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Series GSE135440 Query DataSets for GSE135440
Status Public on Aug 07, 2019
Title PIWI-piRNA pathway mediated transposon repression in Hydra somatic stem cells
Organism Hydra vulgaris
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Transposable elements (TEs) can damage genomes, thus organisms employ a variety of mechanisms to repress TE expression. The PIWI-piRNA pathway is a small RNA pathway that represses TE expression in the germline of animals. Here we explore the function of the pathway in the somatic stem cells of Hydra, a long-lived freshwater cnidarian. Hydra have three stem cell populations, all of which express PIWI proteins; endodermal and ectodermal epithelial stem cells are somatic, whereas the interstitial stem cells have germline competence. To study somatic function of the pathway we isolated piRNAs from Hydra that lack the interstitial lineage and found that these somatic piRNAs map predominantly to TE transcripts and display the conserved sequence signatures typical of germline piRNAs. Three lines of evidence suggest that the PIWI-piRNA pathway represses TEs in Hydra epithelial stem cells. First, epithelial knockdown of the Hydra piwi gene hywi resulted in upregulation of TE expression. Second, degradome sequencing revealed evidence of PIWI-mediated cleavage of TE RNAs in epithelial cells using the ping-pong mechanism. Finally, we demonstrated a direct association between Hywi protein and TE transcripts in epithelial cells using RNA immunoprecipitation. Altogether, our data reveal that the PIWI-piRNA pathway represses TE expression in the somatic cell lineages of Hydra, which we propose contributes to the extreme longevity of the organism. Furthermore, our results, in combination with others, suggest that somatic TE repression is an ancestral function of the PIWI-piRNA pathway.
Overall design Differential gene expression analysis (mRNA-seq) comparing hywi knockdown and wildtype Hydra. Analysis of tissue/cell lineage specific piRNA expression. Degradome sequencing for homeostatic Hydra and epithelialized Hydra.
Contributor(s) Teefy BB, Juliano CE, Siebert S
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Submission date Aug 06, 2019
Last update date Jan 13, 2020
Contact name Celina E Juliano
Organization name University of California Davis
Department MCB
Lab Julianolab
Street address 149 Briggs Hall
City Davis
State/province California
ZIP/Postal code 95616
Country USA
Platforms (2)
GPL25712 Illumina HiSeq 4000 (Hydra vulgaris)
GPL27013 Illumina HiSeq 2000 (Hydra vulgaris)
Samples (12)
GSM4009028 Replicate 1 - hywi knockdown
GSM4009029 Replicate 2 - hywi knockdown
GSM4009030 Replicate 3 - hywi knockdown
BioProject PRJNA558896
SRA SRP217531

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE135440_Degradome_Counts_Matrix.txt.gz 126.9 Kb (ftp)(http) TXT
GSE135440_Differential_Gene_Expression_Count_Matrix.txt.gz 580.5 Kb (ftp)(http) TXT
GSE135440_piRNA_Counts_Matrix.txt.gz 1000.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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