GSE51556

GSE GEO

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The dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome

Organism: 6239

Platform: GPL9269

Samples: 8

Experiment Types:

Expression profiling by high throughput sequencing

Submitted: Oct 22 2013

Last Updated: May 15 2019

Status: Public on Jan 20 2014

Contact: Boyko,,Kakaradov (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA223411 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP031831

Summary

Purpose: The purpose of this experiment is to expand the repertoire of C. elegans edited transcripts and identify the roles of ADR-1 as indirect regulator of editing and ADR-2 as the only active deaminase in vivo. Methods: Strand-specific RNA sequencing of wild-type and adr mutant worms, followed by a novel RNA variant calling and comparative analysis pipeline. Results: Despite lacking deaminase function, ADR-1 affects editing of over 60 adenosines within the 3â UTRs of 16 different mRNAs. Furthermore, ADR-1 interacts directly with ADR-2 substrates, even in the absence of ADR-2; and mutations within its dsRNA binding domains abolished both binding and editing regulation. Conclusions: ADR-1 acts as a major regulator of editing by binding ADR-2 substrates in vivo and raises the possibility that other dsRNA binding proteins, including the inactive human ADARs, regulate RNA editing by deaminase-independent mechanisms.

Overall Design

Strand-specific RNA sequencing of wild-type and adr mutant worms, followed by a novel RNA variant calling and comparative analysis pipeline.

Analysis (14 steps)

View Data Processing

Processing steps for GSE51556

ssRNAseq: The adr-1(-);adr-2(-) sample was sequenced on one lane of Illumina's HiSeq 2000 yielding 216 million single-end 76nt reads.
Each other sample was sequenced on a lane of Illumina GAII yielding between 37 and 42 million reads of the same type.
Illumina Casava1.8.2 software used for basecalling.
Mapping: Sequenced reads were mapped to the C. elegans reference genome (ce10) using TopHat aligner (version 2.0.6) allowing only uniquely-mapped reads with up to two mismatches each with command line options -Mx 1 and -N 2
Variant calling: sites with RNA-DNA differences were identified by SAMtools mpileup (version 0.1.18) tallying up to 1000 alignments per site.
Additional command line options used were -D -I and -g.
Site filters: Annotated SNPs were obtained from Illumina's iGenomes collection for C. elegans (ce10) and unannotated variants were extracted from the adr-1(-);adr-2(-) RNA-Seq dataset.
These genomic variants were filtered from the putative sites in all other strains reducing the number of false-positive predictions.

Showing first 8 steps.

Supplementary Files (1)

GSE51556_RAW.tar Download

GEO Samples (8)

GSM1248093 GSM1248097 GSM1248099 GSM1248101 GSM1248103 GSM1248105 GSM1248107 GSM1248109

Dataset Citations (1)

The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome.

PMID 24508457 · 2014 · Cell reports

Michael C Washburn, Boyko Kakaradov, Balaji Sundararaman, Emily Wheeler, Shawn Hoon, Gene W Yeo, Heather A Hundley

SRA Experiments (8) and Runs (8)

Total: 24814 MB

SRX366861 SRP031831 RNA-Seq SINGLE

GSM1248093: adr1-/adr2- double knockout; Caenorhabditis elegans; RNA-Seq

Sample: SRS492989

BioProject: PRJNA223411

BioSample: SAMN02380468

Platform: ILLUMINA

Instrument: Illumina HiSeq 2000

Organism: Caenorhabditis elegans

Sample attributes

source_name: BB21 adr-1(tm668); adr-2(ok735)

tissue: whole worms

genotype: BB21 adr-1(tm668); adr-2(ok735)

genetic background: N2

Original files (1)

BB21 adr-1(tm668); adr-2(ok735)

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR1015363	209781429	23075957190	12733.94	Sample_ADR12.fastq.gz, SRR1015363, SRR1015363.sralite	SRA

SRX366862 SRP031831 RNA-Seq SINGLE

GSM1248097: adr1- knockout worms; Caenorhabditis elegans; RNA-Seq

Sample: SRS492990

BioProject: PRJNA223411

BioSample: SAMN02380465

Platform: ILLUMINA

Instrument: Illumina Genome Analyzer II

Organism: Caenorhabditis elegans

Sample attributes

source_name: BB19 adr-1(tm668)

tissue: whole worms

genotype: BB19 adr-1(tm668)

genetic background: N2

Original files (1)

BB19 adr-1(tm668)

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR1015364	36479073	2772409548	1663.8	Sample_ADR1.fastq.gz, SRR1015364, SRR1015364.sralite	SRA

SRX366863 SRP031831 RNA-Seq SINGLE

GSM1248099: adr2- knockout worms; Caenorhabditis elegans; RNA-Seq

Sample: SRS492991

BioProject: PRJNA223411

BioSample: SAMN02380470

Platform: ILLUMINA

Instrument: Illumina Genome Analyzer II

Organism: Caenorhabditis elegans

Sample attributes

source_name: BB20 adr-2(ok735)

tissue: whole worms

genotype: BB20 adr-2(ok735)

genetic background: N2

Original files (1)

BB20 adr-2(ok735)

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR1015365	39667230	3014709480	1831.32	Sample_ADR2.fastq.gz, SRR1015365, SRR1015365.sralite	SRA

