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

Data Files (8)

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
—	SRR1015366	RNA-Seq	1.5 GB	link