|
| Status |
Public on Oct 09, 2018 |
| Title |
Heat Shock in C. elegans Induces Downstream of Gene Transcription and Accumulation of Double-Stranded RNA |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We observed that heat shock of Caenorhabditis elegans leads to the formation of nuclear double-stranded RNA (dsRNA) foci, detectable with a dsRNA-specific monoclonal antibody. These foci significantly overlap with nuclear HSF-1 granules. To investigate the molecular mechanism(s) underlying dsRNA foci formation, we used RNA-seq to globally characterize total RNA and immunoprecipitated dsRNA from control and heat-shocked worms. We find antisense transcripts are generally increased after heat shock, and a subset of both sense and antisense transcripts enriched in the dsRNA pool by heat shock overlap with dsRNA transcripts enriched by deletion of tdp-1, which encodes the C. elegans ortholog of TDP-43. Interestingly, transcripts involved in translation are over-represented in the dsRNAs induced by either heat shock or deletion of tdp-1. Also enriched in the dsRNA transcripts are sequences downstream of annotated genes (DoGs), which we globally quantified with a new algorithm. To validate these observations, we used fluorescence in situ hypridization (FISH) to confirm both antisense and downstream of gene transcription for eif-3.B, one of the affected loci we identified.
|
| |
|
| Overall design |
Total of 11 samples: 1 N2 heat shock input RNA input sample with 2 N2 heat shock J2 immunoprecipated samples. The following samples were re-analyzed from GSE61581. 3 tdp1 J2 immunoprecipitated samples and tdp1 total RNA input with 3 N2 J2 immunoprecipitated controls (with N2 input).
|
| |
|
| Contributor(s) |
Melnick M, Gonzales P, Cabral J, Allen MA, Dowell RD, Link CD |
| Citation(s) |
30958820 |
| Submission date |
Oct 08, 2018 |
| Last update date |
May 02, 2019 |
| Contact name |
marko melnick |
| E-mail(s) |
marko.melnick@colorado.edu
|
| Organization name |
University of Colorado at Boulder
|
| Department |
Integrative Physiology
|
| Lab |
Christopher D. Link Lab
|
| Street address |
1725 pleasant st
|
| City |
boulder |
| State/province |
CO |
| ZIP/Postal code |
80309 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
|
| Samples (11)
|
|
| Relations |
| BioProject |
PRJNA495081 |
| SRA |
SRP164589 |
Less...
More...