KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-FLAG (M2) | Sigma-Aldrich | Cat# F3165; RRID: AB_259529 |
| Mouse monoclonal anti-PGK1 | Thermo, Novex | Cat# 459250; RRID: AB_2532235 |
| Mouse monoclonal anti-RPS5/uS7 | Abcam | Cat# ab58345; RRID: AB_2180899 |
| Mouse monoclonal anti-RPL10A/uL1 (for yeast) | Santa Cruz | Cat# sc-100827; RRID: AB_2285311 |
| Rabbit monoclonal anti-RPL10A/uL1 (for mouse) | Abcam | Cat# ab174318; RRID: N/A |
| Rat monoclonal anti-Mouse IgG-HRP (eB144) | Rockland | Cat# 18-8817-31; RRID: AB_2610850 |
| Mouse monoclonal anti-Rabbit IgG-HRP (eB182) | Rockland | Cat# 18-8816-31; RRID: AB_2610847 |
| Sheep Anti-Mouse IgG, HRP Conjugated | GE Healthcare | Cat# NXA931; RRID: AB_772209 |
| Donkey Anti-Rabbit IgG, HRP Conjugated | GE Healthcare | Cat# NA934; RRID: AB_772206 |
| Mouse monoclonal anti-FLAG M2 affinity Gel | Sigma-Aldrich | Cat# A2220; RRID: AB_10063035 |
| Chemicals, peptides, and recombinant proteins | ||
| Cycloheximide | Sigma-Aldrich | Cat# C7698-1G |
| RNase A | Invitrogen | Cat# AM2271 |
| RNA PureLink columns | Ambion | Cat# 12183018 |
| RNA Clean and Concentrator-5 columns | Zymo Research | Cat# R1016 |
| 3xFLAG peptide | Sigma-Aldrich | Cat# F4799-4MG |
| TURBO DNase | Ambion | Cat# AM2238 |
| SUPERase In RNase Inhibitor | Ambion | Cat# AM2696 |
| RNaseOUT | Thermo Fisher | Cat# 10777019 |
| RNasin Plus RNase inhibitor | Promega | Cat# N261A |
| TRIzol | Invitrogen | Cat# 15596 |
| AccuPrime Pfx DNA Polymerase | Invitrogen | Cat# 12344024 |
| KOD Xtreme Hot Start DNA Polymerase | EMD Millipore | Cat# 71975 |
| SuperScript III Reverse Transcriptase | Invitrogen | Cat# 18080044 |
| SuperScript IV Reverse Transcriptase | Invitrogen | Cat# 18090010 |
| iScript Supermix | Bio-Rad | Cat# 1708840 |
| SsoAdvanced SYBR Green supermix | Bio-Rad | Cat# 1725270 |
| CFX384 Touch qPCR machine | Bio-Rad | Cat# 1855485 |
| 5-Fluoroorotic Acid (5-FOA) | Fisher Scientific | Cat# F10501-5.0 |
| Geneticin | GIBCO | Cat# 11811-031 |
| Amino acid supplements (Complete Supplement Mixture, CSM) | Sunrise Science Products | https://sunrisescience.com/products/growth-media/amino-acid-supplement-mixtures/csm-formulations/ |
| Salmon sperm DNA | Sigma | Cat# D1626-5G |
| Poly ethylene glycol (PEG) – MW 8000 | Millipore Sigma | Cat# 6510-OP |
| cOmplete Protease Inhibitor Cocktail, EDTA-free | Roche | Cat# 11836145001 |
| cOmplete Mini Protease Inhibitor Cocktail, EDTA-free | Roche | Cat# 11836170001 |
| Streptavidin Sepharose High Performance | GE Healthcare | Cat# 17-5113-01 |
| Avidin Agarose | Thermo, Pierce | Cat# 20219 |
| SDS-PAGE gels | Bio-Rad | Cat# 567-1095, 456-1096 |
| Semi-dry Trans-Blot Turbo system | Bio-Rad | Cat# 170-4273 |
| Clarity Western ECL Substrate | Bio-Rad | Cat# 170-5061 |
| ChemiDoc MP | Bio-Rad | Cat# 17001402 |
| Tissue Lyser (QIAgen TissueLyser II) | QIAGEN | Cat# 85300 |
| Dulbecco’s Modified Eagle’s Medium | GIBCO | Cat# 11965–118 |
| Fetal calf serum | EMD Millipore | Cat# TMS-013-B |
| Opti-MEM | GIBCO | Cat# 11058-021 |
| Lipofectamine 2000 | Invitrogen | Cat# 11668-019 |
| 1x PBS | GIBCO | Cat# 14190-250 |
| SYBR Gold | Invitrogen | Cat# S11494 |
| GlycoBlue | Ambion | Cat# LSAM9516 |
| Sucrose | Fisher Scientific | Cat# S5-12 |
| Density Gradient Fraction System | Brandel | Cat# BR-188 |
| Acid-Phenol:Chloroform, pH 4.5 | Ambion | Cat# AM9722 |
| Critical commercial assays | ||
