KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-mouse IgG-HRP antibody | GE Healthcare | Cat#:NA931; RRID: AB_772210 |
| Anti-rabbit IgG-HRP antibody | Cell Signaling Technology | Cat#:7074S; RRID: AB_2099233 |
| Mouse monoclonal anti-GAPDH (6C5) antibody | Santa Cruz Biotechnology | Cat#:sc-32233; RRID: AB_627679 |
| Rabbit monoclonal anti-ac4C antibody | Abcam | Cat#:ab25215; RRID: AB_2827750 |
| Rabbit monoclonal anti-m7G antibody | MBL International Corporation | Cat#:RN016M; N/A |
| Rabbit Monoclonal IgG Isotype Control | Cell Signaling Technology | Cat#:3900S; RRID: AB_1550038 |
| Rabbit polyclonal anti-IRF1 antibody | Abcam | Cat#:ab191032; RRID: AB_2904575 |
| Rabbit polyclonal anti-KDM4B antibody | Cell Signaling Technology | Cat#:8639S; RRID: AB_11140642 |
| Rabbit polyclonal anti-KRT80 antibody | ProteinTech | Cat#:16835-1-AP; RRID: AB_1851273 |
| Rabbit polyclonal anti-LMNA antibody | Bethyl Laboratories | Cat#:A303-433A; RRID: AB_10951693 |
| Rabbit polyclonal anti-PXN antibody | ProteinTech | Cat#:10029-1-Ig; RRID: AB_513929 |
| Rabbit polyclonal anti-NAT10 antibody | ProteinTech | Cat#:13365-1-AP; RRID: AB_2148944 |
| Rabbit polyclonal anti-THUMPD1 antibody | Bethyl Laboratories | Cat#:A304-643AT; RRID: AB_2620838 |
| Bacterial and Virus Strains | ||
| N/A | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| 32P-γATP | PerkinElmer | Cat#:BLU502A100UC |
| 32P-αUTP | PerkinElmer | Cat#:BLU007H250UC |
| AMPure XP beads | Beckam Coulter | Cat#:A63881 |
| Acid-Phenol:Chloroform, pH 4.5 | ThermoFisher Scientific | Cat#:AM9722 |
| Bovine Calf Serum (BCS) | HyClone | Cat#:SH30073.03 |
| Bovine Serum Albumin (BSA) | Roches | Cat#:03117332001 |
| Bradford Reagent | BioRad | Cat#:5000205 |
| CIAP | Promega | Cat. #:M2825 |
| Cycloheximide | Sigma-Aldrich | Cat#:C7698 |
| DMEM | ThermoFisher Scientific | Cat#:11995073 |
| DNase I | Sigma-Aldrich | Cat#:4716728001 |
| DNAse-free RNAse A | ThermoFisher Scientific | Cat#:EN0531 |
| E. coli Poly(A) Polymerase | New England Biolabs | Cat#:M0276S |
| ECL Western Blotting Substrate | Promega | Cat#:W1001 |
| Halt™ protease inhibitor cocktail | ThermoFisher Scientific | Cat#:78429 |
| Harringtonine | Abcam | Cat#:ab141941 |
| Illustra™ MicrosSpin™ G-50 Columns | GE Healthcare | Cat#:27-5330-01 |
| L-glutamine | ThermoFisher Scientific | Cat#:25030149 |
| Linear acrylamide | ThermoFisher Scientific | Cat#:AM9520 |
| Lipofectamine 3000 | ThermoFisher Scientific | Cat#:L3000008 |
| Murine RNAse inhibitor | New England Biolabs | Cat#:M0314 |
| N4-acetylcytidine triphosphate (ac4CTP) | Trilink | Custom synthesis |
| Protease Inhibitor Mini Tablets, EDTA-free | ThermoFisher Scientific | Cat#:32955 |
| Preadenylated universal miRNA cloning linker | New England Biolabs | Cat#:S1315S |
| ProSignal Pico ECL Reagent | Genesee Scientific | Cat#:20-300B |
| Propidium iodide | Roche | Cat#:11348639001 |
| Protein G Magnetic Beads | New England Biolabs | Cat#:S1430S |
| Proteinase K, Molecular Biology Grade | New England Biolabs | Cat#:P8107S |
| RNA Clean & concentrator-5 | Zymo Research | Cat#:R1013 |
| RNA Spike-In mix | ThermoFisher Scientific | Cat#:4456740 |
| RNAse A | Millipore | Cat#:111199115001 |
| RNase I | ThermoFisher Scientific | Cat#:EN0601 |
| Superase-In | ThermoFisher Scientific | Cat#:AM2694 |
| T4 Polynucleotide kinase (PNK) | New England Biolabs | Cat#:M0201 |
| T4 RNA ligase 2 | New England Biolabs | Cat#:M0239S |
| TRIzol Reagent | ThermoFisher Scientific | Cat#:15596026 |
| Trypan blue | Lonza | Cat#:17-942E |
| Turbo™ DNAse I | ThermoFisher Scientific | Cat#:AM2239 |
| Critical Commercial Assays | ||
| human/mouse/rat Ribo-Zero Gold rRNA removal | Illumina | Cat#:MRZG12324 |
