| Antibodies |
| mouse anti-GAPDH |
Cell signaling |
Cat# 97166 |
| mouse anti-actin |
Cell signaling |
Cat# 3700S |
| rabbit anti-Rps6 |
Cell signaling |
Cat# 2217L |
| rabbit anti-4E-BP1 |
Cell signaling |
Cat# 9644S |
| rabbit anti-4E-BP2 |
Cell signaling |
Cat# 2845S |
| rabbit anti-phospho-p70 S6 Kinase(T389) |
Cell signaling |
Cat# 9205S |
| rabbit anti-p70 S6 Kinase |
Cell signaling |
Cat# 9202S |
| rabbit anti-phopsho-ULK1(Ser757) |
Cell signaling |
Cat# 6888T |
| rabbit anti-ULK1 |
Cell signaling |
Cat# 8054T |
| rabbit anti-TSC2 |
Cell signaling |
Cat# 4308T |
| rabbit anti-eIF4G |
Cell signaling |
Cat# 2498S |
| rabbit anti-p53 |
Leica Biosystems |
Cat# CM5P-L |
| mouse anti-eIF4E |
BD Biotransduction |
Cat# 610269 |
| anti-phospho-Histone H3 |
Sigma |
Cat# 06-570 |
| Cleaved Caspase-3 |
Cell signaling |
Cat# 9661S |
| Goat anti-rabbit AF568 |
Life Technologies |
Cat# A11036 |
| donkey anti-mouse HRP |
GE Healthcare |
Cat# NA931-1ML |
| donkey anti-rabbit HRP |
GE Healthcare |
Cat# NA934-1ML |
| alkaline phosphatase-conjugated anti-DIG |
Sigma |
Cat# 11093274910 |
|
|
|
| Bacterial and virus strains |
| Ad5 CMV-Cre |
University of Iowa Viral Vector Core Facility |
Cat# Ad5CMVCre |
| Ad5 CMV-empty |
University of Iowa Viral Vector Core Facility |
Cat# Ad5CMVempty |
|
|
|
| Biological samples |
|
|
|
| Chemicals, peptides, and recombinant proteins |
| O-propargyl-puromycin |
Medchem Source LLP |
Cat# JA-1024 |
| L-homopropargylglycine |
Thermo Fisher |
Cat# C10186
|
| 4EGI-1 (eIF4E/eIF4G interaction inhibitor) |
Millipore Sigma |
Cat# 324517 |
| Dimethyl sulfoxide (DMSO, cell culture grade) |
Sigma |
Cat# D2650 |
| Nutlin-3a |
Cayman Chemicals |
Cat#18585 |
| Doxorubicin hydrochloride |
Sigma |
Cat# D1515 |
| TURBO DNase |
Ambion |
Cat# AM2238 |
| SUPERase In RNase Inhibitor |
Ambion |
Cat# AM2696 |
| TRIzol |
Invitrogen |
Cat# 15596 |
| iScript Supermix |
Bio-Rad |
Cat# 1708840 |
| SsoAdvanced SYBR Green supermix |
Bio-Rad |
Cat# 1725270 |
| 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 |
| Dulbecco’s Modified Eagle’s Medium |
GIBCO |
Cat# 11965–118 |
| Fetal calf serum |
EMD Millipore |
Cat# TMS-013-B |
| DMEM/F-12, HEPES, with phenol red |
Thermo Fisher |
Cat# 11330032 |
| Penicillin-Streptomycin Solution 100X |
Thermo Fisher |
Cat# 15140163 |
| Opti-MEM |
GIBCO |
Cat# 11058-021 |
| Lipofectamine 2000 |
Invitrogen |
Cat# 11668-019 |
| Dharmafect I |
Dharmacon |
Cat# T-2001-02 |
| siGENOME smart pool siRNA 4EBP1 |
Dharmacon |
Cat# M-058681-01-0005 |
| siGENOME smart pool siRNA 4EBP2 |
Dharmacon |
Cat# M-044972-01-0005 |
| siGENOME control siRNA #3 |
Dharmacon |
Cat# D-001210-03-05 |
| siGENOME control siRNA #2 (siFluc) |
Dharmacon |
Cat# D-001210-02-05 |
| Zombie Violet Live-Dead Stain |
BioLegend |
Cat# 423113 |
| BM Purple AP substrate |
Sigma |
Cat# 11442074001 |
