KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Histone H3 (tri methyl K9) antibody - ChIP Grade | Abcam | Cat# 8898, Lot# GR285794-2;RRID: AB_306848 |
| Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade | Abcam | Cat# ab5095, Lot# GR231750-1; RRID: AB_304749 |
| Bacterial and Virus Strains | ||
| E. coli OP50 | CGC | NA |
| E. coli HT115(DE3) | CGC | NA |
| Chemicals, Peptides, and Recombinant Proteins | ||
| FORMALDEHYDE 37% MICROFILTERED | Electron Microscopy Sciences | Cat# 15686 |
| TRIzol-REAGENT | Invitrogen | Cat# 15596-018 |
| RNA Fragmentation Reagents | Invitrogen | Cat# AM8740 |
| T4 PNK | NEB | Cat# M0201L |
| T4 RNA Ligase 1 | NEB | Cat# M0204S |
| T4 RNA ligase 2, truncated | NEB | Cat# M0242L |
| Critical Commercial Assays | ||
| KAPA Hyper Prep Kit | KAPABIOSYSTEM | Cat# KK8505 |
| KAPA SYBR FAST Universal 2 × PCR Master Mix | KAPABIOSYSTEM | Cat# KK4602 |
| Deposited Data | ||
| NGS data | This study | NGS: GSE117662 |
| Experimental Models: Organisms/Strains | ||
| C. elegans Bristol strain | CGC | N2 |
| set-32(ok1457) I | (C. elegans Deletion Mutant Consortium, 2012) | VC967 |
| set-32(red11) I | This study | CSS186 |
| nrde-2(gg091) II | (Guang et al., 2010) | YY186 |
| met-2(n4256) III | (Andersen and Horvitz, 2007) | MT13293 |
| hrde-1(tm1200) III | (C. elegans Deletion Mutant Consortium, 2012) | TM1300 |
| set-25(n5021) III | (Andersen and Horvitz, 2007) | MT17463 |
| set-26(tm3526) IV | (C. elegans Deletion Mutant Consortium, 2012) | TM3526 |
| set-9(red8) IV | (Kalinava et al., 2017) | CSS164 |
| set-26(tm3526) set-9(red8) | this study | CSS412 |
| set-32(red11); hrde-1(tm1200) | this study | CSS425 |
| met-2(n4256) set-25(n5021) | (Kalinava et al., 2017) | CSS95 |
| set-32(red11);met-2(n4256) set-25(n5021) | (Kalinava et al., 2017) | CSS419 |
| met-2(n4256) set-25(n5021) hrde-1(tm1200) | this study | CSS400 |
| set-32(red11);met-2(n4256) set-25(n5021) hrde-1(tm1200) | this study | CSS415 |
| Oligonucleotides | ||
| forward qPCR primer for oma-1 mRNA: ctacaggactctgcccatacg | IDT | SG-1016 |
| reverse qPCR primer for oma-1 mRNA: ggcctggcaaacatttctaa | IDT | SG-1019 |
| forward qPCR primer for oma-1 pre-mRNA:ttaatgacc tctgttttaggtg | IDT | SG-1022 |
| reverse qPCR primer for oma-1 pre-mRNA:gaacccaaaa ccatcgaatc | IDT | SG-1023 |
| forward qPCR primer for oma-1 ChIP: acatgtatttttgctcactgtaa | IDT | SG-1018 |
| reverse qPCR primer for oma-1 ChIP: ggcctggcaaacatttctaa | IDT | SG-1019 |
| forward ChIP qPCR primer for an H3K9me3 negative control locus: agccatggcacaaaaagaag | IDT | SG-1044 |
| reverse ChIP qPCR primer for an H3K9me3 negative control locus: tgtggcctgagaagacaaaa | IDT | SG-1045 |
| forward qPCR primer for tba-1 mRNA: TCCAAGCGAG ACCAGGCTTCAG | IDT | SG-1108 |
| reverse qPCR primer for tba-1 mRNA: TCAACACTGCCAT CGCCGCC | IDT | SG-1109 |
| HR oligo for set-32 (red11) CRISPR allele): tcttcgaatatacagacacg aatgttttgaacccgGCTAGCAtgctccgcaagaaacattgcgaaagcatgta ttatgtctcaaaaggaagagaat | IDT | SG-1173 |
| T7 in vitro transcription template oligo for crRNA targeting hrde-1 tm1200 mutation (seed sequence: taatcgtatgTggaaaccg): AAAACAGCATAGCTCTAAAAC cggtttccAcatacgatta CCCTATAGTGAGTCGTATTA | IDT | SG-1285 |
| upstream PCR primer used to generated a 424 bp genomic DNA fragment as template DNA to repair the hrde-1 (tm1200) mutation by CRISPR: aaggagaagttgcccaggag | IDT | SG-1292 |
| downstream PCR primer used to generated a 424 bp genomic DNA fragment as template DNA to repair the hrde-1(tm1200) mutation by CRISPR: atctcggtacctgtcgttgc | IDT | SG-1293 |
| Recombinant DNA | ||
| oma-1 dsRNA feeding plasmid | (Kalinava et al., 2017) | pSG42 |
| Software and Algorithms | ||
| Bowtie 0.12.7 | (Langmead et al., 2009) | NA |