Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA379122 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5342580.fastq.gz | Fastqsanger.gz | |||
| SRR5342590.fastq.gz | Fastqsanger.gz | |||
| SRR5342581.fastq.gz | Fastqsanger.gz | |||
| SRR5342591.fastq.gz | Fastqsanger.gz | |||
| SRR5342582.fastq.gz | Fastqsanger.gz |
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Project description:Coordinated control of mRNA and rRNA processing regulates early mammalian embryogenesis [ChIP-Seq_HTATSF1]
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Project description:Stem cells are regulated by transcriptional networks controlling pluripotency and differentiation. How basic cellular processes like splicing or protein synthesis regulate stem cell function is less well understood. Here, we show that the RNA binding protein HTATSF1 controls protein synthesis by controlling several independent RNA processing steps during ribosome biogenesis. In a complex with ribosomal RNA transcription and processing factors, HTATSF1 regulates ribosomal RNA abundance. By binding to the U2snRNP complex, HTATSF1 also controls intron removal specifically in ribosomal protein transcripts. HTATSF1-mediated control of protein synthesis is essential for the transition from the naïve pre-implantation epiblast to the primed post-implantation epiblast, a stage of low protein synthesis levels, and during further differentiation towards neuroectoderm. Our results identify coordinated regulation of ribosomal RNA and protein biosynthesis by HTATSF1 as an essential mechanism to mediate protein synthesis control during early stages of mammalian embryogenesis.
2018-04-05 | GSE96594 | GEO
Project description:Stem cells are regulated by transcriptional networks controlling pluripotency and differentiation. How basic cellular processes like splicing or protein synthesis regulate stem cell function is less well understood. Here, we show that the RNA binding protein HTATSF1 controls protein synthesis by controlling several independent RNA processing steps during ribosome biogenesis. In a complex with ribosomal RNA transcription and processing factors, HTATSF1 regulates ribosomal RNA abundance. By binding to the U2snRNP complex, HTATSF1 also controls intron removal specifically in ribosomal protein transcripts. HTATSF1-mediated control of protein synthesis is essential for the transition from the naïve pre-implantation epiblast to the primed post-implantation epiblast, a stage of low protein synthesis levels, and during further differentiation towards neuroectoderm. Our results identify coordinated regulation of ribosomal RNA and protein biosynthesis by HTATSF1 as an essential mechanism to mediate protein synthesis control during early stages of mammalian embryogenesis.
2018-04-05 | GSE96593 | GEO
Project description:Stem cells are regulated by transcriptional networks controlling pluripotency and differentiation. How basic cellular processes like splicing or protein synthesis regulate stem cell function is less well understood. Here, we show that the RNA binding protein HTATSF1 controls protein synthesis by controlling several independent RNA processing steps during ribosome biogenesis. In a complex with ribosomal RNA transcription and processing factors, HTATSF1 regulates ribosomal RNA abundance. By binding to the U2snRNP complex, HTATSF1 also controls intron removal specifically in ribosomal protein transcripts. HTATSF1-mediated control of protein synthesis is essential for the transition from the naïve pre-implantation epiblast to the primed post-implantation epiblast, a stage of low protein synthesis levels, and during further differentiation towards neuroectoderm. Our results identify coordinated regulation of ribosomal RNA and protein biosynthesis by HTATSF1 as an essential mechanism to mediate protein synthesis control during early stages of mammalian embryogenesis.
2018-04-05 | GSE96555 | GEO
Project description:During mammalian oocyte growth, chromatin configuration transition from the nonsurrounded nucleolus (NSN) to surrounded nucleolus (SN) type plays a key role in the regulation of gene expression and in acquisition of meiotic and developmental competence by the oocyte. Nonetheless, the mechanism underlying chromatin configuration maturation in oocytes is poorly understood. Here we show that nucleolar protein DCAF13 is an important component of the ribosomal RNA (rRNA)-processing complex and is essential for oocyte NSN–SN transition in mice. A conditional knockout of Dcaf13 in oocytes led to the arrest of oocyte development in the NSN configuration, follicular atresia, premature ovarian failure, and female sterility. The DCAF13 deficiency resulted in pre-rRNA accumulation in oocytes, whereas the total mRNA level was not altered. Further exploration showed that DCAF13 participated in the 18S rRNA processing in growing oocytes. The lack of 18S rRNA because of DCAF13 deletion caused a ribosome assembly disorder and then reduced global protein synthesis. DCAF13 interacted with a protein of the core box C/D ribonucleoprotein, fibrillarin, i.e., a factor of early pre-rRNA processing. When fibrillarin was knocked down in oocytes from primary follicles, the follicle development was inhibited as well, indicating that an rRNA processing defect in the oocyte indeed stunts chromatin configuration transition and follicle development. Taken together, these results elucidated the in vivo function of novel nucleolar protein DCAF13 in maintaining mammalian oogenesis.
