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PAPERCLIP of cultured cells with/without DNA-damaging treatments

ABSTRACT: To identify APA changes in cancer cells in response to DNA damage, PAPERCLIP was performed on HeLa and LN229 cells with/without Doxorubicin treatment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE144054 | GEO | 2021/07/16

REPOSITORIES: GEO

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PAPERCLIP of cultured cells with/without DNA-damaging treatments

Project description:PAPERCLIP of cultured cells with/without DNA-damaging treatments

| PRJNA602664 | ENA

cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation

Project description:Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell-types, but obtaining APA maps from individual cell-types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell-types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2. We further identified a role of APA in switching Araf protein isoforms during microglia activation, impacting production of downstream inflammatory cytokines. Our results demonstrate the broad applicability of cTag-PAPERCLIP and a previously undiscovered role of APA in contributing to protein diversity between different cell-types and cellular states within the brain.

2017-09-13 | GSE94054 | GEO

A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway

Project description:To identify APA changes in Tsc1-cKO mice, cTag-PAPERCLIP was performed on pAAV-Camk2a-iCre injected Tsc1-WT and Tsc1-floxed cTag-PABP mice. To identify CPSF6-dependent PAS, PAPERCLIP was performed on shCPSF6-BE2C cells with/without doxycycline treatment.

2022-08-11 | GSE210768 | GEO

PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage.

Project description:Accurate and precise annotation of 3' UTRs is critical for understanding how mRNAs are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here, we describe a method, poly(A) binding protein-mediated mRNA 3' end retrieval by crosslinking immunoprecipitation (PAPERCLIP), that shows high specificity for mRNA 3' ends and compares favorably with existing 3' end mapping methods. PAPERCLIP uncovers a previously unrecognized role of CstF64/64tau in promoting the usage of a selected group of non-canonical poly(A) sites, the majority of which contain a downstream GUKKU motif. Furthermore, in the mouse brain, PAPERCLIP discovers extended 3' UTR sequences harboring functional miRNA binding sites and reveals developmentally regulated APA shifts, including one in Atp2b2 that is evolutionarily conserved in humans and results in the gain of a functional binding site of miR-137. PAPERCLIP provides a powerful tool to decipher post-transcriptional regulation of mRNAs through APA in vivo.

2016-02-19 | GSE66092 | GEO

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

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.

2022-01-19 | GSE174303 | GEO

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

2022-05-11 | GSE180413 | GEO

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

2022-05-11 | GSE180412 | GEO

Differential 3’ Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types

Project description:Alternative polyadenylation (APA) regulates mRNA translation, stability, and protein localization. However, it is unclear to what extent APA regulates these processes uniquely in specific cell types. Using a new technique, cTag-PAPERCLIP, we discovered significant differences in APA between the principal types of mouse cerebellar neurons, the Purkinje and granule cells, as well as between proliferating and differentiated granule cells. Transcripts that differed in APA in these comparisons were enriched in key neuronal functions and many differed in coding sequence in addition to 3’UTR length.

2018-04-01 | GSE108480 | GEO

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

Project description:Purpose: To identify all of the APA targets of CFIm25 on a global scale and develop an algorithm that can idenitify APA events from standard RNA-seq data Methods: RNA from HeLa cells treated with control siRNA and CFIm25 siRNA were subject to RNA-Seq. Using a custom-designed algorithm to mine RNA-seq data for novel APA events regulated by CFIm25. Results: We identified over 1,400 genes with shortened 3’UTRs after CFIm25 knockdown. Importantly, we show that as a consequence of APA, many of these mRNAs have greatly enhanced protein expression due to the loss of destabilizing features within the 3’UTR. Conclusions: Our study underscored the critical function of the CFIm complex members in governing APA and establish a previously unknown link between APA and metabolic pathways important for tumor progression. Hela cell line mRNA profiles of control treated and CFIm25 Knockdown were generated by RNA-Seq using Illumina GAIIx.

2014-05-15 | E-GEOD-42420 | biostudies-arrayexpress

m6A-seq assays and analysis of breast cancer MDA-MB-231 cells with or without PRMT5 overexpression and Doxrubicin treatment

Project description:We report the application of immunoprecipitation of m6A methylated RNA followed by sequencing (MeRIP-Seq) in breast cancer MDA-MB-231 cells to identify PRMT5-mediated transcriptome-wide methylation patterns for doxorubicin response. Total RNAs from breast cancer cells were extracted with TRIzol. Then, mRNA sequencing and m6A sequencing were simultaneously performed. We find that doxorubicin induced the increasing m6A peaks compared to the control group, whereas inhibited by PRMT5. The transcripts exhibiting m6A methylation alteration by doxorubicin and PRMT5 were enriched for gene ontology (GO) terms related to DNA damage response and repair. The GO terms and KEGG annotations analysis identified BRCA1 signaling as being significantly altered through m6A methylation which induced by doxorubicin but inhibited by PRMT5. This study provides that PRMT5 promotes DNA damage repair through regulating m6A methylation of BRCA1 mRNA.

2022-01-01 | GSE155657 | GEO

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