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| Status |
Public on Jun 06, 2020 |
| Title |
A molecular mechanism to regulate neural-specific A-to-I editing during development |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Using a combination of molecular and genomic approaches we uncover a molecular mechanism that regulates RNA editing in a neural- and development-specific manner. We de novo identified 570 A-to-i editing sites in adult neural RNA-seq data and 6202 sites from re-analyzing L1 neural RNA seq.Comparing editomes during development led to the identification of both neural transcripts that were edited only in one life-stage. The stage-specific editing is largely regulated by differential gene expression during neural development, and proper gene expression of nearly one-third of these differentially expressed genes is dependent on adr-2, the only known A-to-I editing enzyme in C. elegans. However, we also identified a subset of neural transcripts which are edited and expressed throughout development. Interestingly, despite a neural-specific downregulation of adr-2 during development, the majority of sites edited throughout development exhibit increased editing in adult neural cells. Biochemical data suggests that ADR-1, a deaminase deficient member of the Adenosine deaminase acting on RNA (ADAR) family is competing with ADR-2 for binding to specific transcripts early in development. Our data suggest a model where during neural development, ADR-2 levels overcome ADR-1 repression, resulting in increased ADR-2 binding and editing of specific transcripts. Together, our findings reveal tissue- and development-specific regulation of RNA editing and identify a molecular mechanism that regulates ADAR substrate recognition and editing efficiency.
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| Overall design |
High throughput sequencing of adult neural RNA-seq libraries and identification of A-to-I editing sites using SAILOR software
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| Contributor(s) |
Rajendren S, Vadlamani P, Hundley HA |
| Citation missing |
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| |
| Submission date |
Jun 05, 2020 |
| Last update date |
Jun 06, 2020 |
| Contact name |
Heather Ann Hundley |
| E-mail(s) |
[email protected]
|
| Phone |
812-855-0675
|
| Organization name |
Indiana University, Bloomington
|
| Department |
Biology
|
| Lab |
Hundley
|
| Street address |
1001 E 3rd St,
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
|
| Samples (18)
|
|
| Relations |
| BioProject |
PRJNA637637 |
| SRA |
SRP266179 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE151916_Reanalyzed_adr2.L1.merged.sailoroutput.csv.gz |
312.8 Kb |
(ftp)(http) |
CSV |
| GSE151916_Reanalyzed_wt.L1.merged.sailoroutput.csv.gz |
551.0 Kb |
(ftp)(http) |
CSV |
| GSE151916_WT.adultvsL1.counts.txt.gz |
782.1 Kb |
(ftp)(http) |
TXT |
| GSE151916_adr-2.adultvsL1.txt.gz |
765.1 Kb |
(ftp)(http) |
TXT |
| GSE151916_adr1.L1.sailoroutput.csv.gz |
143.2 Kb |
(ftp)(http) |
CSV |
| GSE151916_adr1.adult.merged.sailoroutput.csv.gz |
162.7 Kb |
(ftp)(http) |
CSV |
| GSE151916_adr2.adult.merged.sailoroutput.csv.gz |
77.5 Kb |
(ftp)(http) |
CSV |
| GSE151916_wt.adult.merged.sailoroutput.csv.gz |
101.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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