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. Overall design: 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.