KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| HA antibody | Sigma-Aldrich | H9658 |
| Tubulin antibody | Developmental Studies Hybridoma Bank | E7 |
| Cy3 affiniPure Goat Anti-Mouse IgG (H+L) | Jackson Immunoresearch Laboratories | 115–165-003 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| TRIzol Reagent | Thermoisher Scientific | 15596026 |
| Hybridase Thermostable RNaseH | Lucigen | H39500 |
| TURBO DNase | ThermoFisher Scientific | AM2238 |
| Proteinase K | Agilent | S3004 |
| 5Prime Phase Lock Gel-Heavy | QuantaBio | 2302830 |
| Triton X-100 | Sigma-Aldrich | X100–500ML |
| PMSF | Roche | 10837091001 |
| HALT Protease | ThermoFisher Scientific | 78430 |
| S.P. Cas9 Nuclease V3 | Integrated DNA Technologies | 1081058 |
| Indole-3-acetic acid | Alfa Aesar | A10556 |
| GlycoBlue | ThermoFisher Scientific | AM9515 |
| RNA 5’ Pyrophosphohydrolase | New England Biolabs | M0356S |
| Cap-Clip Acid Pyrophosphatase | CellScript | C-CC15011H |
| T4 polynucleotide kinase | New England Biolabs | MS201S |
| CircLigase ssDNA Ligase | Lucigen | CL4111K |
| Critical Commercial Assays | ||
| SMARTer Stranded RNA-seq | Clontech, Takara | 634838 |
| TruSeq Small RNA Kit | Illumina | RS-200–0012 |
| Nextera DNA Library Preparation Kit | Illumina | MS-102–2001 |
| Nextera XT DNA Library Preparation Kit | Illumina | FC-131–1024 |
| Agencourt Ampure XP | Beckman Coulter | A63880 |
| Qubit dsDNA HS Assay Kit | ThermoFisher Scientific | Q32851 |
| MiSeq Reagent Kit v3 (150-cycle) | Illumina | MS-102–3001 |
| MiSeq Reagent Kit v2 (50-cycle) | Illumina | MS-102–2001 |
| Deposited Data | ||
| All Sequencing Data | This Study | PRJNA724702 |
| Experimental Models: Organisms/Strains | ||
| C. elegans strain: VC2010 (wildtype) | Authors’ lab | PD1074 |
| C. elegans strain: prg-1(cc3504)I | This study | PD3504 |
| C. elegans strain: unc-119(ed3)l ieSi38[Psun-1::TIR1::mRuby::sim-1 3’UTR, cb-unc-119(+)] IV | Caenorhabditis Genetics Center | CA1199 |
| C. elegans strain: prg-1(cc3522[Flag-HA::prg-1])IV; rol-6 (cc3522–2) | This study | PD3522 |
| C. elegans strain: prg-1 (cc3504)I; unc-119(ed3)l; ieSi38[Psun-1::TIR1::mRuby::sim-1 3’UTR, cb-unc-119(+)] IV | This study | PD3523 |
| C. elegans strain: prg-1(cc3504)I suppressor strain with drh-3[S884F] | This study | PD3543 |
| C. elegans strain: prg-1(cc3504)I suppressor strain with rrf-1[R365L] | This study | PD3548 |
| C. elegans strain: prg-1(cc3504)I suppressor strain with ppw-2[E625K] | This study | PD7401 |
| C. elegans strain: prg-1(cc3504)I suppressor strain with hrde-1[Q887Ter] | This study | PD7403 |
| C. elegans strain: prg-1(cc3504)I suppressor strain with hrde-1[Q887Ter] | This study | PD7404 |
| C. elegans strain: prg-1(cc3504)I suppressor strain with dcr-1[S689L] | This study | PD7405 |
| C. elegans strain: prg-1(cc3504)I suppressor strain with pup-1[T1002I] | This study | PD7409 |
| C. elegans strain: prg-1(cc3504)I suppressor strain with pup-2[S689L] | This study | PD7410 |
| C. elegans strain: prg-1(cc3504)I; dcr-1(cc7411)III | This study | PD7415 |
| C. elegans strain: prg-1(cc3504); pup-1(cc7426)III | This study | PD7426 |
| C. elegans strain: prg-1(cc3504)I; hrde-1(cc7420)III | This study | PD7427 |
| C. elegans strain: prg-1(cc3504)I; pup-2(cc7421)III | This study | PD7428 |
| C. elegans strain: eDp20(I;II) | William Schafer, MRC | CB3680 |
| C. elegans strain: wildtype | This study; generated from cross of CB3680 and PD3504 | PD7436 |
| C. elegans strain: eDp20(I;II) | This study; generated from cross of CB3680 and PD3504 | PD7439 |
| C. elegans strain: prg-1(cc3504) I | This study; generated from cross of CB3680 and PD3504 | PD7440 |
| C. elegans strain: prg-1(cc3504) I; eDp20 (I;II) | This study; generated from cross of CB3680 and PD3504 | PD7442 |
| C. elegans strain: ccTi1594[Pmex-5 GFP-gpr-1 smu-1 UTR, cb-unc-119(+), III:680195], unc-119(ed3) III; hjSi20 [myo-2::mCherry::unc-54 UTR] IV. | Authors’ lab | PD2217 |
| C. elegans strain: ccTi1594[Pmex-5 GFP-gpr-1 smu-1UTR, cb-unc-119(+), III:680195] III; umnIs7 [myo-2p::GFP + NeoR, III:9421936] III; prg-1 I. | This study | PD3547 |
| C. elegans strain: unc-119(ed3); ieSi38[Psun-1::TIR1::mRuby::sim-1 3’UTR, cb-unc-119(+)] IV; ccTi1594[Pmex-5 GFP-gpr-1 smu-1UTR, cb-unc-119(+), III:680195] III; umnIs7 [myo-2p::GFP + NeoR, III:9421936] III. ; AID-Flag-HA::prg-1 | This study | PD7399 |
| Software and Algorithms | ||
| Integrative Genome Viewer, v2.3.92 | http://www.broadinstitute.org/igv/ | RRID:SCR_011793 |
| Tophat2 | http://ccb.jhu.edu/software/tophat/index.shtml | RRID:SCR_013035 |
| BWA | http://bio-bwa.sourceforge.net/ | RRID:SCR_010910 |
| cutadapt 2.0 | https://cutadapt.readthedocs.io/en/stable/index.html | RRID:SCR_011841 |
| RStudio 0.98.501 | https://www.rstudio.com/ | RRID:SCR_000432 |
| SAMtools | http://samtools.sourceforge.net/ | RRID:SCR_002105 |
| featureCounts | http://subread.sourceforge.net/ | RRID:SCR_012919 |
| BEDtools | https://github.com/arq5x/bedtools2 | RRID:SCR_006646 |
| Custom Code | N/A | |