Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.
Nabeel S Ganem,
Noa Ben-Asher,
Aidan C Manning,
Sarah N Deffit,
Michael C Washburn,
Emily C Wheeler,
Gene W Yeo,
Orna Ben-Naim Zgayer,
Einav Mantsur,
Heather A Hundley,
Ayelet T Lamm
Cell reports
· 2019
· Vol. 27
(4)
· pp. 1244-1253.e4
Abstract
A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes on the RNA editing process. We performed comprehensive phenotypic, transcriptomics, proteomics, and RNA binding screens on worms mutated in a single ADAR gene. We found that ADR-1 mutants exhibit more-severe phenotypes than ADR-2, and some of them are a result of non-editing functions of ADR-1. We also show that ADR-1 significantly binds edited genes and regulates mRNA expression, whereas the effect on protein levels is minor. In addition, ADR-1 primarily promotes editing by ADR-2 at the L4 stage of development. Our results suggest that ADR-1 has a significant role in the RNA editing process and in altering editing levels that affect RNA expression; loss of ADR-1 results in severe phenotypes.
Publication Types
["Journal Article", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't"]
MeSH Terms
["Adenosine", "Adenosine Deaminase", "Animals", "Caenorhabditis elegans", "Caenorhabditis elegans Proteins", "Inosine", "Mutation", "Phenotype", "Proteome", "RNA Editing", "Transcriptome"]
Funding
P40 OD010440
NIH HHS
(United States)
F32 GM119257
NIGMS NIH HHS
(United States)
R01 GM130759
NIGMS NIH HHS
(United States)
Linked Datasets (1)
Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing
623984 data files
| File | Type | Size |
|---|---|---|
| BB19_embryo_1_131216_CGATGT.fastq.gz | RNA-Seq | 1.4 GB |
| BB19_embryo_1_131216_CGATGT.fastq.gz | RNA-Seq | 1.4 GB |
| BB19_embryo_2_051216_TTAGGC.fastq.gz | RNA-Seq | 1.3 GB |
| BB19_embryo_2_051216_TTAGGC.fastq.gz | RNA-Seq | 1.3 GB |
| BB19_embryo_310816_TTAGGC.fastq.gz | RNA-Seq | 1016.1 MB |
| BB19_embryo_310816_TTAGGC.fastq.gz | RNA-Seq | 1016.1 MB |
| BB19_L4_220816_GCCAAT.fastq.gz | RNA-Seq | 1.3 GB |
| BB19_L4_220816_GCCAAT.fastq.gz | RNA-Seq | 1.3 GB |
| BB19_L4_6_10_16_TAGCTT.fastq.gz | RNA-Seq | 1.3 GB |
| BB19_L4_6_10_16_TAGCTT.fastq.gz | RNA-Seq | 1.3 GB |
| BB19_L4_Ayya_GGCTAC.fastq.gz | RNA-Seq | 1.2 GB |
| BB19_L4_Ayya_GGCTAC.fastq.gz | RNA-Seq | 1.2 GB |
| BB2_E_18_12_16_CAGATC.fastq.gz | RNA-Seq | 1.3 GB |
| BB2_E_18_12_16_CAGATC.fastq.gz | RNA-Seq | 1.3 GB |
| BB2_embryo_070916_TTAGGC.fastq.gz | RNA-Seq | 1.2 GB |
| BB2_embryo_070916_TTAGGC.fastq.gz | RNA-Seq | 1.2 GB |
| BB2_L4_221216_ACAGTG.fastq.gz | RNA-Seq | 1.3 GB |
| BB2_L4_221216_ACAGTG.fastq.gz | RNA-Seq | 1.3 GB |
| BB2_L4_230816_CAGATC.fastq.gz | RNA-Seq | 1.1 GB |
| BB2_L4_230816_CAGATC.fastq.gz | RNA-Seq | 1.1 GB |
| BB2_L4_Ayya_ATCACG.fastq.gz | RNA-Seq | 1.1 GB |
| BB2_L4_Ayya_ATCACG.fastq.gz | RNA-Seq | 1.1 GB |
| BB3_E_19_12_16_GATCAG.fastq.gz | RNA-Seq | 1.2 GB |
| BB3_E_19_12_16_GATCAG.fastq.gz | RNA-Seq | 1.2 GB |
| BB3_embryo_011216_TAGCTT.fastq.gz | RNA-Seq | 1.3 GB |
| BB3_embryo_011216_TAGCTT.fastq.gz | RNA-Seq | 1.3 GB |
| BB3_embryo_230816_ACAGTG.fastq.gz | RNA-Seq | 1.3 GB |
| BB3_embryo_230816_ACAGTG.fastq.gz | RNA-Seq | 1.3 GB |
| BB3_L4_10_10_16_ACTTGA.fastq.gz | RNA-Seq | 1.1 GB |
| BB3_L4_10_10_16_ACTTGA.fastq.gz | RNA-Seq | 1.1 GB |
| BB3_L4_160816_GATCAG.fastq.gz | RNA-Seq | 1.3 GB |
| BB3_L4_160816_GATCAG.fastq.gz | RNA-Seq | 1.3 GB |
