Non-equilibrium pronucleus histones require gametal factor Lsm1 induced major satellite RNA decay
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ABSTRACT:
PROVIDER: PRJNA744199 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15051120_1.fastq.gz | Fastqsanger.gz | |||
| SRR15051120_2.fastq.gz | Fastqsanger.gz | |||
| SRR15051121_1.fastq.gz | Fastqsanger.gz | |||
| SRR15051121_2.fastq.gz | Fastqsanger.gz | |||
| SRR15051122_1.fastq.gz | Fastqsanger.gz |
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Project description:The development of a multicellular organism with various organs and tissues is a complex but highly concerted process, in which cells acquire different identities through exquisite spatiotemporal regulations called cell fate decision. Here, we Lsm1 targets non-coding major satellite RNAs in mouse zygote, which is required for the non-equilibrium epigenetic modification, especially H3K9me3 establishment during early embryo development.
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Project description:Like-SM proteins (Lsm) assemble into heptameric complexes that are conserved in eukaryotes. The Lsm2-8 complex is involved in the function of spliceosomal RNAs, whereas the Lsm1-7/Pat1 complex associates with decapping complexes in the cytoplasm. It was proposed that the role of Lsm1-7 is to recruit the decapping machinery to unstable mRNA that are rapidly deadenylated. However, the role of deadenylation in RNA stability has been challenged by recent studies in yeast and other organisms. To better understand the potential role of Lsm1 in the degradation of unstable transcripts, we investigated the effects of rapid depletion of Lsm1 in an inducible degron system on transcripts degraded by decapping activation during nonsense-mediated mRNA decay (NMD). In contrast to previous studies that used deletion of LSM1, Lsm1 depletion, led to a slight increase in the abundance of NMD substrates, similar to what is observed following a minimal perturbation of decapping.
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Project description:We report the role of LSM1-7 complex in the Arabidopsis tolerance to abiotic stresses. LSM1-7 controls gene expression reprogramming at the post-transcriptional level by promoting the decapping of mRNA. This function is selectively achieve over selected stress-induced transcripts depending on stress nature.
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Project description:Candidatus Nitrosotenuis cloacae strain:LSM1 Genome sequencing and assembly
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Project description:In this study, we aim to understand how the fates of stress-activated mRNAs are determined under stress conditions by isolating individual osmostress-activated mRNA species, quantitating the proteins associated in vivo with each of them, and analyzing how deletion of these proteins impact on the expression of stress-activated genes. By comparison with the proteome associated with individual not stress-related mRNA species, we show specific proteins to be preferentially binding to osmostress-activated mRNAs, notably members of the cytoplasmic Pat1 / Lsm1 – 7 complex. We evaluated the impact of this complex on the stress response by analyzing expression of osmostress-activated genes, production of osmo-protein and, mapping ribosome transit at single nucleotide resolution using 5’-phosphate sequencing of mRNAs in lsm1 and pat1 mutants. We conclude that our biochemical co-purification approach has successfully identified RNA-binding proteins with a particular role in regulating post-transcriptional expression of stress-activated mRNAs.
2018-07-18 | GSE107250 | GEO
Project description:The influence of the extracellular matrix (ECM) within the stem cell niche remains poorly understood. We found that Syndecan-4 (Sdc4) and Frizzled-7 (Fzd7) form a coreceptor complex in satellite cells and that binding of the ECM glycoprotein Fibronectin (FN) to Sdc4 stimulates the ability of Wnt7a to induce the symmetric expansion of satellite stem cells. Newly activated satellite cells dynamically remodel their niche via transient high-level expression of FN. Knockdown of FN in prospectively isolated satellite cells severely impaired their ability to repopulate the satellite cell niche. Conversely, in vivo overexpression of FN with Wnt7a dramatically stimulated the expansion of satellite stem cells in regenerating muscle. Therefore, activating satellite cells remodel their niche through autologous expression of FN that provides feedback to stimulate Wnt7a signaling through the Fzd7/Sdc4 coreceptor complex. Thus, FN and Wnt7a together regulate the homeostatic levels of satellite stem cells and satellite myogenic cells during regenerative myogenesis. The data set contains one microarray of pooled quiescent skeletal muscle satellite cells
2014-07-11 | E-GEOD-59272 | biostudies-arrayexpress
Project description:Nonsense mediated mRNA decay (NMD) is a translation-dependent surveillance pathway that eliminates RNAs with short open reading frames (ORFs) and long 3' untranslated regions (UTRs). Upf1 is the key protein of this degradation pathway and we were interested to purify the associated RNAs. Moreover we have done purifications of two proteins from the general mRNA turnover in yeast : Pab1 and Lsm1 that both bind RNAs poly(A) tails. We have also done a purification with a protein from the small ribosomal subunit (40S) in order to have a look at the translated RNAs.
2022-10-01 | GSE160642 | GEO
Project description:(Abstract of publication submitted currently) To clarify molecular regulation of satellite cells, we performed genome-wide gene expression analysis of quiescent satellite cells isolated from mouse skeletal muscle by flow cytometry. We identified 53 novel quiescent satellite cell-specific genes whose expressions are sharply down-regulated upon activation. The gene list contains a number of cell surface molecules, transcriptional factors, and cytokines and other signal transduction molecules. We further confirmed that Odz4 and calcitonin receptor proteins were expressed by quiescent but not by activated satellite cells in vivo. Importantly, we found that Pax7+/calcitonin receptor+ satellite cells reappear in close association with regenerating myofibers 7 days after muscle damage, often outside the basal lamina. Moreover, an agonist of calcitonin receptor suppressed the activation of quiescent satellite cells on myofibers in in vitro culture, suggesting that calcitonin receptor signaling plays an important role in renewal and maintenance of satellite cells. Our results show the gene expression profile of quiescent satellite cells for the first time and reveal the temporal and spatial reappearance of a satellite cell pool. Experiment Overall Design: Satellite cells and non-satellite cells were examined. Totally three types of cells (groups), the satellite cells in quiescent and activated states and the non-satellite cells, were compared. Each has 4 replicates.
2008-06-12 | E-GEOD-3483 | biostudies-arrayexpress
Project description:Following skeletal muscle injury, muscle stem cells (satellite cells) are activated, proliferate, and differentiate to form myofibers. We show that mRNA decay protein AUF1 regulates satellite cell function through targeted degradation of specific mRNAs. AUF1 targets certain mRNAs containing 3 AU-rich elements (AREs) for rapid decay. Auf1-/- (KO) mice undergo accelerated skeletal muscle wasting with age and impaired muscle repair following injury. Satellite cell mRNA analysis and regeneration studies demonstrate that auf1-/- satellite cell self-renewal is impaired due to increased stability and overexpression of ARE-mRNAs. Control of ARE-mRNA decay by AUF1 and potentially other ARE-binding proteins represents a mechanism for adult stem cell regulation and is implicated in human muscle wasting diseases. We report the RNA transcript expression profiles from sorted satellite cells isolated from wild type (WT) and AUF1-null (KO) mice hindlimb muscles Examination of RNA transcript expression from satellite cells of two genotypes Please note that mice are bred through a C57BL/6 strain of 129 background.
2016-07-21 | E-GEOD-83555 | biostudies-arrayexpress