The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells

Abstract

PIWI proteins and PIWI-interacting RNAs (piRNAs) play a central role in repressing transposable elements in animal germ cells. It is thought that piRNAs are mainly produced from discrete genomic loci named piRNA clusters, which often contain many “dead” transposon remnants from past invasions and have heterochromatic features. In the genome of silkworm ovary-derived cultured cells called BmN4, a well-established model for piRNA research, torimochi was previously annotated as a unique and specialized genomic region that can capture transgenes and produce new piRNAs bearing a trans-silencing activity. However, the sequence identity of torimochi has remained elusive. Here, we carefully characterized torimochi by utilizing the updated silkworm genome sequence and the long-read sequencer MinION. We found that torimochi is in fact a full-length gypsy-like LTR retrotransposon, which is exceptionally active and has massively expanded its copy number in BmN4 cells. Many copies of torimochi in BmN4 cells have features of open chromatin and the ability to produce piRNAs. Therefore, torimochi may represent a young, growing piRNA cluster, which is still “alive” and active in transposition yet capable of trapping other transposable elements to produce de novo piRNAs. (185 words)

Autonomous Shaping of the piRNA Sequence Repertoire by Competition between Adjacent Ping-Pong Sites

“…When analyzing our previous small RNA sequencing data derived from silkworm BmN4 cells 15,26 , we noticed that some but not all piRNAs show different production patterns depending on when the libraries were constructed. To gain a precise understanding of this observation, we decided to conduct a comparative analysis of small RNA sequencing data from two sibling BmN4 cell lines that were 7 years apart; one cell line, Naive20, was continuously cultured from 2013 to 2020, while the other cell line, Naive13, was stored in a deep freezer during that entire period (Figure 1A).…”

“…When analyzing our previous small RNA sequencing data derived from silkworm BmN4 cells 15,26 , we noticed that some but not all piRNAs show different production patterns depending on when the libraries were constructed.…”

“…Deep sequencing data obtained in this study are accessible through the provided accession number DRA017494 (DDBJ). The Drosophila P element piRNA and DNA sequences (SRP007937) were reported previously 26 .…”

A potential role of inefficient and non-specific piRNA production from the whole transcriptome

“…We envision that the primitive piRNA biogenesis pathway initiates this adaptation process by generating a small pool of piRNAs de novo. These primitive piRNAs can then act as the seed for the ping-pong and phased piRNA pathways as long as both sense and antisense transcripts are abundantly available, perhaps even before the new transposons are captured by piRNA clusters for established silencing (30)(31)(32)(33)(34). In this way, the primitive piRNA biogenesis pathway may act as a primitive sensor for aberrantly abundant transcripts in the germline.…”

The sixth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements

“…When the cells were in vitro differentiated into non-gonadal cells (i.e., adipocytes), the expression of torimochi decreased, whereas other TEs were derepressed. Taken together, they proposed that torimochi , an unfragmented active transposon, integrates with a BmN4-specific activation mechanism and serves as a model for nascent piRNA cluster formation [ 11 ].…”