KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse Anti-Actin Monoclonal Antibody, Unconjugated, Clone AC-40 | Sigma-Aldrich | Sigma-Aldrich Cat# A4700, RRID:AB_476730 |
| Rabbit anti-LIN-28 polyclonal antibody | Eric Moss labSeggerson et al. 2002 | n/a |
| IRDye 800CW Goat anti-Mouse | LI-COR | LI-COR Biosciences Cat# 827-08364, RRID:AB_10793856 |
| IRDye 680RD Goat anti-Rabbit | LI-COR | LI-COR Biosciences Cat# 926-68171, RRID:AB_10956389 |
| Bacterial and Virus Strains | ||
| OP50-1 | RRID:WB-STRAIN:OP50-1 | |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Alt-R® S.p. Cas9 Nuclease | Integrated DNA Technologies (IDT) | Cat#1081058 |
| Restriction enzyme SfiI | New England Biolabs | Cat#R0123S |
| Restriction enzyme AatII | New England Biolabs | Cat#R0117S |
| Critical Commercial Assays | ||
| QuikChangeXL site-directed mutagenesis kit | Agilent Technologies | Cat#200516 |
| Custom Stellaris RNA-FISH probes for lep-5 labeled with Quasar570 (sequences in STAR methods) | Biosearch Technologies | https://www.biosearchtech.com/products/rna-fish |
| Custom Stellaris RNA-Fish probes for lin-44 labeled with Quasar670 (sequences in STAR methods) | Biosearch Technologies | https://www.biosearchtech.com/products/rna-fish |
| RNeasy micro kit | Qiagen | Cat#74004 |
| double-primed RNA to cDNA EcoDry Premix | Takara/Clontech | Cat #639547 |
| iQ SYBR Green Supermix | BioRad | Cat#1708882 |
| GFP-Trap MA and | Chromotek | Cat#gtma-20 |
| Binding control for GFP-Trap MA | Chromotek | Cat#bmab-20 |
| Experimental Models: Organisms/Strains | ||
| C. elegans CB4088 = him-5(e1490)V | CGC | https://cgc.umn.edu/strain/CB4088 |
| C. elegans DF135 = him-5(e1490) V; lep-5(ny10) X | This paper | n/a |
| C. elegans DF137 = him-5(e1490) V; lep-5(ny10) X; fsIs2[Pdmd-3::yfp + CC::GFP] | This paper | n/a |
| C. elegans DF174 = him-5(e1490) V; lep-5(ny10) X ; nyEx23[Plin-41::NLS::GFP + rol-6] | This paper | n/a |
| C. elegans DF213 = him-5(e1490) V; zaIs3[let-7(+) + myo-3::GFP] made by crossing CT19 with CB4088 | This paper | n/a |
| C. elegans DF223 = him-5(e1490) V; lep-5(ny10)X; zaIs3[let-7(+) + myo-3::GFP] | This paper | n/a |
| C. elegans DF235 = him-5(e1490) V; lep-5(ny10) X; wIs78[unc-119(+) + ajm-1::GFP + scm::GFP + F58E10(+)] | This paper | n/a |
| C. elegans DF237 = him-5(e1490) V; maIs108[lin-28::gfp + rol-6] | This paper | n/a |
| C. elegans DF293 = lep-2(ny23) IV; him-5(e1490) V; nyEx53[lep-2>GFP::lep-2b + pRF4] | This paper | n/a |
| C. elegans DF282 = lin-41(tn1541[GFP::tev::s::lin-41]) I; him-5(e1490) V | This paper | n/a |
| C. elegans DF302 = him-5(e1490) V; nyEx61[lep-5>GFP + rol-6] | This paper | n/a |
| C. elegans DF271 = him-5(e1490) V ; nyEx56[lin-28::Dendra2::lin-28_3'UTR + rol-6] | Herrera et al. 2016 | n/a |
| C. elegans EM122 = him-5(e1490) V ; unc-18(e81) dpy6(e14) X | CGC | https://cgc.umn.edu/strain/EM122 |
| C. elegans UR290 = him-5(e1490) V; lep-5(fs8) X | This paper | n/a |
| C. elegans UR1140 = him-5(e1490) V; lep-5(fs18) X | This paper | n/a |
| UR157 = fsIs2[dmd-3promxln2::YFP + CCGFP] I; him-5(e1490) V | This paper | n/a |
| C. elegans UR1141 = him-5(e1490) V; lep-5(fs19) X | This paper | n/a |
| C. elegans UR1207 = him-5(e1490) V; lep-5(fs21) X | This paper | n/a |
| C. elegans UR1208 = him-5(e1490) V; lep-5(fs22) X | This paper | n/a |
| C. elegans UR1211 = him-5(e1490) V; lep-5(fs21 fs25) X | This paper | n/a |
| C. elegans UR1226 = lin-41(ma104) I ; him-5(e1490)V; lep-5(fs8) X | This paper | n/a |
| Oligonucleotides | ||
| See Table S1 for list of oligonucleotides | ||
| Recombinant DNA | ||
| Gateway vector pDONR™P4-P1R | Life Technologies | Not available (replaced by new product) |
| RNAi feeding clone for C. elegans lin-14: Ahringer library sjj_T25C12.1 | Source BioScience | sjj_T25C12.1 |
