|
| Status |
Public on Nov 26, 2012 |
| Title |
RNAi triggered by specialized machinery silences developmental genes and retrotransposons (RNA-Seq) |
| Organisms |
Schizosaccharomyces pombe; Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
RNAi is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. In the absence of the exosome, transcripts are processed preferentially by the RNAi machinery, revealing widespread occurrence of siRNA clusters and corresponding increase in heterochromatin modifications across large domains. We show that the generation of siRNAs and heterochromatin assembly by RNAi is triggered by a mechanism involving the canonical poly(A) polymerase Pla1 and an associated RNA surveillance factor Red1, which also activate the exosome. Remarkably, siRNA production and heterochromatin modifications at genes are regulated by environmental growth conditions, and by developmental signals that induce gene expression during sexual differentiation. Our analyses uncover interplay between RNAi and the exosome that is conserved in higher eukaryotes, and show that differentiation signals modulate RNAi silencing to regulate developmental genes.
|
| |
|
| Overall design |
We sequenced 7 samples from Schizosaccharomyces pombe and 2 samples from Drosophila melanogaster.
|
| |
|
| Contributor(s) |
Yamanaka S, Mehta S, Shuang F, Fuchs RT, Rong Y, Robb GB |
| Citation(s) |
23151475 |
| Submission date |
Oct 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shiv Grewal |
| Phone |
2407607553
|
| Organization name |
NCI
|
| Department |
LBMB
|
| Lab |
Shiv Grewal
|
| Street address |
NCI bldg 37 Rm 6068 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
| GPL15167 |
Illumina Genome Analyzer IIx (Schizosaccharomyces pombe) |
| GPL16192 |
Illumina MiSeq (Schizosaccharomyces pombe) |
|
| Samples (9)
|
|
| This SubSeries is part of SuperSeries: |
| GSE41643 |
RNAi triggered by specialized machinery silences developmental genes and retrotransposons |
|
| Relations |
| BioProject |
PRJNA177799 |
| SRA |
SRP016495 |
Less...
More...