SRX366864 SRP031831 RNA-Seq SINGLE

GSM1248101: N2 wild type worms; Caenorhabditis elegans; RNA-Seq

Sample: SRS492992

BioProject: PRJNA223411

BioSample: SAMN02380464

Platform: ILLUMINA

Instrument: Illumina Genome Analyzer II

Organism: Caenorhabditis elegans

Sample attributes

source_name: Bristol strain N2

tissue: whole worms

genotype: wild type

genetic background: N2

Original files (1)

Bristol strain N2

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR1015366	34542067	2625197092	1583.79	SRR1015366, SRR1015366.sralite	SRA

SRX366865 SRP031831 RNA-Seq SINGLE

GSM1248103: adr1/adr2 double mutant; Caenorhabditis elegans; RNA-Seq

Sample: SRS492993

BioProject: PRJNA223411

BioSample: SAMN02380466

Platform: ILLUMINA

Instrument: Illumina Genome Analyzer II

Organism: Caenorhabditis elegans

Sample attributes

source_name: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD1 (K223E, K224A, and K227A) and dsRBD2 (K583E, K584A and K587A)]

tissue: whole worms

genotype: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD1 (K223E, K224A, and K227A) and dsRBD2 (K583E, K584A and K587A)]

genetic background: N2

Original files (1)

BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD1 (K223E, K224A, and K227A) and dsRBD2 (K583E, K584A and K587A)]

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR1015367	38361013	2915436988	1726.79	Sample_DS12MT.fastq.gz, SRR1015367, SRR1015367.sralite	SRA

SRX366866 SRP031831 RNA-Seq SINGLE

GSM1248105: adr1 dsRBD mutant; Caenorhabditis elegans; RNA-Seq

Sample: SRS492994

BioProject: PRJNA223411

BioSample: SAMN02380471

Platform: ILLUMINA

Instrument: Illumina Genome Analyzer II

Organism: Caenorhabditis elegans

Sample attributes

source_name: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD1 (K223E, K224A, and K227A)]

tissue: whole worms

genotype: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD1 (K223E, K224A, and K227A)]

genetic background: N2

Original files (1)

BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD1 (K223E, K224A, and K227A)]

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR1015368	38703417	2941459692	1763.92	Sample_DS1MT.fastq.gz, SRR1015368, SRR1015368.sralite	SRA

SRX366867 SRP031831 RNA-Seq SINGLE

GSM1248107: adr2 dsRBD mutant; Caenorhabditis elegans; RNA-Seq

Sample: SRS492995

BioProject: PRJNA223411

BioSample: SAMN02380469

Platform: ILLUMINA

Instrument: Illumina Genome Analyzer II

Organism: Caenorhabditis elegans

Sample attributes

source_name: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD2 (K583E, K584A and K587A)]

tissue: whole worms

genotype: BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD2 (K583E, K584A and K587A)]

genetic background: N2

Original files (1)

BB21 adr-1(tm668) + blmEx2[3X FLAG-adr-1 genomic with mutations in dsRBD2 (K583E, K584A and K587A)]

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR1015369	37625864	2859565664	1700.47	Sample_DS2MT.fastq.gz, SRR1015369, SRR1015369.sralite	SRA

SRX366868 SRP031831 RNA-Seq SINGLE

GSM1248109: FLAG ADR1- rescue; Caenorhabditis elegans; RNA-Seq

Sample: SRS492996

BioProject: PRJNA223411

BioSample: SAMN02380467

Platform: ILLUMINA

Instrument: Illumina Genome Analyzer II

Organism: Caenorhabditis elegans

Sample attributes

source_name: BB21 adr-1(tm668) + blmEx1[ 3XFLAG-adr-1 genomic, rab3::gfp::unc-54]

tissue: whole worms

genotype: BB21 adr-1(tm668) + blmEx1[ 3XFLAG-adr-1 genomic, rab3::gfp::unc-54]

genetic background: N2

Original files (1)

BB21 adr-1(tm668) + blmEx1[ 3XFLAG-adr-1 genomic, rab3::gfp::unc-54]

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR1015370	39313335	2987813460	1810.13	Sample_WADR1.fastq.gz, SRR1015370, SRR1015370.sralite	SRA

Linked Publications (1)

The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome.

Cell reports · 2014

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome.

Cell reports · 2014

Data Files (16)

Accession	File Name	Stored Type	Size	Download
—	Sample_ADR12.fastq.gz	RNA-Seq	12.4 GB	link
—	Sample_ADR1.fastq.gz	RNA-Seq	1.6 GB	link
—	Sample_ADR2.fastq.gz	RNA-Seq	1.8 GB	link
—	Sample_DS12MT.fastq.gz	RNA-Seq	1.7 GB	link
—	Sample_DS1MT.fastq.gz	RNA-Seq	1.7 GB	link
—	Sample_DS2MT.fastq.gz	RNA-Seq	1.7 GB	link
—	Sample_WADR1.fastq.gz	RNA-Seq	1.8 GB	link
—	SRR1015363_GSM1248093	RNA-Seq	12.4 GB	link
—	SRR1015364_GSM1248097	RNA-Seq	1.6 GB	link
—	SRR1015365_GSM1248099	RNA-Seq	1.8 GB	link
—	SRR1015366	RNA-Seq	1.5 GB	link
—	SRR1015366_GSM1248101	RNA-Seq	1.5 GB	link
—	SRR1015367_GSM1248103	RNA-Seq	1.7 GB	link
—	SRR1015368_GSM1248105	RNA-Seq	1.7 GB	link
—	SRR1015369_GSM1248107	RNA-Seq	1.7 GB	link
—	SRR1015370_GSM1248109	RNA-Seq	1.8 GB	link