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Transcriptome-wide map of SRSF9 bining in the presence and absence of ADAR2 in HEK293T cells

ABSTRACT: Transcriptome-wide map of SRSF9 bining in the presence and absence of ADAR2 in HEK293T cells

PROVIDER: PRJNA422807 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6384872_1.fastq.gz	Fastqsanger.gz
	SRR6384872_2.fastq.gz	Fastqsanger.gz
	SRR6384873_1.fastq.gz	Fastqsanger.gz
	SRR6384873_2.fastq.gz	Fastqsanger.gz
	SRR6384874_1.fastq.gz	Fastqsanger.gz

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Transcriptome-wide map of SRSF9 bining in the presence and absence of ADAR2 in HEK293T cells

Project description:Here, we show that the splicing factor SRSF9 selectively controls the editing of many brain-specific sites in mammals. SRSF9 is more lowly expressed in the mammalian brain than in non-brain tissues. Gene perturbation experiments and minigene analysis of candidate sites demonstrated that SRSF9 could robustly repress A-to-I editing by ADAR2. We found that SRSF9 biochemically interacted with ADAR2 in the nucleus via its RRM2 domain alone. Additionally, this interaction required the presence of the RNA substrate and disrupted the formation of ADAR2 dimers. Using transcriptome-wide location analysis and genome-wide RNA profiling, we identified 1,328 editing sites that are regulated directly by SRSF9. Importantly, we showed that this SRSF9 regulon is significantly enriched for brain-specific editing sites despite our unbiased approach. We further provide evidence that SRSF9 prevents cells from undergoing apoptosis possibly through the inhibition of ADAR2-mediated editing. Collectively, our results highlighted the importance of SRSF9 as an editing regulator and suggested that other splicing factors may also be involved in regulating RNA editing.

2018-06-21 | GSE108125 | GEO

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.

2018-06-21 | GSE108126 | GEO

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

2018-06-21 | GSE114970 | GEO

ADAR2 in HEK293T cells

Project description:ADAR2 in HEK293T cells

| PRJNA422795 | ENA

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

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

| PRJNA422806 | ENA

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

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

| PRJNA473370 | ENA

Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9

Project description:Adenosine DeAminases acting on RNA (ADAR) catalyzes adenosine-to-inosine (A-to-I) conversion within RNA duplex structures. While A-to-I editing is often dynamically regulated in a spatial-temporal manner, the mechanisms underlying its tissue-selective restriction remain elusive. We have previously reported that transcripts of voltage-gated calcium channel CaV1.3 are subject to brain-selective A-to-I RNA editing by ADAR2. Here, we show that editing of CaV1.3 mRNA is dependent on a 40 bp RNA duplex formed between exon 41 and an evolutionarily conserved editing site complementary sequence (ECS) located within the preceding intron. Heterologous expression of a mouse minigene that contained the ECS, intermediate intronic sequence and exon 41 with ADAR2 yielded robust editing. Interestingly, editing of CaV1.3 was potently inhibited by serine/arginine-rich splicing factor 9 (SRSF9). Mechanistically, the inhibitory effect of SRSF9 required direct RNA interaction. Selective down-regulation of SRSF9 in neurons provides a basis for the neuron-specific editing of CaV1.3 transcripts.

2018-04-17 | GSE113193 | GEO

MiRNAinU118_Cells_Inactive_vs_ active_ Adar2

Project description:MicroRNA expression profile of NB U118 cells transfected with a plasmid directing an inactive Adar2 vs an active Adar2 - 3 biological replicates 1 Condition experiment, 3 biological replicates, 2 replicates/array

2015-02-28 | E-GEOD-63694 | biostudies-arrayexpress

MiRNAinU118_Cells_Inactive_vs_ active_ Adar2

Project description:MicroRNA expression profile of NB U118 cells transfected with a plasmid directing an inactive Adar2 vs an active Adar2 - 3 biological replicates

2015-02-28 | GSE63694 | GEO

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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