 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 05, 2017 |
| Title |
Natural variation of piRNA expression affects immunity to transposable elements |
| Organism |
Drosophila melanogaster |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements. The permissivity to I-element activity of R females, called reactivity, varies considerably in natural R populations, indicating the existence of a strong natural polymorphism in defense systems targeting transposons. To reveal the nature of such polymorphisms, we compared ovarian small RNAs between R strains with low and high reactivity and show that reactivity negatively correlates with the ancestral I-element-specific piRNA content. Analysis of piRNA clusters containing remnants of I-elements shows increased expression of the piRNA precursors and enrichment by the Heterochromatin Protein 1 homolog, Rhino, in weak R strains, which is in accordance with stronger piRNA expression by these regions. To explore the nature of the differences in piRNA production, we focused on two R strains, weak and strong, and showed that the efficiency of maternal inheritance of piRNAs as well as the I-element copy number are very similar in both strains. At the same time, germline and somatic uni-strand piRNA clusters generate more piRNAs in strains with low reactivity, suggesting the relationship between the efficiency of primary piRNA production and variable response to TE invasions. The strength of adaptive genome defense is likely driven by naturally occurring polymorphisms in the rapidly evolving piRNA pathway proteins. We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric retrotransposon HeT-A, which we have observed in one particular transposon-resistant R strain.
|
| |
|
| Overall design |
The fractions of small RNAs (19-29 nt) from ovaries of four R strains of Drosophila melanogaster, and from embryos of two R strains of Drosophila melanogaster, were sequenced using Illumina HiSeq 2000.
|
| |
|
| Contributor(s) |
Ryazansky S, Radion E, Mironova A, Akulenko N, Abramov Y, Morgunova V, Kordyukova M, Olovnikov I, Kalmykova A |
| Citation(s) |
28448516 |
| Submission date |
Jun 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sergei Ryazansky |
| E-mail(s) |
s.ryazansky@gmail.com
|
| Phone |
+7-499-196-81-73
|
| Organization name |
Institute of Molecular Genetics
|
| Department |
Department of Molecular Genetics of Cell
|
| Street address |
Kurchatov sq., 2
|
| City |
Moscow |
| ZIP/Postal code |
123182 |
| Country |
Russia |
| |
|
| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
|
| Samples (7)
|
| GSM2199449 |
Small RNAs from ovaries of Paris R strain |
| GSM2199450 |
Small RNAs from ovaries of Misy R strain |
| GSM2199451 |
Small RNAs from ovaries of cn bw; e R strain |
| GSM2199452 |
Small RNAs from ovaries of Zola R strain |
| GSM2199453 |
Small RNAs from embryos of Paris R strain |
| GSM2199454 |
Small RNAs from embryos of Misy R strain |
| GSM2472381 |
Small RNAs from ovaries of Zola R strain 2 |
|
| Relations |
| BioProject |
PRJNA325554 |
| SRA |
SRP076499 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE83316_RAW.tar |
128.8 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...