| LightCycler 480 SYBR Green I Master | Roche | Cat#:04887352001 |
| Luciferase assay reagent | Promega | Cat#:E1500 |
| MEGAscript T7 Transcription Kit | ThermoFisher Scientific | Cat#:AM1334 |
| Nano-Glo® Luciferase Assay System | Promega | Cat#:N1120 |
| Nano-Glo Dual-Luciferase Reporter System | Promega | Cat#:N1610 |
| NEBNext® Magnesium RNA Fragmentation buffer | New England Biolabs | Cat#:E6150 |
| NEBNext® rRNA Depletion Kit | New England Biolabs | Cat#:E6310L |
| NEBNext® UltraII™ Directional RNA Library Prep Kit | New England Biolabs | Cat#:E7770S |
| NorthernMax kit | ThermoFisher Scientific | Cat#:AM1940 |
| NorthernMax Prehyb/Hyb buffer | ThermoFisher Scientific | Cat#:AM8677 |
| ONE-Glo EX Reagent | Promega | Cat#:E8110 |
| PowerUp SYBR Green Master Mix | ThermoFisher Scientific | Cat#:A25777 |
| ProSignal Pico ECL Reagent | Genesee Scientific | Cat#:20-300B |
| Q5 Hot Start High-Fidelity | New England Biolabs | Cat#:M0493S |
| Rabbit Reticulocyte Lysate | Promega | Cat#:L4960 |
| SuperScript IV First-Stranded Synthesis System | ThermoFisher Scientific | Cat#:18091050 |
| SuperSignal ELISA Femto Maximum Sensitivity Substrate | ThermoFisher Scientific | Cat#:37075 |
| TransIT-mRNA Transfection Kit | Mirus | Cat#:MIR2250 |
| Vaccinia Capping System | New England Biolabs | Cat#:M2080S |
| Deposited Data | ||
| Raw and processed RedaC:T-seq data | This Study | GEO: GSE162043 |
| Raw and processed HR Ribo-seq-seq data | This Study | GEO: GSE162043 |
| Rabbit Reticulocyte RNA-seq | This Study | GEO: GSE162043 |
| Cryo-EM data | This Study | ac4C 80s ribosome: PDB:7UCK and EMDB:EMD-26445 AUG 80s ribosome: PDB:7UCJ and EMDB:EMD-26444 |
| Experimental Models: Cell Lines | ||
| Human: HeLa | ATCC | Cat#:CCL-2; RRID: CVCL_0030 |
| Human: NAT10+/+ | Arango et. al. 2018 | N/A |
| Human: Flp-In Trex 293 | ThermoFisher Scientific | Cat. #:R71007 RRID: CVCL_U427 |
| Human: Flp-In Trex 293 NAT10-FL | Arango et. al. 2018 | N/A |
| Oligonucleotides | ||
| ON-TARGETplus siRNAs against PXN | Dharmacon | Cat.#:L-005163-00-0005 |
| ON-TARGETplus siRNAs against KRT80 | Dharmacon | Cat.#:L-018941-02-0005 |
| ON-TARGETplus siRNAs Control | Dharmacon | Cat.#:D-001810-10 |
| Oligonucleotide sequences used in this study | This Study | Table S1 |
| Recombinant DNA | ||
| pNL1.1PGK | Promega | Cat#:N1441 |
| pcDNA/FRT | ThermoFisher Scientific | Cat#:V6010-20 |
| pcDNA/FRT-NAT10-FL | Arango et al., 2018 | |
| pcDNA/FRT-NAT10-ΔHel | Arango et al., 2018 | |
| Software and Algorithms | ||
| BEDtools | Quinlan, 2014 | RRID:SCR_006646 |
| Bowtie2 v.00.14 | Langmead and Salzberg, 2012 | RRID:SCR_016368 |
| Cutadapt v 2.0 | Martin, 2011 | RRID:SCR_011841 |
| DeepTools | Ramírez et al., 2014 | RRID:SCR_016366 |
| DESeq2 | Love et al., 2014 | RRID:SCR_017673 |
| Fastx_clipper v.0.014 | http://hannonlab.cshl.edu/fastx_toolkit/ | |
| Hisat2 v2.2.1.0 | Kim et al., 2015 | RRID:SCR_015530 |
| HTSeq v 0.6.1p1 | Anders et al., 2015 | RRID:SCR_005514 |
| ImageJ | National Center for Microscopy and Imaging Research | RRID:SCR_001935 |
| ImageLab | BioRad | http://www.biorad.com/en-us/product/image-lab-software?ID=KRE6P5E8Z |
| MACS2 | Zhang et al., 2008 | RRID:SCR_013291 |
| MFOLD v3.6 | Zuker, 2003 | RRID:SCR_008543 |
| Mpileup v 1.10 | Li et al., 2009 | RRID:SCR_002105 |
| PRISM 7 | GraphPad Software, Inc. | RRID:SCR_002798 |
| Relion v 3.0 | Zivanov et al., 2018 | RRID:SCR_016274 |
| Ribo-TISH | Zhang et al., 2017 | https://github.com/zhpn1024/ribotish |
| Rstudio v 3.6 | Rstudio | RRID:SCR_000432 |
| STAR v. 2.5.4.a | Dobin et al., 2013 | RRID:SCR_019993 |
| Tophat2 v.2.1.1 | Trapnell et al., 2009 | RRID:SCR_013035 |
| ViennaRNA tool v 2.4.18 | Lorenz et al., 2011 | https://www.tbi.univie.ac.at/RNA/# |