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Analysis of canonical A-to-I RNA editing in Drosophila using ICE-seq

ABSTRACT: Analysis of canonical A-to-I RNA editing in Drosophila using ICE-seq

PROVIDER: PRJNA259668 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1560490.fastq.gz	Fastqsanger.gz
	SRR1560500.fastq.gz	Fastqsanger.gz
	SRR1560491.fastq.gz	Fastqsanger.gz
	SRR1560501.fastq.gz	Fastqsanger.gz
	SRR1560482.fastq.gz	Fastqsanger.gz

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Analysis of canonical A-to-I RNA editing in Drosophila using ICE-seq

Project description:The predominant form of RNA editing in animals is the enzymatic conversion of adenosine to inosine that is sequenced in cDNA as guanine. While RNA editing should be identifiable from RNA-seq data alone, genomic SNPs as well as sequencing and mapping errors result in a high false-positive rate. We used Inosine Chemical Erasing (ICE) with deep sequencing (ICE-seq) in order to validate A-to-I RNA editing genome-wide without the need for the sequencing of the underlying genomic DNA. We called RNA editing events in the head transcriptome of the reference strain of Drosophila melanogaster and six resequenced strains of Drosophila yakuba using the Illumina HiSeq and NextSeq platforms. We compared RNA editing sites reported in other studies and measured the level of conservation between D. melanogaster and D. yakuba. We found that while some of the best-studied editing sites in D. melanogaster are also edited in D. yakuba, we also detect a significant amount of species-specific editing in genes with different Gene Ontology enrichments, which suggests that the biological function of RNA editing in the two Drosophila species is diverging.

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Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila

Project description:The RNA editing enzyme ADAR chemically modifies adenosine (A) to inosine (I), which is interpreted by the ribosome as a guanosine. Here we assess cotranscriptional A-to-I editing in Drosophila, by isolating nascent RNA from adult fly heads and subjecting samples to high-throughput sequencing. There are a large number of edited sites within nascent exons. Nascent RNA from an ADAR null mutant strain was also sequenced, indicating that almost all A-to-I events require ADAR. Moreover, mRNA editing levels correlate with editing levels within the cognate nascent RNA sequence, indicating that the extent of editing is set cotranscriptionally. Surprisingly, the nascent data also identify an excess of intronic over exonic editing sites. These intronic sites occur preferentially within introns that are poorly spliced cotranscriptionally, suggesting a link between editing and splicing. We conclude that ADAR-mediated editing is more widespread than previously indicated and largely occurs cotranscriptionally. GSM914095: Fly genomic DNA sequencing. Sequenced on the Illumina GA II. GSM914102-GSM914113: Fly head nascent RNA profiles over 6 time points of a 12hr light:dark cycle in duplicate; sequenced on the Illumina GA II. GSM914114-GSM914119: Fly head nascent RNA profiles of yw, FM7, ADAR0 males in duplicate; sequenced on the HiSeq2000. GSM915213-GSM915214: Fly head mRNA profiles over 2 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II. GSM915215-GSM915220: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; paired-end sequenced on the Illumina GA II. GSM915221-GSM91526: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II.

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A-to-I RNA Editing in Drosophila

Project description:A-to-I RNA Editing in Drosophila

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Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain

Project description:We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using RNA-seq, we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control.

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