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FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [TRAP-seq, RNA-seq]

ABSTRACT: We report cell-type and compartment-specific TRAP-seq, RNAseq, FMRP-CLIP, and PAPERCLIP from CA1 hippocampal neurons. We use TRAP-seq and PAPERCLIP data to precisely define the dendritic transcriptome, including mRNAs that harbor APA and AS events that are differentially localized. Further, we use FMRP-CLIP in order to define mRNAs that undergo compartment-specific regulation by FMRP.

ORGANISM(S): Mus musculus

PROVIDER: GSE174303 | GEO | 2022/01/19

REPOSITORIES: GEO

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FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [FMRP-CLIP]

Project description:We report cell-type and compartment-specific TRAP-seq, RNAseq, FMRP-CLIP, and PAPERCLIP from CA1 hippocampal neurons. We use TRAP-seq and PAPERCLIP data to precisely define the dendritic transcriptome, including mRNAs that harbor APA and AS events that are differentially localized. Further, we use FMRP-CLIP in order to define mRNAs that undergo compartment-specific regulation by FMRP.

2022-05-11 | GSE180412 | GEO

FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [PAPERCLIP]

2022-05-11 | GSE180413 | GEO

FMRP cTag CLIP from mouse CA1 pyramidal neurons

Project description:Loss of the neuronal RNA binding protein FMRP causes Fragile X Syndrome (FXS), the most common cause of inherited intellectual disability, yet it is unknown which brain regions and cell types within them contribute to disease pathophysiology. We used conditional tagging of FMRP and CLIP (cTag FMRP CLIP) to examine FMRP targets specifically in CA1 hippocampal neurons, a critical cell type for learning and memory known to have altered synaptic function in FXS. Integrating this data with analysis of ribosome-bound transcripts from the same neuronal population revealed CA1-enriched binding of autism-relevant mRNAs, and unexpected CA1-specific regulation of transcripts encoding circadian proteins.

2020-01-07 | GSE127846 | GEO

FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [FMRP-CLIP]

Project description:FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [FMRP-CLIP]

| PRJNA748080 | ENA

The Fragile X Mental Retardation Protein (FMRP) controls diacylglycerol kinase in neurons

Project description:In this study, we sought to identify the mRNAs associated to FMRP protein in mouse cortical neuron using a cross linking immunoprecipitation and microarray (CLIP-microarray). The mRNAs crosslinked at 254 nm to FMRP in mouse cortical neurons cultured 8 days in vitro (8 DIV) were immunoprecipitated with H120 anti-FMRP (Santa Cruz) and reverse transcribed to labeled cDNAs with Ovation Pico WTA system V2 (Nugen) and hybridized on Mouse Gene 1.0ST (Affymetrix) We analyzed total RNA (Input) and FMRP-CLIPed RNA (Clip) from 10 primary cortical neuron mouse cultures (5 Wt Input, 5 FMR1-KO Input, 5 Wt Clip, 5 FMR1-KO Clip). Array data was processed by Affymetrix Exon Array Computational Tool. No technical replicates were performed.

2016-06-01 | E-GEOD-51649 | biostudies-arrayexpress

FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [PAPERCLIP]

Project description:FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons [PAPERCLIP]

| PRJNA748085 | ENA

FMRP cTag CLIP from mouse CA1 pyramidal neurons

Project description:FMRP cTag CLIP from mouse CA1 pyramidal neurons

| PRJNA525639 | ENA

The Fragile X Mental Retardation Protein (FMRP) controls diacylglycerol kinase in neurons

2016-06-01 | GSE51649 | GEO

FMRP-associated MOV10 facilitates and antagonizes miRNA-mediated regulation

Project description:The fragile X mental retardation protein FMRP is an RNA binding protein that regulates translation of its bound mRNAs through incompletely defined mechanisms. FMRP has been linked to the microRNA pathway and we show here that it is associated with MOV10, a putative helicase that is also associated with the microRNA pathway. We show that FMRP associates with MOV10 in an RNA-dependent manner and facilitates MOV10-association with RNAs in brain. We identified the RNA sequences recognized by MOV10 using iCLIP and found an increased number of G-quadruplexes in the CLIP sites. We provide evidence that MOV10 facilitates microRNA-mediated translation regulation and also has the novel role of increasing the expression of a subset of RNAs by sterically hindering Argonaute2 association. In summary, we have identified a new mechanism for FMRP-mediated translational regulation through its association with MOV10. Comparison of MOV10 siRNA knockdown, irrelevant siRNA control and MOV10 overexpression on total RNA levels

2014-11-20 | E-GEOD-50499 | biostudies-arrayexpress

HITS-CLIP analysis of FMRP mRNA binding sites from P11-P25 mouse brain polysomes

Project description:FMRP loss-of-function causes Fragile X Syndrome (FXS) and autistic features. FMRP is a polyribosome-associated neuronal RNA-binding protein, suggesting that it plays a key role in regulating neuronal translation, but there has been little consensus regarding either its RNA targets or mechanism of action. Here we use high throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) to identify FMRP interactions with mouse brain polyribosomal mRNAs. FMRP interacts with the coding region of transcripts encoding pre- and postsynaptic proteins, and transcripts implicated in autism spectrum disorders

2013-03-15 | GSE45148 | GEO

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