Transcriptomics analysis of gene expression in control and Ddx3xb knockdown zebrafish embryos
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE169163 | GEO | 2022/06/03
REPOSITORIES: GEO
Similar Datasets
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE181503 | GEO
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE169168 | GEO
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE169166 | GEO
Project description:We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.
2022-06-03 | GSE169161 | GEO
Project description:Compacted heterochromatin blocks are prevalent in differentiated cells and present a barrier to cellular reprogramming. It remains obscure how heterochromatin remodeling is orchestrated during cell differentiation. Here we find that the evolutionarily conserved homeodomain transcription factor Prospero (Pros)/Prox1 ensures neuronal differentiation by driving heterochromatin domain condensation and expansion. Intriguingly, in mitotically dividing Drosophila neural precursors, Pros is retained at H3K9me3+ pericentromeric heterochromatin regions of chromosomes via liquid-liquid phase separation (LLPS). During mitotic exit of neural precursors, mitotically retained Pros recruits and concentrates heterochromatin protein 1 (HP1) into phase-separated condensates and drives heterochromatin compaction. This establishes a transcriptionally repressive chromatin environment that guarantees cell-cycle exit and terminal neuronal differentiation. Importantly, mammalian Prox1 employs a similar “mitotic-implantation-ensured heterochromatin condensation” strategy to reinforce neuronal differentiation. Together, our results unveiled a new paradigm whereby mitotic implantation of a transcription factor via LLPS remodels H3K9me3+ heterochromatin and drives timely and irreversible terminal differentiation.
2019-12-21 | GSE136413 | GEO
Project description:We report that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with viral RNA. N-protein condenses with specific RNA genomic elements under physiological buffer conditions and condensation is enhanced at human body temperatures (33°C and 37°C) and reduced at room temperature (22°C). RNA sequence and structure in specific genomic regions regulate N-protein condensation while other genomic regions promote condensate dissolution, potentially preventing aggregation of the large genome. At low concentrations, N-protein preferentially crosslinks to specific regions characterized by single-stranded RNA flanked by structured elements and these features specify the location, number, and strength of N-protein binding sites (valency). Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is RNA sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules, and presents a screenable process for identifying antiviral compounds effective against SARS-CoV-2.
2020-12-17 | GSE162569 | GEO
Project description:Background: Metazoan embryos undergo a maternal-to-zygotic transition (MZT) during which a subset of maternal gene products is eliminated and the zygotic genome becomes transcriptionally active. RNA-binding proteins (RBPs) and the microRNA-induced silencing complex (miRISC) â of which Argonaute 1 (AGO1) is a key component in Drosophila â target maternal mRNAs for degradation. The Drosophila Smaug, Brain tumor (BRAT) and Pumilio (PUM) RBPs direct the degradation of maternal mRNAs. Here we elucidate Smaugâs roles in regulation of miRNAs and miRISC during the MZT. Results: By global analysis of small RNAs at several stages during the MZT, we show that the vast majority of all miRNA species encoded by the Drosophila genome (85%) are expressed during the MZT. Whereas a subset of these miRNAs is loaded into oocytes by the mother and stays at constant levels during the MZT, dozens of miRNA species are either newly synthesized or re-expressed in the early embryo. Loss of Smaug has a profound effect on miRNAs but little effect on piRNAs or siRNAs. Smaug is required for production of new miRNAs during the MZT; Smaug-bound AGO1 reflects the constellation and abundance of the miRNAs present in early embryos; and Smaug is required for the increase in AGO1 protein levels that occurs during the MZT. As a consequence of low miRISC activity in smaug mutants, maternal mRNAs that are normally targeted for degradation by zygotic miRNAs fail to be cleared. BRAT and PUM share target mRNAs with miRISC during the MZT while the miR-309 miRNA family coregulates targets of BRAT but not PUM. Conclusions: Smaug controls the MZT through direct targeting of a subset of maternal mRNAs for degradation and, indirectly, through production and function of miRNAs and miRISC, which control clearance of a distinct subset of maternal mRNAs. BRAT and/or PUM function together with miRISC during the latter process. With respect to miRISC-dependent transcript degradation, Smaug is required (1) for the synthesis of miRNAs, (2) for synthesis and stabilization of AGO1, and (3) for action of AGO1 in association with its bound miRNAs. In smaug mutants a large number of maternal mRNAs persist and the MZT fails. Examination of miRNA expresssion at different time points in wild type and smuag mutant early embryos .
2016-09-06 | E-GEOD-82194 | biostudies-arrayexpress
Project description:During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNAbound proteome. This protein constellation consists of many conserved RBPs, with additional embryo- and stage-specific mRNA interactors that likely reflect the dynamics of RNA-protein interactions during MZT. The enrichment of numerous splicing factors like hnRNP proteins before ZGA was surprising, because maternal mRNAs were found to be fully spliced. To address potentially unique roles of RBPs in embryogenesis, we focused on hnRNP A1. iCLIP and subsequent mRNA reporter assays revealed a function for hnRNP A1 in the regulation of poly(A) tail length and translation of maternal mRNAs through sequence-specific association with 3’UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that hnRNP A1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-miR-430 transcripts, which we validated experimentally. The shift from cytoplasmic to nuclear RNA targets was accompanied by a dramatic translocation of hnRNP A1 and other pre-mRNA splicing factors to the nucleus in a transcription-dependent manner. Thus, our study identifies global changes in RNA-protein interactions during vertebrate MZT and shows that hnRNP A1 RNA-binding activities are spatially and temporally coordinated to regulate RNA metabolism during early development.
2017-03-27 | PXD006098 | Pride
Project description:We found that CPSF6, a component of the CFIm, can form liquid-liquid phase separation (LLPS) and the elevated LLPS induces the preferential usage of the distal poly(A) sites. CLK2, a kinase upregulated in cancer cells, destructs LLPS of CPSF6 by phosphorylating its arginine/serine-like domain. Albeit higher expression of CPSF6 in cancer, the reduction of LLPS leads to shortening 3’ UTR of cell cycle related genes and then promotes cell proliferation. These results reveal that LLPS regulation of CPSF6 is a fine tuning way of APA in cancer cells and provide a new mechanism for APA regulation by regulating LLPS of 3’ end processing factors through post-translational modification.
2023-09-05 | GSE212519 | GEO
Project description:Intron retention (IR) constitutes a less explored form of alternative splicing, wherein introns are retained within mature mRNA transcripts. Our investigation demonstrates that the CDC-like kinase 2 (CLK2) undergoes liquid-liquid phase separation (LLPS) within nuclear speckles in response to heat shock (HS). The formation of CLK2 condensates depends on the intrinsically disordered region (IDR) located within the N-terminal amino acids 1-148. Phosphorylation at residue T343 sustains CLK2 kinase activity and facilitates autophosphorylation, thus inhibiting the LLPS activity of the IDR. These CLK2 condensates initiate the reorganization of nuclear speckles, transforming them into larger, rounded structures. Moreover, these condensates facilitate the recruitment of splicing factors into these compartments, potentially restricting their access to mRNA for intron splicing. Consequently, the formation of CLK2 condensates promotes the IR.
2024-07-15 | GSE271918 | GEO