| Ribo-Zero Gold rRNA Removal Kit (Yeast) | Illumina | Cat# MRZY1306 |
| NextFlex Rapid Directional qRNA-Seq Library Prep Kit | Perkin Elmer, Bioo Scientific | Cat# NOVA-5130-01D |
| ProteoExtract Protein Precipitation Kit | EMD Millipore | Cat#539180 |
| Dual-Luciferase Reporter Assay System | Promega | Cat# E1980 |
| GloMax-Multi | Promega | Cat# E7081 |
| MEGAscript T7 Transcription Kit | Ambion | Cat# AM1333 |
| MEGAscript SP6 Transcription Kit | Ambion | Cat# AM1330 |
| MasterPure Yeast RNA Purification Kit | Epicenter | Cat# MPY03100 |
| QIAquick Gel Extraction Kit | QIAgen | Cat# 28706 |
| Monarch Gel Extraction Kit | NEB | Cat# T1020S |
| NEBuilder HiFi DNA Assembly Master Mix | NEB | Cat# E2621S |
| QIAquick PCR Purification Kit | QIAgen | Cat# 28106 |
| G-50 Mini Quick Spin Sephadex RNA columns | Roche | Cat# 11814427001 |
| Oligotex mRNA Mini Kit | QIAgen | Cat# 70022 |
| Poly(A) Purist MAG kit | Invitrogen | Cat# AM1922 |
| NEBNext Magnesium RNA Fragmentation Module | NEB | Cat# E6150S |
| RNA 6000 Pico Chip | Agilent | Cat# 5067-1513 |
| High Sensitivity DNA Assay | Agilent | Cat# 5067-4626 |
| Deposited data | ||
| Raw and analyzed VELCRO-IP RNA-seq data | This paper | GEO: GSE141382 |
| Mouse reference transcriptome mm9 knownGene | UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTables |
| Mouse mm9 knownCanonical annotation | UCSC Genome Browser | https://genome.ucsc.edu/cgi-bin/hgTables |
| Experimental models: cell lines | ||
| C3H/10T1/2 mouse cells | ATCC | Cat# CCL-226 |
| Experimental models: organisms/strains | ||
| Yeast (S. cerevisiae) strains used: see Table S2 | This paper | N/A |
| Oligonucleotides | ||
| Oligonucleotides for genome editing, cloning, qRT-PCR analysis, in vitro transcription, see Table S3 | This paper | N/A |
| Synthesized oligonucleotides | Twist Bioscience | N/A |
| Recombinant DNA | ||
| Plasmids used and generated, see Table S1 | This paper | N/A |
| Software and algorithms | ||
| Agilent 2100 Bioanalyzer Expert software | Agilent | https://www.agilent.com/ |
| Cutadapt | Martin, 2011 | https://cutadapt.readthedocs.io/en/stable/ |
| FastQC | Babraham Bioinformatics | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| deepTools | Ramírez et al., 2016 | https://github.com/deeptools/deepTools/ |
| UMI-tools | Smith et al., 2017 | https://github.com/CGATOxford/UMI-tools |
| Locfdr | Efron, 2010 | https://cran.r-project.org/web/packages/locfdr/index.html |
| STAR RNA-Seq aligner | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| bedtools | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| Samtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| TMM | Robinson and Oshlack, 2010 | N/A |
| wiggleplotR | Alasoo et al., 2015 | https://bioconductor.org/packages/release/bioc/html/wiggleplotr.html |
| voom | Law et al., 2014 | N/A |
| limma | Ritchie et al., 2015 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| topGO | Alexa et al., 2006 | https://bioconductor.org/packages/release/bioc/html/topGO.html |
| MAFFT, MView | EMBL-EBI webtools | https://www.ebi.ac.uk/Tools/msa/mafft/ |
| Vienna RNAfold | RNAfold WebServer | http://rna.tbi.univie.ac.at |
| VARNA | RNA structure visualization | http://varna.lri.fr |
| R | R Foundation | https://www.r-project.org/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Prism | GraphPad Software Inc. | Version 8.0 |