| RNAi feeding clone for C. elegans lin-41: Ahringer library sjj_C12C8.3 | Source BioScience | sjj_C12C8.3 |
| RNAi feeding clone for C. elegans lin-28: Vidal library GHR-11014@G03 | Source BioScience | GHR-11014@G03 |
| L4440 control plasmid for RNAi feeding experiments | Addgene | RRID:Addgene_1654 |
| pRF4[rol-6(d)] | ||
| Punc-122::GFP C. elegans expression vector | Addgene | RRID:Addgene_19325 |
| GFP::NLS C. elegans expression vector | Addgene | RRID:Addgene_1622 |
| Dendra2 C. elegans expression vector | Addgene | RRID:Addgene_40077 |
| Fosmid clones WRM062bG06, WRM0629cE12, WRM0628aE08 and WRM0640cA10 | Source BioScience | https://www.sourcebioscience.com/ |
| Software and Algorithms | ||
| imageJ | https://imagej.nih.gov | |
| ChopChop | Labun et al., 2016; Montague et al., 2014 | http://chopchop.cbu.uib.no |
| CRISPOR | Haeussler et al., 2016 | http://crispor.tefor.net |
| ApE | Doench et al., 2014 | http://jorgensen.biology.utah.edu/wayned/ape/ |
| LIMMA | https://bioconductor.org/packages/release/bioc/html/limma.html | |
| HMMER 3.1b2 | Eddy, 2011 | http://hmmer.org |
| MAFFT v7.266 | Katoh and Standley, 2013 | https://mafft.cbrc.jp/alignment/software/ |
| Jalview 2.9.0b2 | Waterhouse et al., 2009 | http://www.jalview.org |
| TurboFold | Harmanci et al., 2011 | http://rna.urmc.rochester.edu/RNAstructure.html |
| VARNA | Darty et al., 2009 | http://varna.lri.fr |
| CARNA | Raden et al., 2018; Sorescu et al., 2012 | http://rna.informatik.uni-freiburg.de |
| RNAalifold | http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAalifold.cgi | |
| TargetScan | http://www.targetscan.org/worm_52/ | |
| Online MicroRNA prediction tool | Kertesz et al. 2007 | https://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html |
| microRNA.org | http://www.microrna.org/microrna/home.do | |
| Other | ||
| Genome sequence of Caenorhabditis afra | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. brenneri | https://wormbase.org/species/c_brenneri#4--10 | |
| Genome sequence of C. briggsae | https://wormbase.org/species/c_briggsae#0--10 | |
| Genome sequence of C. doughertyi | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. japonica | https://wormbase.org/species/c_japonica#0--10 | |
| Genome sequence of C. kamaaina | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. latens | https://parasite.wormbase.org/Caenorhabditis_latens_prjna248912/Info/Index | |
| Genome sequence of C. macrosperma | nematode.org | |
| Genome sequence of C. nigoni | https://parasite.wormbase.org/Caenorhabditis_nigoni_prjna384657/Info/Index | |
| Genome sequence of C. nouraguensis | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. remanei | https://wormbase.org/species/c_remanei#0--10 | |
| Genome sequence of C. sinica | https://parasite.wormbase.org/Caenorhabditis_sinica_prjna194557/Info/Index | |
| Genome sequence of C. sp. 28 | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. sp. 29 | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. sp. 32 | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. sp. 40 | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. tropicalis | https://parasite.wormbase.org/Caenorhabditis_tropicalis_prjna53597/Info/Index | |
| Genome sequence of C. wallacei | nematode.org | |
| Genome sequence of C. angaria | https://wormbase.org/species/all#0123--10 | |
| Genome sequence of C. castelli | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. sp. 38 | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. pilcata | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. virilis | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. sp. 43 | http://ensembl.caenorhabditis.org/index.html | |
| Genome sequence of C. sp. 31 | http://ensembl.caenorhabditis.org/index.html | |