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| Status |
Public on Jan 08, 2024 |
| Title |
Autonomous transposons tune their sequences to ensure somatic suppression [polyA_S2] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Transposable elements (TEs) are a major constituent of human genes, occupying approximately half of the intronic space. During pre-mRNA synthesis, intronŁic TEs are transcribed along with their host genes but rarely contribute to the final mRNA product as they are spliced out together with the intron and rapidly degraded. Paradoxically, TEs are an abundant source of RNA-processing signals through which they can create new introns (Huff et al. 2016), and functional (Cosby et al. 2021) or non-functional chimeric transcripts (Clayton et al. 2020). The rarity of these events impliesy the existence of a resilient splicing code that is able to suppress TE-exonization without compromising host pre-mRNA processing. Here we show that SAFB proteins play a unique dual role in defence against TEs by preventing retrotransposition of L1 elements as well as their exonization when they land into genes by coating their adenosine-rich RNA. The suppressive activity of SAFB extends to neuro-, muscle- and testis-specific giant protein-coding cassette exons of ANK3, MAP4 and CLIP1, nested genes as well as Tigger DNA transposons, which are all enriched with adenosine/purine-rich sequences that act as splicing-enhancers in SAFB depleted cells. In mice and flies, SAFB additionally suppresses LTR/ERV elements, which are active in mice and flies, but no longer in humans. Splicing events suppressed by SAFB in somatic cells are activated in the testis, coinciding with low SAFB expression in post-meiotic spermatids. Reminiscent of the division of labour between innate and adaptive immune systems that fight external pathogens, our results uncover SAFB proteins as an RNA-based, pattern-guided, non-adaptive defence system against TEs in the soma, complementing the RNA-based, adaptive Piwi-piRNA pathway of the germline.
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| Overall design |
Gene expression profiling of Saf-B-depleted D. melanogaster S2 cells, and a control treatment. poly(A)+ RNAs were sequenced in three biological replicates per treatment (6 libraries in total).
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| Contributor(s) |
Ilik IA, Glažar P, Aktas T |
| Citation(s) |
38355802 |
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| Submission date |
Jan 19, 2023 |
| Last update date |
Apr 11, 2024 |
| Contact name |
IBRAHIM AVSAR ILIK |
| E-mail(s) |
ilik@molgen.mpg.de
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| Organization name |
Max-Planck-Institut für molekulare Genetik
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| Lab |
OWL Aktas
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| Street address |
Ihnestraße 63-73
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| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
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| Platforms (1) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE223263 |
Autonomous transposons tune their sequences to ensure somatic suppression. |
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| Relations |
| BioProject |
PRJNA925494 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE223262_RAW.tar |
36.8 Mb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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