| LysoTracker Red DND-99 |
Invitrogen |
Cat# L7528 |
| Alizarin Red S |
Sigma |
A5533 |
| Alcian Blue 8GX |
Sigma |
A5268 |
| HBSS |
Thermo Fisher |
14025-076 |
| Cycloheximide |
Sigma-Aldrich |
C7698 |
| Halt Protease and Phosphatase Inhibitor Cocktail |
Thermo Fisher |
78442 |
| Acid-Phenol: Chloroform, pH 4.5 (with IAA, 125:24:1) |
Thermo Fisher |
AM9722 |
| Complete Protease Inhibitor EDTA-free |
Sigma-Aldrich |
11836170001 |
| TRIzol LS |
Thermo Fisher |
10296010 |
| RNase A |
Thermo Fisher |
AM2271 |
| RNase T1 |
Thermo Fisher |
EN0541 |
| GlycoBlue Coprecipitant |
Thermo Fisher |
AM9515 |
| 10 bp DNA ladder |
Invitrogen |
10821015 |
| T4 PNK |
NEB |
M0201S |
| Universal miRNA Cloning Linker |
NEB |
S1315S |
| T4 RNA Ligase 2, truncated KQ |
NEB |
M0373S |
| 5’-Deadenylase |
NEB |
M0331S |
| RecJ Exonuclease |
Lucigen/Epicentre |
RJ411250 |
|
|
|
| Critical commercial assays |
| Dual-Luciferase Reporter Assay System |
Promega |
Cat# E1980 |
| Monarch Gel Extraction Kit |
NEB |
Cat# T1020S |
| NEBuilder HiFi DNA Assembly Master Mix |
NEB |
Cat# E2621S |
| RNA Clean and Concentrator-5 columns |
Zymo Research |
Cat# R1016 |
| RNA PureLink columns |
Ambion |
Cat# 12183018 |
| mMESSAGE mMACHINE® T7 Transcription Kit |
Ambion |
Cat# AM 1344 |
| Poly(A) Polymerase Tailing Kit |
Lucigen |
Cat# PAP5104H |
| Agarose beads |
Jena Biosciences |
Cat# AC-100S |
| γ-aminophenyl-m7GTP (C10-spacer)-agarose beads |
Jena Biosciences |
Cat# AC-155S |
| Click-iT EdU Alexa Fluor 488 flow Cytometry Assay Kit |
Thermo Fisher |
Cat# C10425
|
| FITC Annexin V and propidium iodide staining kit |
BioLegend |
Cat# 640914 |
| Click-iT™ Plus Alexa Fluor™ 555 Picolyl Azide Toolkit |
Thermo Fisher |
Cat# C10642
|
| Direct-zol Micro Kit |
Zymo |
R2060 |
| Ribo-Zero Gold rRNA Removal Kit (H/M/R) |
Illumina |
MRZG126 |
| SuperScript III |
Thermo Fisher |
18080-044 |
| CircLigase |
Illumina |
CL4115K |
| Phusion High-Fidelity DNA Polymerase |
Thermo Fisher |
F530S |
|
|
|
| Deposited data |
| Ribosome profiling (ribosome footprints and RNA-Seq) data from E10.5 Rps6lox/+;Trp53+/+; Prx1Cre;Rps6lox/+;Trp53+/+; Rps6lox/+;Trp53−/−; Prx1Cre;Rps6lox/+;Trp53−/− embryonic limb buds |
This paper |
GEO: GSE135722
|
| p53 ChIP-seq in primary MEFs |
(Kenzelmann Broz et al., 2013) |
GEO: GSE46240
|
|
|
|
| Experimental models: cell lines |
| NIH3T3 |
ATCC |
CAT#CRL-1658 |
| C3H10T1/2 |
ATCC |
CAT#CCL-226 |
| Mouse embryonic fibroblasts (Trp53LSL-WT/LSL-WT)
|
(Brady et al., 2011) |
N/A |
| Mouse embryonic fibroblasts (Trp53LSL-25,26,53,54/LSL-25,26,53,54)
|
(Brady et al., 2011) |
N/A |
|
|
|
| Experimental Models: organisms/strains |
| Mouse: Rps6lox
|
(Volarevic et al., 2000) |
N/A |
| Mouse: Prx1Cre
|
(Logan et al., 2002); Jackson Laboratories |
JAX: 005584 |
| Mouse: Msx2Cre
|
(Sun et al., 2000); Jackson Laboratories |
JAX: 027892 |
