Transposable elements (TE) are DNA sequences that are ubiquitous in eukaryotes, constituting about half of the eukaryotic genome. TEs replicate and insert their sequence into other loci of the genome to increase their copy number. Because of this potentially harmful action, TE expression is normally suppressed through the host defence pathways.
A body of research revealed that TEs become activated, for example, due to changes in epigenetic status of the chromatin upon differentiation, stress, and oncogenesis. A number of diseases, such as neurological and inflammatory diseases and a variety of cancers are attributed to uncontrolled expression of TEs. However, the molecular effects of TE activation and whether and how it causes diseases remain unclear.
piRNA pathway is an evolutionarily conserved defence mechanism against TEs. Effector proteins Argonaute, which are loaded with small RNA called piRNA, bind TE mRNA to silence its expression. In fruit flies, piRNA pathway is active in ovarian somatic cells and is required for silencing ~15 different gypsy-class LTR retrotransposons. Defective piRNA pathway causes female sterility and severe morphological abnormalities in ovary development. One can deplete piRNA pathway genes in a cell-type specific manner or use tissue culture cells derived from ovarian somatic cells (OSCs) to specifically study the effect of TE overexpression in the relevant cell type. In this study, we individually depleted ~20 piRNA pathway genes in OSCs and measured the impact of TE activation on the host gene expression by High-throughput RNA sequencing. The panel of knockdown led to a varying degree of TE activation, which allowed us to extract host genes whose expression co-variates with those of TEs. Through this analysis, we built a gene network that is associated with TE activation and predicted how TE activation leads to morphological defects in ovaries. We also discuss the caveats of measuring TE expression from RNA sequencing data along with host mRNAs and how various quality control filters influence the gene network analysis.