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Unbiased identification of trans regulators of ADAR and A-to-I RNA editing

ABSTRACT: Unbiased identification of trans regulators of ADAR and A-to-I RNA editing

PROVIDER: PRJNA541311 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9019510_1.fastq.gz	Fastqsanger.gz
	SRR9019510_2.fastq.gz	Fastqsanger.gz
	SRR9019520_1.fastq.gz	Fastqsanger.gz
	SRR9019520_2.fastq.gz	Fastqsanger.gz
	SRR9019530_1.fastq.gz	Fastqsanger.gz

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Identification of trans regulators of ADAR and A-to-I RNA editing using RNA-seq

Project description:A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We performed RNA-seq on M17 and HeLa cells with overexpression of different candidate Adar regulators and GFP as a control to assay editing level differences between overexpression and control.

2019-05-07 | GSE130770 | GEO

Identification of trans regulators of ADAR and A-to-I RNA editing using mmPCR-seq

Project description:A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We performed mmPCRseq on H239T and H293TAdar2OE cells with overexpression of different candidate Adar regulators and GFP as a control to assay editing level differences between overexpression and control.

2019-05-07 | GSE130769 | GEO

Identification of trans regulators of ADAR and A-to-I RNA editing using mmPCR-seq

Project description:Identification of trans regulators of ADAR and A-to-I RNA editing using mmPCR-seq

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Identification of trans regulators of ADAR and A-to-I RNA editing using RNA-seq

Project description:Identification of trans regulators of ADAR and A-to-I RNA editing using RNA-seq

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Unbiased Identification of trans Regulators of ADAR and A-to-I RNA Editing.

Project description:Adenosine-to-inosine RNA editing is catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes that deaminate adenosine to inosine. Although many RNA editing sites are known, few trans regulators have been identified. We perform BioID followed by mass spectrometry to identify trans regulators of ADAR1 and ADAR2 in HeLa and M17 neuroblastoma cells. We identify known and novel ADAR-interacting proteins. Using ENCODE data, we validate and characterize a subset of the novel interactors as global or site-specific RNA editing regulators. Our set of novel trans regulators includes all four members of the DZF-domain-containing family of proteins: ILF3, ILF2, STRBP, and ZFR. We show that these proteins interact with each ADAR and modulate RNA editing levels. We find ILF3 is a broadly influential negative regulator of editing. This work demonstrates the broad roles that RNA binding proteins play in regulating editing levels, and establishes DZF-domain-containing proteins as a group of highly influential RNA editing regulators.

| S-EPMC7306178 | biostudies-literature

Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) [expression]

Project description:Alternative mRNA splicing is a major mechanism for gene regulation and transcriptome diversity. Despite the extent of the phenomenon, the regulation and specificity of the splicing machinery are only partially understood. Adenosine-to-inosine (A-to-I) RNA editing of pre-mRNA by ADAR enzymes has been linked to splicing regulation in several cases. Here we used bioinformatics approaches, RNA-seq and exon-specific microarray of ADAR knockdown cells to globally examine how ADAR and its A-to-I RNA editing activity influence alternative mRNA splicing. Although A-to-I RNA editing only rarely targets canonical splicing acceptor, donor, and branch sites, it was found to affect splicing regulatory elements (SREs) within exons. Cassette exons were found to be significantly enriched with A-to-I RNA editing sites compared with constitutive exons. RNA-seq and exon-specific microarray revealed that ADAR knockdown in hepatocarcinoma and myelogenous leukemia cell lines leads to global changes in gene expression, with hundreds of genes changing their splicing patterns in both cell lines. This global change in splicing pattern cannot be explained by putative editing sites alone. Genes showing significant changes in their splicing pattern are frequently involved in RNA processing and splicing activity. Analysis of recently published RNA-seq data from glioblastoma cell lines showed similar results. Our global analysis reveals that ADAR plays a major role in splicing regulation. Although direct editing of the splicing motifs does occur, we suggest it is not likely to be the primary mechanism for ADAR-mediated regulation of alternative splicing. Rather, this regulation is achieved by modulating trans-acting factors involved in the splicing machinery. HepG2 and K562 cell lines were stably transfected with plasmids containing siRNA designed to specifically knock down ADAR expression (ADAR KD). This in order to examine how ADAR affects alternative splicing globally.

2013-06-15 | E-GEOD-47945 | biostudies-arrayexpress

Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) [RNA-seq]

2013-06-17 | E-GEOD-47997 | biostudies-arrayexpress

Unbiased identification of trans regulators of ADAR and A-to-I RNA editing

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-05-07 | GSE130771 | GEO

CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo

Project description:RNA base editing represents a promising alternative for genome editing. Recent approaches harness the endogenous RNA editing enzyme ADAR to circumvent problems related to the ectopic expression of an editing enzyme, but they suffer from sequence restriction, lack of efficiency, and bystander editing. Here, we present in‐silico optimized CLUSTER guide RNAs, which bind their target mRNAs in a multivalent fashion and thereby enable editing with unprecedented precision as shown by next generation sequencing. CLUSTER guide RNAs can be genetically encoded and manufactured into viruses to work in various cell lines. They achieve on‐target editing on endogenous transcripts like GUSB and NUP43 with yields up to 45% without bystander editing and have been shown to recruit endogenous ADAR in vivo. The CLUSTER approach tremendously enlarges the sequence space available for guide RNA design and opens new avenues for drug development in the field of RNA base editing.

2021-09-20 | GSE184244 | GEO

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Project description:Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE, uninjected wild-type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128-cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf, a separate batch of uninjected control, as well as Adar KD and OE samples were generated in three replicates.

2022-08-02 | GSE182714 | GEO

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