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Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines [array]

ABSTRACT: Cancer stem cells (CSC) dictate tumor cell heterogeneity in diverse cancer types and arise, in part, from microRNA (miRNA)-dependent alteration of gene expression. The let-7 miRNA family induces differentiation by silencing genes that maintain stemness and is repressed by the RNA-binding proteins LIN28A/B, which preserve stemness in normal embryonic and malignant cells. Here, we observed that LIN28A/B is undetectable in glioma stem cells (GSC) whereas let-7 and, paradoxically, their target genes are highly expressed. Using photoactivatable-ribonucloside-enchanced crosslinking and immunoprecipitation (PAR-CLIP), we show that insulin-like growth factor-2 mRNA-binding protein 2 (IMP2) protects let-7 target genes from silencing and provides a mechanistically distinct alternative to LIN28A/B toward both GSC and neural stem cell specification. Our observations define the RNA-binding repertoire of IMP2 and identify a mechanism by which it supports GSC maintenance.

ORGANISM(S): Homo sapiens

PROVIDER: GSE73846 | GEO | 2016/05/12

SECONDARY ACCESSION(S): PRJNA298215

REPOSITORIES: GEO

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Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines [HTS]

Project description:Cancer stem cells (CSC) dictate tumor cell heterogeneity in diverse cancer types and arise, in part, from microRNA (miRNA)-dependent alteration of gene expression. The let-7 miRNA family induces differentiation by silencing genes that maintain stemness and is repressed by the RNA-binding proteins LIN28A/B, which preserve stemness in normal embryonic and malignant cells. Here, we observed that LIN28A/B is undetectable in glioma stem cells (GSC) whereas let-7 and, paradoxically, their target genes are highly expressed. Using photoactivatable-ribonucloside-enchanced crosslinking and immunoprecipitation (PAR-CLIP), we show that insulin-like growth factor-2 mRNA-binding protein 2 (IMP2) protects let-7 target genes from silencing and provides a mechanistically distinct alternative to LIN28A/B toward both GSC and neural stem cell specification. Our observations define the RNA-binding repertoire of IMP2 and identify a mechanism by which it supports GSC maintenance.

2016-05-12 | GSE73845 | GEO

IMP2/IGF2BP2 HITS-CLIP from E13.5 mouse brain

Project description:HITS-CLIP is performed for the RNA-binding protein, IMP2/IGF2BP2, from E13.5 mouse brain.

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IMP2 axonal localization, RNA interactome, and function in development of axon trajectories

Project description:RNA-based regulatory mechanisms play important roles in the development and plasticity of neural circuits and neurologic disease. Developing axons provide a well suited model to study RNA-based regulation, and contain specific subsets of mRNAs that are locally translated and have roles in axon pathfinding. However, the RNA-binding proteins involved in axon pathfinding, and their corresponding mRNA targets, are still largely unknown. Here we find that the RNA-binding protein IMP2 (Igf2bp2) is strikingly enriched in developing axon tracts, including in spinal commissural axons. We used the HITS-CLIP approach to perform a genome-wide identification of RNAs that interact directly with IMP2 in the native context of developing brain. This IMP2 interactome was highly enriched for mRNA targets related to axon guidance. Accordingly, IMP2 knockdown in the developing spinal cord led to strong defects in commissural axon trajectories at the midline intermediate target. These results reveal a highly distinctive axonal enrichment of IMP2, show that it interacts with a network of axon guidance-related mRNAs, and reveal its requirement for normal axon pathfinding during vertebrate development. CLIP-seq

2016-08-02 | E-GEOD-83822 | biostudies-arrayexpress

Next Generation Sequencing (NGS) analysis of mice pancreatic islets from control and IMP2 islet specific knockout (Rip2;IMP2).

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2023-06-11 | GSE152424 | GEO

Quantitative proteomes of Imp2 KO mouse 2-cell-stage embryos

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The m6A reader IMP2 directs autoimmune inflammation through an IL-17- and TNFa-dependent C/EBP transcription factor axis

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IMP2 axonal localization, RNA interactome, and function in development of axon trajectories

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LIN28A-mediated regulation of microRNA biogenesis in mouse embryonic stem cell (A3-1) [Agilent]

Project description:LIN28A is a highly-conserved RNA-binding protein which is known to be involved in embryonic development, stem cell maintenance and proliferation. LIN28A is expressed in various types of cancer, and they are associated with advanced tumor malignancy. In embryonic stem cell, LIN28A specifically binds to let-7 precursors to suppress biogenesis of the let-7 microRNA family. In addition, LIN28A was reported to bind several mRNAs such as Oct4, cyclin A/B and histone H2A to activate their translation. For comprehensive understanding of the interaction between LIN28A and their target RNAs, we exploited UV-crosslinking and immunoprecipitation (CLIP) to capture their in vivo binding to target RNAs. LIN28A-binding RNAs were identified in a mouse embryonic stem cell line using multiple monoclonal and polyclonal antibodies. The result shows that LIN28 preferentially binds to let-7 precursors through GGAG binding motif, which is consistent with our previous results. We also identified that LIN28A binding is enriched in a certain subset of mRNAs. To understand the function of the novel LIN28A-mRNA binding, we carried out ribosome profiling from LIN28A-depleted mouse embryonic stem cells. Examination of miRNA level in embryonic stem cell treated with siRNA for GFP or for Lin28a

2012-10-25 | E-GEOD-37112 | biostudies-arrayexpress

A Long Non-coding RNA, LncMyoD, Regulates Skeletal Muscle Differentiation by Blocking IMP2-mediated mRNA Translation

Project description:Increasing evidence suggests that Long non-coding RNAs (LncRNAs) represent a new class of regulators of stem cells. However, the roles of LncRNAs in stem cell maintenance and myogenesis remain largely unexamined. For this study, hundreds of novel intergenic LncRNAs were identified that are expressed in myoblasts and regulated during differentiation. One of these LncRNAs, termed LncMyoD, is encoded next to the Myod gene and is directly activated by MyoD during myoblast differentiation. Knockdown of LncMyoD strongly inhibits terminal muscle differentiation largely due to a failure to exit the cell cycle. LncMyoD directly binds to IGF2-mRNA-binding-protein 2 (IMP2) and negatively regulates IMP2-mediated translation of proliferation genes such as N-Ras and c-Myc. While the RNA sequence of LncMyoD is not well-conserved between human and mouse, its locus, gene structure and function is preserved. The MyoD-LncMyoD-IMP2 pathway elucidates a mechanism as to how MyoD blocks proliferation to create a permissive state for differentiation. In order to perform an unbiased search for downstream signaling pathways perturbed by LncMyodD downregulation, microarrays were performed on myoblasts treated with control vs LncMyoD shRNAs. Total RNA was extracted using the TRIzol reagent (Invitrogen) and purified with Qiagen RNeasy separation columns (Qiagen) from myoblasts treated with control vs. LncMyoD shRNA. First-strand cDNA was synthesized and hybridized to GeneChip Mouse Genome 430 2.0 Array (Affymetrix).

2015-08-11 | E-GEOD-68842 | biostudies-arrayexpress

Effect of IMP2 overexpression in murine liver

Project description:Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis

| PRJEB21164 | ENA