Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse Anti-beta Actin Monoclonal Antibody, HRP Conjugated, Clone AC-15 | Abcam | Cat# ab49900, RRID:AB_867494 |
| Peroxidase-AffiniPure Goat Anti-Rabbit IgG (H+L) (min X Hu,Ms,Rat Sr Prot) antibody | Jackson Immunoresearch Labs. | Cat# 111-035-144, RRID:AB_2307391 |
| Rabbit Anti-ALG-1 polyclonal antibody | (Vasquez-Rifo et al., 2012) | N/A |
| Rabbit Anti-AIN-1 polyclonal antibody | (Jannot et al., 2016) | N/A |
| Rabbit Anti-DCR-1 polyclonal antibody | (Duchaine et al., 2006) | N/A |
| Mouse Anti-Ubiquitin Antibody (P4D1) monoclonal antibody | Santa Cruz | Cat# sc-8017, RRID:AB_628423 |
| Mouse Anti-HA.11 Monoclonal Antibody, Unconjugated, Clone 16B12 | Covance | Cat# MMS-101P-500, RRID:AB_291261 |
| IRDye 800CW Goat anti-Mouse IgG | Li-Cor Biosciences | Cat# 925-32210, RRID: AB_2687825 |
| Bacterial and virus strains | ||
| E. coli strain: OP50 | Caenorhabditis Genetics Center | CGC: OP50, RRID: WB-STRAIN:WBStrain00041969 |
| E. coli strain: HT115(DE3) | Caenorhabditis Genetics Center | CGC: HT115(DE3), RRID: WB-STRAIN:WBStrain00041080 |
| Chemicals, peptides, and recombinant proteins | ||
| Biotin-MFTNQLQRISNDAGMPIV-OH | This study | N/A |
| Biotin-MFTNQLQRIANDAGMPIV-OH | This study | N/A |
| Firefly D-Luciferin | PJK GmbH | Cat# 102111 |
| MG-132 | Sigma-Aldrich | Cat# 474790 |
| Tri Reagent | Sigma-Aldrich | Cat# T9424 |
| Critical commercial assays | ||
| TaqMan Universal PCR Master Mix, no AmpErase UNG | Thermo Fisher Scientific | Cat# 4324018 |
| Taqman MicroRNA Assay | Thermo Fisher Scientific | Cat# 4440886 |
| Q5 Site-Directed Mutagenesis Kit | New England Biolabs | Cat# E0554S |
| Dynabeads M-280 Streptavidin | Thermo Fisher Scientific | Cat# 11205D |
| Dynabeads Protein G for Immunoprecipitation | Thermo Fisher Scientific | Cat# 10004D |
| Anti-FLAG M2 Magnetic Beads | Sigma Aldrich | Cat# M8823 |
| High-Capacity cDNA Reverse Transcription Kit | Thermo Fisher Scientific | Cat# 4368814 |
| Edit-R tracrRNA | Horizon Discovery | Cat# U-002005 |
| Edit-R crRNA | Horizon Discovery | Cat# Custom0280 |
| QIAseq miRNA Library Kit | Qiagen | Cat# 331505 |
| Takyon No Rox SYBR MasterMix dTTP Blue | Eurogentec | Cat# UF-NSMT-B0701 |
| Deposited data | ||
| Small RNA sequencing reads from Caenorhabditis elegans adult worms (total RNA and ALG-1 IP) | This study | GEO: GSE198352 |
| Small RNA sequencing reads at different time points during larval development | This study | GEO: GSE174368 |
| Experimental models: Cell lines | ||
| Human: HEK293T cells | ATCC | RRID:CVCL_0063 |
| Experimental models: Organisms/strains | ||
| Strain N2 Bristol (WT) | Caenorhabditis Genetics Center | CGC: N2, RRID:WB-STRAIN:WBStrain00000001 |
| Strain VC446: alg-1(gk214) X | Caenorhabditis Genetics Center | CGC: VC446, RRID: WB-STRAIN: WBStrain00035775 |
| Strain KG532: kin-2(ce179) X | Caenorhabditis Genetics Center | CGC: KG532, RRID:WB-STRAIN:WBStrain00023482 |
