Characterization of factors that underlie transcriptional silencing in C. elegans oocytes.

While it has been appreciated for decades that prophase-arrested oocytes are transcriptionally silenced on a global level, the molecular pathways that promote silencing have remained elusive. Previous work in C. elegans has shown that both topoisomerase II (TOP-2) and condensin II collaborate with the H3K9me heterochromatin pathway to silence gene expression in the germline during L1 starvation, and that the PIE-1 protein silences the genome in the P-lineage of early embryos. Here, we show that all three of these silencing systems, TOP-2/condensin II, H3K9me, and PIE-1, are required for transcriptional repression in oocytes. We find that H3K9me3 marks increase dramatically on chromatin during silencing, and that silencing is under cell cycle control. We also find that PIE-1 localizes to the nucleolus just prior to silencing, and that nucleolar dissolution during silencing is dependent on TOP-2/condensin II. Our data identify both the molecular components and the trigger for genome silencing in oocytes and establish a link between PIE-1 nucleolar residency and its ability to repress transcription.

A global chromatin compaction pathway that represses germline gene expression during starvation.

While much is known about how transcription is controlled at individual genes, comparatively little is known about how cells regulate gene expression on a genome-wide level. Here, we identify a molecular pathway in the C. elegans germline that controls transcription globally in response to nutritional stress. We report that when embryos hatch into L1 larvae, they sense the nutritional status of their environment, and if food is unavailable, they repress gene expression via a global chromatin compaction (GCC) pathway. GCC is triggered by the energy-sensing kinase AMPK and is mediated by a novel mechanism that involves the topoisomerase II/condensin II axis acting upstream of heterochromatin assembly. When the GCC pathway is inactivated, then transcription persists during starvation. These results define a new mode of whole-genome control of transcription.

Programmed DNA Breaks Activate the Germline Genome in Caenorhabditis elegans.

In Caenorhabditis elegans, the primordial germ cells Z2 and Z3 are born during early embryogenesis and then held in a transcriptionally quiescent state where the genome is highly compacted. When hatched L1s feed, the germline genome decompacts, and RNAPII is abruptly and globally activated. A previously documented yet unexplained feature of germline genome activation in the worm is the appearance of numerous DNA breaks coincident with RNAPII transcription. Here, we show that the DNA breaks are induced by topoisomerase II and that they function to recruit the RUVB complex to chromosomes so that RUVB can decompact the chromatin. DNA break- and RUVB-mediated decompaction is required for zygotic genome activation. This work highlights the importance of global chromatin decompaction in the rapid induction of gene expression and shows that one way cells achieve global decompaction is through programmed DNA breaks.