2019-01-01 | GSE114967 | GEO
Project description:Embryogenesis entails dramatic shifts in mRNA translation and turnover to account for gene expression differences during proliferation and cellular differentiation. Codon identity modulates mRNA stability during early vertebrate embryogenesis, but how the composition of tRNA pools adapts to the embryo s translational demand is unknown. By quantitatively profiling the tRNA repertoires of zebrafish embryos during the maternal-to-zygotic transition, here we find that maternal and zygotic tRNA pools are distinct. We show that translational activation during embryogenesis and tRNA gene derepression are temporally coordinated by TORC1 activity, which increases at gastrulation and inactivates the RNA polymerase III repressor Maf1a/b in vivo. Reshaping of tRNA pools results in differential tRNA anticodon supply, but these changes do not alter decoding rates in zebrafish embryos. Instead, our data indicate that tRNA repertoires reflect the inherent codon bias of the zebrafish mRNA transcriptome, and tRNA levels are boosted at gastrulation to ensure efficient translation as embryos enter differentiation.
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Project description:Ribosome biogenesis, which takes place mainly in the nucleolus, involves coordinated expression of pre-ribosomal RNAs (pre-rRNAs) and ribosomal proteins, pre-rRNA processing, and subunit assembly with the aid of numerous assembly factors. Our previous study showed that the Arabidopsis thaliana protein arginine methyltransferase AtPRMT3 regulates pre-rRNA processing; however, the underlying molecular mechanism remains unknown. Here, we report that AtPRMT3 interacts with Ribosomal Protein S2 (RPS2), facilitating processing of the 90S/Small Subunit (SSU) processome and repressing nucleolar stress. We isolated an intragenic suppressor of atprmt3-2, which rescues the developmental defects of atprmt3-2 while produces a putative truncated AtPRMT3 protein bearing the entire N-terminus but lacking an intact enzymatic activity domain. We further identified RPS2 as an interacting partner of AtPRMT3, and found that loss-of-function rps2a2b mutants were phenotypically reminiscent of atprmt3, showing pleiotropic developmental defects and aberrant pre-rRNA processing. RPS2B binds directly to pre-rRNAs in the nucleus, and such binding is enhanced in atprmt3-2. Consistently, multiple components of the 90S/SSU processome were more enriched by RPS2B in atprmt3-2, which accounts for early pre-rRNA processing defects and results in nucleolar stress. Collectively, our study uncovered a novel mechanism by which AtPRMT3 cooperates with RPS2B to facilitate the dynamic assembly/disassembly of the 90S/SSU processome during ribosome biogenesis and repress nucleolar stress.
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Project description:Maternal RNA degradation is critical for embryogenesis and is tightly controlled by maternal RNA-binding proteins. Fragile X mental-retardation protein (FMR1) binds target mRNAs to form ribonucleoprotein (RNP) complexes/granules that control various biological processes, including early embryogenesis. However, how FMR1 recognizes target mRNAs and how FMR1-RNP granule assembly/disassembly regulates FMR1-associated mRNAs remain elusive. Here we show that Drosophila FMR1 preferentially binds mRNAs containing m6A-marked “AGACU” motif with high affinity to contributes to maternal RNA degradation. The high-affinity binding largely depends on a hydrophobic network within FMR1 KH2 domain. Importantly, this binding greatly induces FMR1 granule condensation to efficiently recruit unmodified mRNAs. The degradation of maternal mRNAs then causes granule de-condensation, allowing normal embryogenesis. Our findings reveal that sequence-specific mRNAs instruct FMR1-RNP granules to undergo a dynamic phase-switch, thus contributes to maternal mRNA decay. This mechanism may represent a general principle that regulated RNP-granules control RNA processing and normal development.
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