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RIP-Chip Analysis of hnRNP K in Xenopus juvenile brain

ABSTRACT: Cells use their wide variety of RNPs to integrate the expression of functionally inter-related proteins by forming RNP complexes with cis-elements that are shared among co-regulated RNAs. In this study, we identified the the associated mRNAs that co-precipitated with hnRNP K in developing juvenile frog brain. three replicates of immunoprecipitation experiments for both hnRNP K and beta-galactosidase(control)

ORGANISM(S): Xenopus laevis

SUBMITTER: Ben Szaro

PROVIDER: E-GEOD-25207 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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hnRNP K post-transcriptionally co-regulates multiple cytoskeletal genes needed for axonogenesis.

Liu Yuanyuan Y Szaro Ben G BG

Development (Cambridge, England) 20110701 14

The RNA-binding protein, hnRNP K, is essential for axonogenesis. Suppressing its expression in Xenopus embryos yields terminally specified neurons with severely disorganized microtubules, microfilaments and neurofilaments, raising the hypothesis that hnRNP K post-transcriptionally regulates multiple transcripts of proteins that organize the axonal cytoskeleton. To identify downstream candidates for this regulation, RNAs that co-immunoprecipitated from juvenile brain with hnRNP K were identified ...[more]

PMID: 21693523

Similar Datasets

RIP-Chip Analysis of hnRNP K in Xenopus juvenile brain

Project description:Cells use their wide variety of RNPs to integrate the expression of functionally inter-related proteins by forming RNP complexes with cis-elements that are shared among co-regulated RNAs. In this study, we identified the the associated mRNAs that co-precipitated with hnRNP K in developing juvenile frog brain.

2011-07-06 | GSE25207 | GEO

Rip-Chip profiling of HnRNP A1 nuclear complexes in HuR WT and HuR KO cells

Project description:Post-transcriptional regulatory networks are dependent on the interplay of many RNA-binding proteins having a major role in mRNA processing events in mammals. We have been interested in the concerted action of the two RNA-binding proteins hnRNP A1 and HuR, both stable components of immunoselected hnRNP complexes and having a major nuclear localization. Specifically, we present here the application of the RNA-immunoprecipitation (RIP)-Chip technology to identify a population of nuclear transcripts associated with hnRNP A1-RNPs as isolated from the nuclear extract of either HuR WT or HuR-depleted (KO) mouse embryonic fibroblast (MEF) cells. The outcome of this analysis was a list of target genes regulated via HuR for their association (either increased or reduced) with the nuclear hnRNP A1-RNP complexes. Real time PCR analysis was applied to validate a selected number of nuclear mRNA transcripts, as well as to identify pre-spliced transcripts (in addition to their mature mRNA counterpart) within the isolated nuclear hnRNP A1-RNPs. The differentially enriched mRNAs were found to belong to GO categories relevant to biological processes anticipated for hnRNP A1 and HuR (such as transport, transcription, translation, apoptosis and cell cycle) indicative of their concerted function in mRNA metabolism.

2013-11-01 | GSE49225 | GEO

Rip-Chip profiling of HnRNP A1 nuclear complexes in HuR WT and HuR KO cells

2013-11-01 | E-GEOD-49225 | biostudies-arrayexpress

Widespread specific intron-retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts

Project description:Many essential cellular processes require RNA to interact with protein(s) to form ribonucleic protein complexes (RNPs). For example, all cellular proteins are produced by the ribosome - a large and stable RNP, gene splicing requires a choreography of numerous small and large RNPs, even the replication of telomeric DNA requires an RNP. All these examples are stable RNPs that exhibit specific sedimentation rates (e.g., in a sucrose gradient) based on the composition of RNA and protein. In this study we aimed to identify RNAs components of RNPs on a transcriptome-wide scale. Using sucrose-gradient followed by sequencing we identified 1,057 RNA transcripts that are likely to be components of cellular RNPs. Our approach determined that RNP are not due to the cellular abundance nor length of the constituent RNA transcripts. The RNPs identified were predominantly nuclear, containing a specified retained intron and resistant to RNA degradation. Collectively our study reveals a widespread phenomena of a specific intron being retained in a stable nuclear RNP.

