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Overexpression of RNA deaminase ADAR2 in Th17 cells

ABSTRACT: Overexpression of RNA deaminase ADAR2 in Th17 cells

PROVIDER: PRJNA943423 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23817300_1.fastq.gz	Fastqsanger.gz
	SRR23817300_2.fastq.gz	Fastqsanger.gz
	SRR23817301_1.fastq.gz	Fastqsanger.gz
	SRR23817301_2.fastq.gz	Fastqsanger.gz
	SRR23817302_1.fastq.gz	Fastqsanger.gz

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Overexpression of RNA deaminase ADAR2 in Th17 cells

Project description:ADAR2 is induced upon T cell activation and its immunological function is not known. Here, we performed RNA-seq on control and Th17 cells overexpressing wildtype or catalytic dead ADAR2 to identify A-to-I edited transcripts that are targets of ADAR2.

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Knockdown of RNA deaminase ADAR2 in Th17 cells

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Knockdown of RNA deaminase ADAR2 in Th17 cells

Project description:ADAR2 is induced upon T cell activation and its immunological function is not known. Here, we performed RNA-seq on Cas9+ control and Th17 cells expressing the PSIN empty vector control or guide RNAs against the ATG start codon or ADAR2 to identify ADAR2 dependent A-to-I edited transcripts.

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Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing HEK 293T cells Transcriptomes

Project description:Purpose: A-to-I RNA editing is critical for many cellular processes. The sites of A-I RNA editing can be identified through RNA-seq and matching the reads to the annotated database like RADAR. The goals of this study is to compare A-I RNA editing profile among wild type, ADAR2 overexpressing and ADAR2+SRSF9 overexpressing 293T cells to evaluate the influence of SRSF9 repressive action on A-I RNA editing Methods: A-I RNA editing profile and gene expression profiles were generated by deep sequencing from all the samples, using NEBNext® Ultra™ Directional RNA Library Prep Kit. The sequence reads that passed quality filters were analyzed for identifying the A-I RNA editing sites using RADAR Database Results: Upon overexpression of ADAR2, we found that 18,174 sites were differentially edited compared to control cells, of which 97.0% showed a significant increase in their editing levels as expected (P < 0.05, Fisher’s test). Furthermore, when we overexpressed both ADAR2 and SRSF9 together, we found that 6,994 sites were differentially edited compared to overexpression of the deaminase alone (P < 0.05, Fisher’s test). Importantly, the editing of 92.5% of these sites was down-regulated, consistent with the function of SRSF9 as a repressor of editing. Conclusions: Our study reports a detailed analysis of the effect of SRSF9 on A-I RNA editing of ADAR2-specific targets. We Conclude that this SRSF9 regulon is significantly enriched for brain-specific editing sites despite our unbiased approach.

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Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing SH-Sy5y cells Transcriptomes

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Transcriptomic studies of mouse naïve and Th17 cell from wildtype or DDX5 deficient background [RNA-seq]

Project description:Gene expression in naïve and Th17 cell were characterized. We report a notable dynamic change in the expression of genes encoding RNA editing enzymes. Birefly, the transcript encoding ADAR2 (Adarb1) was significantly upregulated in Th17 cells, and the transcript encoding ADAR1 (Adar) was downregulated during the polarization from naive to Th17 cells. The altered expression of RNA editing genes results in the dynamic A-to-I editing in naive and Th17 cells. In addtion, loss of DDX5 dysregulated ADAR2 expression, resulting in altered A-to-I editing on a subset of Th17 transcripts.

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Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA base-editing activity, functionality and specificity

Project description:We use RNA-seq to study the transcriptome wide specificity profiles of A-to-I RNA editing by split-ADAR2 constructs.

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Changes in gene expression and RNA editing in Adar2-WT and Adar2-KO Mouse embryonic Fibroblasts (MEFs)

Project description:Purpose: Measure gene expression and RNA editing changes in Adar-WT and Adar2-KO MEFs Methods: Performed PolyA+ RNA-seq (single end, one sample each) of Adar2-WT and Adar2-KO MEFs Results: Observed changes in editing and gene expression of several genes Conclusion: Adar2 influences gene expression and editing of transcripts

2016-12-23 | GSE74746 | GEO

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Project description:We overexpressed ADAR1, ADAR2 and AIMP2 in HEK293 cells and examined editing using RNA-seq.

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