Complex Genetic Interactions between Piwi and HP1a in the Repression of Transposable Elements and Tissue-Specific Genes in the Ovarian Germline

Abstract

Insertions of transposable elements (TEs) in eukaryotic genomes are usually associated with repressive chromatin, which spreads to neighbouring genomic sequences. In ovaries of Drosophila melanogaster, the Piwi-piRNA pathway plays a key role in the transcriptional silencing of TEs considered to be exerted mostly through the establishment of H3K9me3 histone marks recruiting Heterochromatin Protein 1a (HP1a). Here, using RNA-seq, we investigated the expression of TEs and the adjacent genomic regions upon Piwi and HP1a germline knockdowns sharing a similar genetic background. We found that the depletion of Piwi and HP1a led to the derepression of only partially overlapping TE sets. Several TEs were silenced predominantly by HP1a, whereas the upregulation of some other TEs was more pronounced upon Piwi knockdown and, surprisingly, was diminished upon a Piwi/HP1a double-knockdown. We revealed that HP1a loss influenced the expression of thousands of protein-coding genes mostly not adjacent to TE insertions and, in particular, downregulated a putative transcriptional factor required for TE activation. Nevertheless, our results indicate that Piwi and HP1a cooperatively exert repressive effects on the transcription of euchromatic loci flanking the insertions of some Piwi-regulated TEs. We suggest that this mechanism controls the silencing of a small set of TE-adjacent tissue-specific genes, preventing their inappropriate expression in ovaries.

What Are the Functional Roles of Piwi Proteins and piRNAs in Insects?

“…RNAi-mediated knockdown of Piwi, Aub or Ago3 does not affect strongly oogenesis although follicles degenerate in Aub/Ago3 double mutants at the late stage [ 34 , 41 ]. However, specific knockdown of Aub and Ago3 in the female germline causes female sterility and disruption of embryonic axis formation [ 33 , 42 ].…”

“…Another mechanism by which Piwi can regulate gene expression is by the spreading of repressive chromatin marks from transposon insertions into neighboring cellular genes [ 41 ]. Since genes that are adjacent to transposable elements show higher expression in ovaries than in other tissues, Piwi may also function to prevent the ectopic transcription of inappropriate genes that occurs concomitantly with the transcriptional silencing of mobile elements [ 41 ].…”