| Mouse: Tsc2lox
|
(Hernandez et al., 2007); Jackson laboratories |
JAX: 027458 |
| Mouse: Trp53null
|
(Jacks et al., 1994) |
N/A |
| Mouse: RosamTmG
|
(Muzumdar et al., 2007) |
N/A |
|
|
|
| Oligonucleotides |
| Oligonucleotides for ribosome profiling, RT-qPCR, ChIP-PCR, see Table S2
|
This paper |
N/A |
|
|
|
| Recombinant DNA |
| pGL3-Pkm-FLB-stop |
This Paper |
N/A |
| pGL3-Cnot10-FLB-stop |
This Paper |
N/A |
| pGL3-Mdm4-FLB-stop |
This Paper |
N/A |
| pGL3-Rnf10-FLB-stop |
This Paper |
N/A |
| pGL3-Megf8-FLB-stop |
This Paper |
N/A |
| pGL3-Col2a1-FLB-stop |
This Paper |
N/A |
| pGL3-Gli2-FLB-stop |
This Paper |
N/A |
| pGL4.23 |
Promega |
CAT#E8411 |
| pGL4.23-p53-4EBP1_delMiniP |
This Paper |
N/A |
| pGL4.23-Delp53-4EBP1_delMiniP |
This Paper |
N/A |
|
|
|
| Software and algorithms |
| ImageJ |
NIH |
https://imagej.nih.gov/ij/ |
| Prism |
Graphpad Software Inc. |
Version 8.0 |
| FlowJo |
BD Biosciences |
Version 10.7.1 |
| Volocity |
Quroum Technologies |
Version 6.3.1 |
| UMI-tools |
(Smith et al., 2017) |
https://github.com/CGATOxford/UMI-tools |
| FASTX-Toolkit |
http://hannonlab.cshl.edu/fastx_toolkit/ |
http://hannonlab.cshl.edu/fastx_toolkit/ |
| cutadapt |
(Martin, 2011) |
https://cutadapt.readthedocs.io/en/stable/ |
| bowtie2 |
(Langmead and Salzberg, 2012) |
http://bowtie-bio.sourceforge.net/bowtie2/ |
| voom |
(Law et al., 2014) |
https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/voom |
| limma |
(Ritchie et al., 2015) |
https://bioconductor.org/packages/release/bioc/html/limma.html |
| Camera |
(Wu and Smyth, 2012) |
https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/camera |
| Enrichment Map |
(Merico et al., 2010) |
http://apps.cytoscape.org/apps/enrichmentmap |
| Cytoscape |
https://cytoscape.org/ |
https://cytoscape.org/ |
| RStudio |
https://rstudio.com/ |
https://www.rstudio.com/ |
| samtools |
(Li et al., 2009) |
http://www.htslib.org/ |
| Mouse GRCm38/mm10 UCSC/GENCODE VM20 knownCanonical annotation |
https://genome.ucsc.edu/ |
https://genome.ucsc.edu/ |
| Enrichment Map Mouse Gene Sets |
http://download.baderlab.org/EM_Genesets/current_release/Mouse/entrezgene/ |
http://download.baderlab.org/EM_Genesets/current_release/Mouse/entrezgene/ |
| ggplot2 |
(Wickham, 2016) |
https://ggplot2.tidyverse.org/ |
|
|
|
| Other |
| Density Gradient Fraction System |
Brandel |
Cat# BR-188 |
| CFX384 Touch qPCR machine |
Bio-Rad |
Cat# 1855485 |
| ChemiDoc MP |
Bio-Rad |
Cat# 17001402 |
| Biocomp Model 108 Gradient Master |
BioComp |
N/A |
| LSRII Flow Cytometer |
BD Biosciences |
N/A |
| NovoCyte Quanteon Flow Cytometer |
Agilent Technologies |
N/A |
| CFX384 Touch Real-Time PCR Detection System |
Bio-Rad |
Cat# 1855485 |
| GloMax-Multi Plate Reader |
Promega |
Cat# E7081 |
| SW-60 rotor |
Beckman |
Cat# 335649 |
| TLA 120.2 rotor |
Beckman |
Cat# 357656 |
|
|
|
