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. Author manuscript; available in PMC: 2022 Apr 6.
Published in final edited form as: Cell Rep. 2020 Oct 13;33(2):108262. doi: 10.1016/j.celrep.2020.108262

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Mouse monoclonal anti-GFP Roche Cat. #11814460001: RRID: AB_390913
Rabbit polyclonal anti-GFP In house N/A
Rabbit polyclonal anti-HsGIGYF1 Bethyl laboratories Cat. #A304-132A-M
Rabbit polyclonal anti-HsGIGYF2 Bethyl laboratories Cat. #A303-731A
Rabbit polyclonal anti-HsZNF598 Bethyl laboratories Cat. #A305-108A
Rabbit polyclonal anti-Hs4EHP In house N/A
Mouse monoclonal anti-HA (HRP) Roche Cat. #12013819001: RRID: AB_390917
Mouse monoclonal anti-Tubulin Sigma Aldrich Cat. #T6199: RRID: AB_477583
Mouse monoclonal anti-V5 LSBio LifeSpan BioSciences, Inc. Cat. #LS-C57305: RRID: AB_1512087
Anti-RENT1 (UPF1) Bethyl laboratories Cat. #A301-902A: RRID: AB_1524122
Anti-R-LUC Abcam Cat. #ab185925
Donkey polyclonal anti-rabbit IgG (HRP) GE Healthcare Cat. #NA934V
Sheep polyclonal anti-mouse IgG (HRP) GE Healthcare Cat. #RPN4201
Chemicals, Peptides, and Recombinant Proteins
Lipofectamine 2000 Thermo Scientific Cat. #11668-019
DMEM In house N/A
FBS Thermo Scientific Cat. #10270-106
Penicillin-Streptomycin Thermo Scientific Cat. #15140-122
L-Glutamine Thermo Scientific Cat. #25030-024
Agarose Thermo Scientific Cat. #16500-500
Low melting Agarose Serva Electrophoresis Cat. #11384
Phusion DNA polymerase Thermo Scientific Cat. #F-530XL
IgG beads GE Healthcare Cat. #17-0885-04
Streptavidin beads GE Healthcare Cat. #17-5113-01
TRIzol Thermo Scientific Cat. #15596018
TriFast FL Peqlab Biotechnologies Cat. #30-2120
P:C:I, stabilized PanReac AppliChem Cat. #A0889,0100
RiboLock Thermo Scientific Cat. #EO0381
dNTPs Thermo Scientific Cat. #R0141, #R0171, #R0161, #R0152
RevertAid H Minus reverse transcriptase Thermo Scientific Cat. #EP0451
Actinomycin D Sigma Aldrich Cat. #A9415
Puromycin Serva Electrophoresis Cat. #33835
Harringtonine Sigma Aldrich Cat. #SML1091
Protease Inhibitor (cOmplete, EDTA-free) Roche Cat. #05056489001
Yeast RNA Roche Cat. #10109223001
Nitrocellulose Transfer Membrane Santa Cruz Biotechnology Cat. #sc-3724
Luminol Roth Cat. #4203.1
P-Coumaric acid Sigma Aldrich Cat. #C9008
GeneScreen Plus nylon Membrane Perkin Elmer Cat. #NEF1018001PK
Cycloheximide Serva Electrophoresis Cat. #10700
Nocodazole Sigma Aldrich Cat #M1404
TurboDNase Thermo Scientific Cat. #AM2238
RNA Clean & Concentrator Kit Zymo Research Cat. #R1015
Zymoclean Gel DNA Recovery Kit Zymo Research Cat. #D4007
MicroSpin S-400 HR Columns GE Healthcare Cat. #27514001
RNaseI Thermo Scientific Cat. #AM2294
SUPERase Inhibitor Thermo Scientific Cat. #AM2694
Ribo-Zero Gold rRNA Removal Kit Illumina discontinued
SYBR Gold Thermo Scientific Cat. #S11494
