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| Status |
Public on Aug 23, 2022 |
| Title |
Comparative analysis of piRNA sequences, targets and functions in Caenorhabditis nematodes |
| Organisms |
Caenorhabditis briggsae; Caenorhabditis elegans |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. briggsae. piRNA sequences in C. briggsae are extremely divergent from their counterparts in C. elegans, yet both species adopt similar genomic organization and transcription program that drive piRNA expression. By examining production of Piwi-dependent secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to C. elegans, small RNAs mapped to ribosomal RNAs or histone transcripts are not hyper-accumulated in C. briggsae. Instead, we found that fewer introns in transcripts are associated with hyper-accumulation of small RNAs. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
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| Overall design |
Small RNA high-throughput sequencing was done using RNA from adult wild type and prg-1 mutant animals in C. elegans and C. briggsae. C. briggsae PRG-1 IP was preformed using adult animals. Differential gene expression analysis, and other analyses, was done to identify C. briggsae piRNA loci, as well as smRNA abundance changes between wild type and prg-1 mutants.
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| Web link |
https://doi.org/10.1080/15476286.2022.2149170
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| |
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| Contributor(s) |
Pastore B, Hertz HL, Tang W |
| Citation(s) |
36412988 |
| |
| Submission date |
May 18, 2022 |
| Last update date |
Dec 09, 2022 |
| Contact name |
Wen Tang |
| E-mail(s) |
tang.542@osu.edu
|
| Organization name |
The Ohio State University
|
| Department |
Department of Biological Chemistry and Pharmacology
|
| Street address |
1060 Carmack Rd
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
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| Platforms (3) |
| GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
| GPL21214 |
Illumina HiSeq 2500 (Caenorhabditis briggsae) |
| GPL29990 |
Illumina NovaSeq 6000 (Caenorhabditis briggsae) |
|
| Samples (12)
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| GSM6166102 |
C. briggsae PRG-1 input replicate 2 |
| GSM6166103 |
C. briggsae smRNA sequencing wild type replicate 1 |
| GSM6166104 |
C. briggsae smRNA sequencing wild type replicate 2 |
| GSM6166105 |
C. briggsae smRNA sequencing prg-1 replicate 1 |
| GSM6166106 |
C. briggsae smRNA sequencing prg-1 replicate 2 |
| GSM6166107 |
C. elegans smRNA sequencing wild type replicate 1 |
| GSM6166108 |
C. elegans smRNA sequencing wild type replicate 2 |
| GSM6166109 |
C. elegans smRNA sequencing prg-1 replicate 1 |
| GSM6166110 |
C. elegans smRNA sequencing prg-1 replicate 2 |
|
| Relations |
| BioProject |
PRJNA839379 |
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