| BB3_L4_Ayya_CTTGTA.fastq.gz | RNA-Seq | 1.3 GB |
| BB3_L4_Ayya_CTTGTA.fastq.gz | RNA-Seq | 1.3 GB |
| GSF-896-134-Input-24June_S6_R1_001.fastq.gz | RIP-Seq | 1009.6 MB |
| GSF-896-134-Input-24June_S6_R1_001.fastq.gz | RIP-Seq | 1009.6 MB |
| GSF-896-134-Input-30Mar_S3_R1_001.fastq.gz | RIP-Seq | 1.8 GB |
| GSF-896-134-Input-30Mar_S3_R1_001.fastq.gz | RIP-Seq | 1.8 GB |
| GSF-896-134-RIP-24June_S15_R1_001.fastq.gz | RIP-Seq | 760.1 MB |
| GSF-896-134-RIP-24June_S15_R1_001.fastq.gz | RIP-Seq | 760.1 MB |
| GSF-896-134-RIP-30Mar_S12_R1_001.fastq.gz | RIP-Seq | 792.5 MB |
| GSF-896-134-RIP-30Mar_S12_R1_001.fastq.gz | RIP-Seq | 792.5 MB |
| GSF-896-76-Input-24June_S4_R1_001.fastq.gz | RIP-Seq | 955.5 MB |
| GSF-896-76-Input-24June_S4_R1_001.fastq.gz | RIP-Seq | 955.5 MB |
| GSF-896-76-Input-30Mar_S1_R1_001.fastq.gz | RIP-Seq | 1.7 GB |
| GSF-896-76-Input-30Mar_S1_R1_001.fastq.gz | RIP-Seq | 1.7 GB |
| GSF-896-76-RIP-24June_S13_R1_001.fastq.gz | RIP-Seq | 780.0 MB |
| GSF-896-76-RIP-24June_S13_R1_001.fastq.gz | RIP-Seq | 780.0 MB |
| GSF-896-76-RIP-30Mar_S10_R1_001.fastq.gz | RIP-Seq | 782.0 MB |
| GSF-896-76-RIP-30Mar_S10_R1_001.fastq.gz | RIP-Seq | 782.0 MB |
| GSF-896-Adr-1-Input-24June_S5_R1_001.fastq.gz | RIP-Seq | 849.7 MB |
| GSF-896-Adr-1-Input-24June_S5_R1_001.fastq.gz | RIP-Seq | 849.7 MB |
| GSF-896-Adr-1-Input-30Mar_S2_R1_001.fastq.gz | RIP-Seq | 2.0 GB |
| GSF-896-Adr-1-Input-30Mar_S2_R1_001.fastq.gz | RIP-Seq | 2.0 GB |
| GSF-896-Adr-1-RIP-24June_S14_R1_001.fastq.gz | RIP-Seq | 785.4 MB |
| GSF-896-Adr-1-RIP-24June_S14_R1_001.fastq.gz | RIP-Seq | 785.4 MB |
| GSF-896-Adr1-RIP-30Mar_S11_R1_001.fastq.gz | RIP-Seq | 783.8 MB |
| GSF-896-Adr1-RIP-30Mar_S11_R1_001.fastq.gz | RIP-Seq | 783.8 MB |
| N2_E_15_12_16_CGATGT.fastq.gz | RNA-Seq | 1.3 GB |
| N2_E_15_12_16_CGATGT.fastq.gz | RNA-Seq | 1.3 GB |
| N2_E_15_9_16_CGATGT.fastq.gz | RNA-Seq | 1.2 GB |
| N2_E_15_9_16_CGATGT.fastq.gz | RNA-Seq | 1.2 GB |
| N2_embryo_111216_TAGCTT.fastq.gz | RNA-Seq | 1.3 GB |
| N2_embryo_111216_TAGCTT.fastq.gz | RNA-Seq | 1.3 GB |
| N2_embryo_230816_ATCACG.fastq.gz | RNA-Seq | 1.1 GB |
| N2_embryo_230816_ATCACG.fastq.gz | RNA-Seq | 1.1 GB |
| N2_L4_18_9_16_ATCACG.fastq.gz | RNA-Seq | 1.1 GB |
| N2_L4_18_9_16_ATCACG.fastq.gz | RNA-Seq | 1.1 GB |
| N2_L4_220816_ATCACG.fastq.gz | RNA-Seq | 1.2 GB |
| N2_L4_220816_ATCACG.fastq.gz | RNA-Seq | 1.2 GB |
| N2_L4_AYYA_TTAGGC.fastq.gz | RNA-Seq | 1.1 GB |
| N2_L4_AYYA_TTAGGC.fastq.gz | RNA-Seq | 1.1 GB |
| RB886_E_11_9_16_ACAGTG.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_E_11_9_16_ACAGTG.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_E_15_12_16_TTAGGC.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_E_15_12_16_TTAGGC.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_embryo_110916_CGATGT.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_embryo_110916_CGATGT.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_L4_160816_TGACCA.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_L4_160816_TGACCA.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_L4_20_9_16_TGACCA.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_L4_20_9_16_TGACCA.fastq.gz | RNA-Seq | 1.2 GB |
| RB886_L4_Ayya_GCCAAT.fastq.gz | RNA-Seq | 1.1 GB |
| RB886_L4_Ayya_GCCAAT.fastq.gz | RNA-Seq | 1.1 GB |
Analysis Pipelines (1)
GSE110701 Data Processing
7 steps
geo_data_processing
GSE110701