Two parallel pathways recruit the H3K9me3 HMT in somatic cells, requiring the Argonaut NRDE-3, or the MBT-domain protein, LIN-61 (smallRNA-seq)

The establishment and maintenance of chromatin domains shape the epigenetic memory of a cell, with histone H3 lysine 9 methylation defining repressed heterochromatin. We show that in C. elegans the SET-25 (SUV39/G9a) HMT that catalyzes H3K9me1-3, is able to establish repressed domains de novo. We identify here two distinct pathways that recruit SET-25 to its targets. One requires LIN-61 (L3MBTL2), a conserved protein with 4 MBT domains that recognizes H3K9me2 deposited by the HMT MET-2 (SETDB1). The second pathway is MET-2-independent and requires a somatic Argonaut NRDE-3 and 22nt small nuclear RNAs. This NRDE-3 pathway targets ~10% of all SET-25-modified loci genome-wide including intact RNA and DNA transposons. Removal of both pathways in the met-2;nrde-3 double mutant synergistically derepresses transposons in early embryos and elevates embryonic lethality. The redundancy of these pathways illustrates the key role played by chromatin-mediated silencing in protecting the genome against inherent threats. Small RNA purification from early embryos was performed using the Norgen Single Cell RNA purification kit (51800). Total small RNA was treated with 1 mlTAP (Lucigen) for 1h at 37°C, to allow sequencing of all small RNA species. Library preparation including size selection was performed using the QiaSeq miRNA library. Single-end 50-bp reads were generated using an Illumina HiSeq 2500. Adapter sequences were removed using the fastx_clipper and collapsed using the fastx_collapser functions implemented in the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The R package QuasR was used to map reads to the C. elegans genome (WS220), normalized to total number of reads and subsequently subseted according to read lengths.