies-arrayexpress
Project description:mRNA degradation critically contributes to liver development and function. The CCR4-NOT complex serves as a major deadenylase that initiates mRNA degradation. We used microarrays to identify deregulated genes in the livers lacking Cnot3, a core subunit of the CCR4-NOT complex.
2019-02-21 | GSE120910 | GEO
Project description:mRNA degradation critically contributes to liver development and function. The CCR4-NOT complex serves as a major deadenylase that initiates mRNA degradation. We used microarrays to identify deregulated genes in the livers lacking CNOT3, a core subunit of the CCR4-NOT complex.
2019-02-21 | GSE114508 | GEO