Somatic piRNAs and Transposons are Differentially Expressed Coincident with Skeletal Muscle Atrophy and Programmed Cell Death.

Junko Tsuji,Zhiping Weng,Christine Brown,Subhanita Ghosh,Lawrence M Schwartz,William E Theurkauf,Travis Thomson

doi:10.3389/fgene.2021.775369

Abstract

PIWI-interacting RNAs (piRNAs) are small single-stranded RNAs that can repress transposon expression via epigenetic silencing and transcript degradation. They have been identified predominantly in the ovary and testis, where they serve essential roles in transposon silencing in order to protect the integrity of the genome in the germline. The potential expression of piRNAs in somatic cells has been controversial. In the present study we demonstrate the expression of piRNAs derived from both genic and transposon RNAs in the intersegmental muscles (ISMs) from the tobacco hawkmoth Manduca sexta. These piRNAs are abundantly expressed, ∼27 nt long, map antisense to transposons, are oxidation resistant, exhibit a 5’ uridine bias, and amplify via the canonical ping-pong pathway. An RNA-seq analysis demonstrated that 19 piRNA pathway genes are expressed in the ISMs and are developmentally regulated. The abundance of piRNAs does not change when the muscles initiate developmentally-regulated atrophy, but are repressed coincident with the commitment of the muscles undergo programmed cell death at the end of metamorphosis. This change in piRNA expression is correlated with the repression of several retrotransposons and the induction of specific DNA transposons. The developmentally-regulated changes in the expression of piRNAs, piRNA pathway genes, and transposons are all regulated by 20-hydroxyecdysone, the steroid hormone that controls the timing of ISM death. Taken together, these data provide compelling evidence for the existence of piRNA in somatic tissues and suggest that they may play roles in developmental processes such as programmed cell death.

Highlights

Small silencing RNAs are powerful regulators of gene expression
The biogenesis and function of PIWI-interacting RNAs (piRNAs) has been well studied in the fruit fly Drosophila melanogaster (Huang, Fejes Toth et al, 2017). piRNAs are processed from long transcripts that can be up to hundreds of kilobases long that are transcribed from discrete genomic loci termed “piRNA clusters” (Brennecke et al, 2007; Malone et al, 2009; Thomson and Lin 2009). piRNAs are amplified via reciprocal target cleavages by PIWI proteins, a mechanism known as the ping-pong cycle (Brennecke et al, 2007; Gunawardane et al, 2007)
Based on piRNA pathway genes characterized in Drosophila, we identified all 19 of the genes we sought in the intersegmental muscles (ISMs), plus two small RNA biogenesis pathway factors

Summary

Introduction

Small silencing RNAs are powerful regulators of gene expression. They can lead to epigenetic silencing of transcription, transcript degradation, and inhibition of mRNA translation. Because PIWI proteins cleave the phosphodiester bond between the nucleotides in the target RNA that pair with the 10th and the 11th nucleotides of the guide piRNA, and 3′ cleavage products is subsequently made into another piRNA, there is an enrichment of piRNAs that perfectly reverse complement each other in their first 10 nucleotides, the hallmark of the ping-pong cycle This process typically creates piRNAs with a uridine residue as the first nucleotide of the primary piRNA, and complementarity over the first 10 nt of post-transcriptionally amplified piRNAs (Brennecke et al, 2007; Cora et al, 2014; Wang et al, 2014; Stein et al, 2019)

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Results

Conclusion