| Strain MJS218: alg-1(gk214) Ex[alg-1p::lambdaN::mCherry::alg-1::alg-1 3'UTR; prf4(rol-6(su1006))] | (Quévillon Huberdeau et al., 2017) | N/A |
| Strain MJS258: alg-1(gk214) Ex[λN::mcherry::alg-1(S642E); prf4(rol-6(su1006))] | This paper | N/A |
| Strain MJS259: alg-1(gk214) Ex[λN::mcherry::alg-1(S642A); prf4(rol-6(su1006))] | This paper | N/A |
| Strain MJS275: alg-1(qbc23[S642A]) X | This paper | N/A |
| Strain MJS306: alg-1(qbc46[S642E]) X | This paper | N/A |
| Strain HW1939: xeSi296[Peft-3::luc::gfp::unc-54 3'UTR, unc-119(+)] II | (Meeuse et al., 2020) | N/A |
| Strain HW3060: xeSi296[Peft-3::luc::gfp::unc-54 3'UTR, unc-119(+)] II; alg-1(qbc23[S642A]) X | This paper | N/A |
| Strain HW3061: xeSi296[Peft-3::luc::gfp::unc-54 3'UTR, unc-119(+)] II; alg-1(qbc46[S642E]) X | This paper | N/A |
| Strain MJS237: qbcSi03[Palg-1::GFP::cog-1-boxb-cb-unc-19(+)] IV; alg-1(qbc18[lambdaN::alg-1]) X | (Quévillon Huberdeau et al., 2017) | N/A |
| Strain MJS345: qbcSi03[alg-1p::GFP::cog-1-boxb;cb-unc-119(+)] IV; alg-1(qbc66[λN::alg-1(S642E)] X | This paper | N/A |
| Strain MJS349: qbcSi03[alg-1p::GFP::cog-1-boxb;cb-unc-119(+)] IV; alg-1(qbc67[λN::alg-1(S642A)] X | This paper | N/A |
| Strain MJS446: alg-2(ok304) II; kin-2(qbc92[R92C]) X | This paper | N/A |
| Strain MJS 447: alg-2(ok304) II; kin-2(qbc92[R92C]) alg-1(qbc67[S642A]) X | This paper | N/A |
| Oligonucleotides | ||
| Primers used for cloning are listed in Table S2. | This study | N/A |
| CRISPR RNA and repair templates to generate alg-1(S642A), alg-1(S642E), alg-1(Y693E) and kin-2(R92C) are listed in Table S2. | This study | N/A |
| Primers for RT-qPCR are listed in Table S2. | This study | N/A |
| Recombinant DNA | ||
| Plasmid L4440: untargeted RNAi vector | Addgene | Cat# 1654 |
| Plasmid MSP163: RNAi vector targeting alg-2 | (Bouasker and Simard, 2012) | N/A |
| Plasmid MSP437: RNAi vector targeting kin-2 | This paper | N/A |
| Plasmid MSP186: alg-1p::lambdaN::mCherry::alg-1::alg-1 3'UTR | Jannot et al. 2016 | N/A |
| Plasmid MSP438: alg-1p::lambdaN::mCherry::alg-1(S642A)::alg-1 3'UTR | This study | N/A |
| Plasmid MSP439: alg-1p::lambdaN::mCherry::alg-1(S642E)::alg-1 3'UTR | This study | N/A |
| Software and algorithms | ||
| Bowtie (version 0.12.7) | Langmead, B. et al, 2009 | http://bowtie-bio.sourceforge.net/index.shtml |
| Bowtie (version 1.2.2) | Langmead, B. et al, 2009 | http://bowtie-bio.sourceforge.net/index.shtml |
| Cutadapt (version 2.3) | Martin,M. et al., 2011 | https://cutadapt.readthedocs.io/en/v2.3/ |
| Samtools (version 1.9) | Li, H. et al, 2009 | https://sourceforge.net/projects/samtools/files/samtools/1.9/ |
| HTSeq (version 0.11.2) | Anders, S. et al, 2015 | https://htseq.readthedocs.io/en/master/ |
| Image Lab | Bio-Rad | https://www.bio-rad.com/en-ca/product/image-lab-software?ID=KRE6P5E8Z |
| Other | ||
| Breathable sealing membrane (Breathe-EASIER) | Diversified Biotech | Cat# BERM-2000 |
| Luminometer | Berthold Technologies | Centro XS3 LB 960 |
| Gel Imaging System | Bio-Rad | ChemiDoc XRS+ System |