Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis

Abstract

The PIWI-interacting RNA (piRNA) pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. In Drosophila, piRNAs are intergenerationally inherited through the maternal lineage, and this has demonstrated importance in the specification of piRNA source loci and in silencing of I- and P-elements in the germ cells of daughters. Maternally inherited Piwi protein enters somatic nuclei in early embryos prior to zygotic genome activation and persists therein for roughly half of the time required to complete embryonic development. To investigate the role of the piRNA pathway in the embryonic soma, we created a conditionally unstable Piwi protein. This enabled maternally deposited Piwi to be cleared from newly laid embryos within 30 minutes and well ahead of the activation of zygotic transcription. Examination of RNA and protein profiles over time, and correlation with patterns of H3K9me3 deposition, suggests a role for maternally deposited Piwi in attenuating zygotic transposon expression in somatic cells of the developing embryo. In particular, robust deposition of piRNAs targeting roo, an element whose expression is mainly restricted to embryonic development, results in the deposition of transient heterochromatic marks at active roo insertions. We hypothesize that roo, an extremely successful mobile element, may have adopted a lifestyle of expression in the embryonic soma to evade silencing in germ cells.

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

“…The 297 element was shown to be especially active in embryos where it is regulated by Piwi-induced H3K9me3 deposition [24]. Insertions of 297 are also associated with H3K9me3 in ovaries, albeit to a lesser extent compared to embryos [24]. These data suggest that these TEs can be targeted by piRNAs produced specifically in somatic tissues, where they are capable of the strongest transcription.…”

“…Our results indicate that piRNA-independent targeting of TEs by HP1a can also operate in ovarian germ cells given that some TEs are upregulated upon HP1a-or double-GKD but not upon Piwi loss (Figure S4). Interestingly, the H3K9me3 marks deposited at the roo element by the piRNA pathway in Drosophila embryos have been shown to not be epigenetically inherited during the subsequent cell divisions, making unlikely the possibility that the repressive chromatin state can be established by Piwi, and then is maintained by HP1a in a Piwi-independent manner [24]. To our knowledge, apart from piRNAs, no other molecular mechanisms by which euchromatic TE insertions in Drosophila can be recognised and repressed at the chromatin level have been described so far.…”

“…Interestingly, the highest transcription levels of the 297 and 412 TEs were previously observed in somatic tissues [24,56,57]. The 297 element was shown to be especially active in embryos where it is regulated by Piwi-induced H3K9me3 deposition [24]. Insertions of 297 are also associated with H3K9me3 in ovaries, albeit to a lesser extent compared to embryos [24].…”

“…It should be noted that insertions of 297 and 412 are highly abundant: in the euchromatin of the analysed genome, we found 51 and 46 insertions of the 297 and 412 elements, respectively (Table S3). Interestingly, the highest transcription levels of the 297 and 412 TEs were previously observed in somatic tissues [24,56,57]. The 297 element was shown to be especially active in embryos where it is regulated by Piwi-induced H3K9me3 deposition [24].…”

“…Despite the fact that TEs occupy a smaller part of the Drosophila melanogaster genome, they are extremely diverse in this organism, belonging to more than 120 families constituting three main groups: LINE and LTR retrotransposons and DNA transposons (for review, see References [22,23]). Different TE families are characterised by distinct temporal and spatial patterns of expression and transposition activity, which, in turn, can determine the differences in the mechanisms aimed at their regulation [24][25][26][27][28]. TEs tend to be especially active in gonadal cells, which is required for the implementation of their biological strategy to infect the genomes of gametes and thereby transfer new TE copies to the next generation of host organisms.…”