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C. elegans DLC-1 is a component of diverse ribonucleoprotein complexes

ABSTRACT: C. elegans DLC-1 is a component of diverse ribonucleoprotein complexes

PROVIDER: PRJNA474476 | ENA |

REPOSITORIES: ENA

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C. elegans DLC-1 is a component of diverse ribonucleoprotein complexes

Project description:Ribonucleoprotein complexes, which contain mRNAs and their regulator proteins, carry out post-transcriptional control of gene expression. The function of many RNA-binding proteins depends on their association with cofactors. Here we use a genomic approach to identify transcripts associated with DLC-1, a protein previously identified as a cofactor of two unrelated RNA-binding proteins that act in the C. elegans germline. Among the 2732 potential DLC-1 targets, most are germline mRNAs. Removal of DLC-1 affects expression of its targets, meg-1 and meg-3. We propose that DLC-1 acts as a cofactor for multiple ribonucleoprotein complexes, thus making diverse contributions to RNA regulation in the germline.

2018-10-01 | GSE115281 | GEO

Systematic discovery of endogenous human ribonucleoprotein complexes

Project description:An exploration of human protein complexes in the presence and absence of RNA reveals endogenous ribonucleoprotein complexes

2019-09-19 | GSE137651 | GEO

Systematic discovery of endogenous human ribonucleoprotein complexes

Project description:Systematic discovery of endogenous human ribonucleoprotein complexes

| PRJNA566149 | ENA

Saturating mutagenesis with assembled CRISPR-Cas9 ribonucleoprotein complexes.

Project description:Saturating mutagenesis with assembled CRISPR-Cas9 ribonucleoprotein complexes.

| PRJEB12161 | ENA

Saturating mutagenesis with assembled CRISPR-Cas9 ribonucleoprotein complexes.

Project description:The CRISPR-Cas9 system enables efficient sequence-specific mutagenesis for creating germline mutants of model organisms. Key constraints in vivo remain the expression and delivery of active Cas9-guideRNA ribonucleoprotein complexes (RNPs) with minimal toxicity, variable mutagenesis efficiencies depending on targeting sequence, and high mutation mosaicism. Here, we established in vitro-assembled, fluorescent Cas9-sgRNA RNPs in stabilizing salt solution to achieve maximal mutagenesis efficiency in zebrafish embryos. Sequence analysis of targeted loci in individual embryos reveals highly efficient bi-allelic mutagenesis that reaches saturation at several tested gene loci. Such virtually complete mutagenesis reveals preliminary loss-of-function phenotypes for candidate genes in somatic mutant embryos for subsequent generation of stable germline mutants. We further show efficient targeting of functional non-coding elements in gene-regulatory regions using saturating mutagenesis towards uncovering functional control elements in transgenic reporters and endogenous genes. Our results suggest that in vitro assembled, fluorescent Cas9-sgRNA RNPs provide a rapid reverse-genetics tool for direct and scalable loss-of-function studies beyond zebrafish applications.

2016-05-01 | E-MTAB-4143 | biostudies-arrayexpress

The scaffolding role of RNA in ribonucleoprotein complexes: TRA2A recruitment in FXTAS disease

Project description:The scaffolding role of RNA in ribonucleoprotein complexes: TRA2A recruitment in FXTAS disease

| PRJNA496616 | ENA

The scaffolding role of RNA in ribonucleoprotein complexes: TRA2A recruitment in FXTAS disease

Project description:The scaffolding role of RNA in ribonucleoprotein complexes: TRA2A recruitment in FXTAS disease

| PRJNA422212 | ENA

Genome-wide distribution of the three condensin complexes in C. elegans

Project description:Condensins are multi-subunit protein complexes that regulate chromosome structure throughout cell-cycle. Metazoans contain two types of condensin complexes (I and II) with essential and distinct functions. In C. elegans a third type of condensin (IDC) functions as part of the X chromosome dosage compensation complex1,2. We mapped genome-wide binding sites of the three condensin types in C. elegans embryos. Characteristics of condensin binding are similar between condensin types. ChIP-seq profiles of C. elegans subunits of the three condensins in 3-6 replicates from mixed stage embryos, controls are included, and RNA-Seq profiles of C. elegans in 5 replicates from mixed staged embryos. Additionally, ChIP-seq profiles of the condensin II subunit KLE-2 in 6 replicates from L3 with controls, and RNA-Seq profiles of KLE-2 mutants in 3 replicates each from L3.

2013-09-16 | E-GEOD-45678 | biostudies-arrayexpress

LIN-41 and OMA ribonucleoprotein complexes mediate a translational repression-to-activation switch controlling oocyte meiotic maturation and the oocyte-to-embryo transition in Caenorhabditis elegans

Project description:An extended meiotic prophase is a hallmark of oogenesis. Hormonal signaling activates the CDK1/cyclin B kinase to promote oocyte meiotic maturation, which involves nuclear and cytoplasmic events. Nuclear maturation encompasses nuclear envelope breakdown, meiotic spindle assembly, and chromosome segregation. Cytoplasmic maturation involves major changes in oocyte protein translation and cytoplasmic organelles and is poorly understood. In the nematode Caenorhabditis elegans, sperm release the major sperm protein (MSP) hormone to promote oocyte growth and meiotic maturation. Large translational regulatory ribonucleoprotein (RNP) complexes containing the RNA-binding proteins OMA-1, OMA-2, and LIN-41 regulate meiotic maturation downstream of MSP signaling. To understand the control of translation during meiotic maturation, we purified LIN-41-containing RNPs and characterized their protein and RNA components. Protein constituents of LIN-41 RNPs include essential RNA-binding proteins, the GLD-2 cytoplasmic poly(A) polymerase, the CCR4-NOT deadenylase complex, and translation initiation factors. RNA sequencing defined mRNAs associated with both LIN-41 and OMA-1, as well as sets of mRNAs associated with either LIN-41 or OMA-1. Genetic and genomic evidence suggests that GLD-2, which is a component of LIN-41 RNPs, stimulates the efficient translation of many LIN-41-associated transcripts. We analyzed the translational regulation of two transcripts specifically associated with LIN-41 that encode the RNA regulators SPN-4 and MEG-1. We found that LIN-41 represses translation of spn-4 and meg-1, whereas OMA-1 and OMA-2 promote their expression. Upon their synthesis, SPN-4 and MEG-1 assemble into LIN-41 RNPs prior to their functions in the embryo. This study defines a translational repression-to-activation switch as a key element of cytoplasmic maturation.

2017-06-02 | GSE98130 | GEO

Genome-wide distribution of the three condensin complexes in C. elegans

2013-09-16 | GSE45678 | GEO

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