2025-08-11 | GSE284687 | GEO

Genome-wide maps of hnRNP UL1 binding on DNA during the inflammatory process.

Project description:We performed ChIP-seq with antibody targeting hnRNP UL1 at 0, 4h and 10h following LPS stimulation in RAW 264.7 cells. NGS and data analysis were done by Novogen China Co. Ltd. We found that hnRNP UL1 binds to chromatin DNA broadly and dynamically during inflammatory response. hnRNP UL1 binds to genes' promoter mainly. And NF-κB binding sites (κB sites) were significantly enriched in the motifs bound by hnRNP UL1.

2022-06-01 | GSE196201 | GEO

Analysis of hnRNP K interacting RNAs in myeloid KG-1a cells

Project description:HNRNPK is part of the minimally deleted region (MDR) in AML del(9q). To understand the function of hnRNP K in pathogenesis of this AML subtype, we analyzed the function of hnRNP K as an RNA binding protein in myeloid cells. Co-immunoprecipitated RNAs from hnRNP K and non-related control immunoprecipitation as well as input RNA were subjected to next generation sequencing. This analysis revealed an interaction of hnRNP K with 1076 RNAs, among them many mRNAs encoding transcription factors involved in myeloid differentiation and AML pathogenesis.

2024-01-31 | GSE180831 | GEO

hnRNP A1 iCLIP

Project description:hnRNP A1 iCLIP

| PRJEB9546 | ENA

Expression data from HeLa cells after hnRNP L knockdown (versus luciferase control), including cycloheximide treatment

Project description:Transient siRNA-mediated knockdown of hnRNP L, followed by cycloheximide treatment to eliminate NMD. Supplementary files GSE37561_activated_exon.txt and GSE37561_repressed_exon.txt list exons predicted to be activated and repressed by hnRNPL, respectively. 3 biological replicates of hnRNP L (luciferase) knockdown samples

2014-02-13 | E-GEOD-37561 | biostudies-arrayexpress

L-bodies are novel RNA-protein condensates driving RNA transport in Xenopus oocytes

Project description:RNP granules are membrane-less compartments within cells, formed by phase separation, that function as regulatory hubs for diverse biological processes. However, the mechanisms by which RNAs and proteins interact to promote RNP granule assembly and function in vivo remain unclear. In Xenopus laevis oocytes, maternal mRNAs are transported as large RNPs to the vegetal hemisphere of the developing oocyte, where local translation is critical for proper embryonic patterning. Here, we demonstrate that vegetal transport RNPs represent a new class of cytoplasmic RNP granule, termed Localization-bodies (L-bodies). We show that L-bodies are multiphase RNP granules, containing a dynamic liquid-like protein-containing phase surrounding a non-dynamic RNA-containing substructure. Our results support a role for RNA as a critical scaffold component within these RNP granules and suggest that cis-elements within localized mRNAs may drive subcellular RNA localization through control over phase behavior.

2020-09-20 | GSE158246 | GEO

hnRNP-K targets open chromatin in mouse embryonic stem cells in concert with multiple regulators

Project description:The transcription factor Oct4 plays a key regulatory role in the induction and maintenance of cellular pluripotency. With this paper, we show that ubiquitous and multifunctional poly(C) DNA/RNA-binding protein hnRNP-K occupies Oct4 (Pou5f1) enhancers in embryonic stem cells (ESCs) but is dispensable for the initiation, maintenance, and downregulation of Oct4 gene expression. Nevertheless, hnRNP-K has an essential cell-autonomous function in ESCs to maintain their proliferation and viability. To better understand mechanisms of hnRNP-K action in ESCs we have performed ChIP-seq analysis of genome-wide binding of hnRNP-K and identified several thousands of hnRNP-K target sites that are frequently co-occupied by pluripotency-related and common factors (Oct4, TBP, Sox2, Nanog, Otx2, etc.), as well as active histone marks. Furthermore, hnRNP-K localizes exclusively within open chromatin, implying its role in the onset and/or maintenance of this chromatin state.

2019-04-09 | GSE129471 | GEO

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