Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila melanogaster genome

Transposable elements (TEs) are genetic parasites that can potentially threaten the stability of the genomes they colonize. Nonetheless, TEs persist within genomes and are rarely fully eliminated, diverse TE families coexisting in various copy numbers. The TE replication strategies that enable host organisms to tolerate and accommodate the extensive diversity of TEs, while minimizing harm to the host and avoiding mutual competition among TEs, remain poorly understood. Here, by studying the spontaneous or experimental mobilization of four Drosophila LTR RetroTransposable Elements (LTR-RTEs), we reveal that each of them preferentially targets open chromatin regions characterized by specific epigenetic features. Among these, gtwin and ZAM are expressed in distinct cell types within female somatic gonadal tissues and inserted into the distinct accessible chromatin landscapes of the corresponding stages of embryogenesis. These findings suggest that individual LTR-RTEs exploit unique biological niches, enabling their coexistence within the tightly regulated ecosystem of the same host genome. For ther ATAC-seq, Purified PGC cells and somatic cells by flow cytometry. ATAC-Seq experiments were performed using the ATAC-Seq kit from Diagenode (catalogue no. C01080002). Input material was between 100,000 to 130,000 cryopreserved PGCs (GFP positive) cells or somatic (GFP negative) cells isolated from whole embryos. For Small-RNA sequencing, Small RNAs from ovaries collected at permissive (25°C) and non-permissive (20°C) temperature, for Piwi-sKD, were isolated using TraPR ion exchange spin columns (Lexogen, Catalog Nr.128.08). The libraries were performed by MGX-Biocampus Montpellier plateform using the NEBNext® Small RNA Library Prep Set for Illumina® from NEB. 150 nt paired-end read (28 bp for R1 and 90 bp for R2) sequencing on NOVASEQ 6000 apparatus was performed by MGX. Only the R2 file contains informations.