SuperScript II reverse transcriptase Thermo Scientific Cat. #18064014
SuperScript III reverse transcriptase Thermo Scientific Cat. #18080044
T4 Polynucleotide kinase NEB Cat. #M0201S
GlycoBlue Thermo Scientific Cat. #AM9515
T4 RNA Ligase 2, truncated K227Q NEB Cat. #M0351S
5′ DNA Adenylation Kit NEB Cat. #E2610S
T4 RNA Ligase 1 NEB Cat. #M0204S
Critical Commercial Assays
RNeasy Mini Kit QIAGEN Cat. #74104
Dual-luciferase reporter assay Promega Cat. #E1960
iTaq Sybr Green Supermix Biorad Cat. #170-8885
Wizard SV Genomic DNA Purification System Promega Cat. #A2360
TruSeq RNA sample Prep Kit Illumina Cat. #RS-122-2002
Deposited Data
Raw and analyzed RNA-Seq and Ribo-Seq data – WT, 4EHP-null and GIGYF1/2-null HEK293T cells This study GEO: GSE144841
Raw and analyzed RNA-Seq and Ribo-Seq data – WT and ZNF598-null HEK293T cells This study GSE149279
Harringtonine and LTM treated HEK293 cells Lee et al., 2012 SRA: SRA056377
Monosome and disome profiling of HEK293 cells Han et al., 2020 GEO: GSE145723
Monosome and disome profiling in mESCs Tuck et al., 2020 GEO: GSE134020
Source imaging data This study – Mendeley data https://doi.Org/10.17632/dk55r385cj.1
Experimental Models: Cell Lines
HEK293T DSMZ ACC 635
GIGYF1/2 KO Peter et al., 2017 N/A
4EHP KO Räsch et al., 2020 N/A
ZNF598 KO This study N/A
Oligonucleotides
Oligonucleotides, see Table S7 This study N/A
Recombinant DNA
pλN-HA-C1-HseIF4E2 (4EHP) Peter et al., 2017 Uniprot: O60573-1
pλN-HA-C1-HseIF4E2 W124A (cap*) Peter et al., 2017 N/A
pλN-HA-C1-HseIF4E2 R103L, E149L (S*) Peter et al., 2017 N/A
pT7-V5-SBP-C1-HseIF4E2 (4EHP) Peter et al., 2017 N/A
pT7-V5-SBP- C1-HseIF4E2 W124A (cap*) Peter et al., 2017 N/A
pT7-V5-SBP- C1-HseIF4E2 R103L, E149L (S*) Peter et al., 2017 N/A
pT7-EGFP-C1-HsGIGYF1 Peter et al., 2017 Uniprot: O60573-1
pT7-EGFP-C1-HsGIGYF1 Y39AY41A M46A L47A (C*) Peter et al., 2017 N/A
pT7-EGFP-C1-HsGIGYF1 Y479A F490A W498A F504A (GYF*) Peter et al., 2017 N/A
pT7-EGFP-C1-HsGIGYF1 W294A, F306A, F312A (DDX6*) Peter et al., 2019 N/A
pT7-EGFP-C1-HsGIGYF2 Peter et al., 2017 Uniprot: Q6Y7W6-1
pT7-EGFP-C1-HsGIGYF2 Y41A Y43A M48A L49A (C*) Peter et al., 2017 N/A
pT7-EGFP-C1-HsGIGYF2 Y538A, F549A, W557A, F563A (GYF*) Peter et al., 2017 N/A
pT7-EGFP-C1-HsGIGYF2 W288A, F300A, F306A (DDX6*) Peter et al., 2019 N/A
pT7-EGFP-C1-HsGIGYF2 C-term (7191299) This study N/A
pEGFP-N3-F-Luc-EGFP Lazzaretti et al., 2009 N/A
pCIneo-HsDBNDD2-HA This study Uniprot: Q9BQY9-2
pCIneo-HsDBNDD2-STOP3-HA This study N/A
pCIneo-HsDBNDD2-STOP18-HA This study N/A
pCIneo-HsDBNDD2-STOP39-HA This study N/A
pCIneo-HsDBNDD2-STOP79-HA This study N/A
pCIneo-HsDBNDD2-STOP89-HA This study N/A
pCIneo-HsDBNDD2-FED25-AAA-HA This study N/A
pCIneo-HsDBNDD2-DPN4-AAA-HA This study N/A
pCIneo-R-Luc-HsDBNDD2 3′ UTR This study N/A
pCIneo-HsLGALS3BP-HA This study Uniprot: Q08380-1
pCIneo-HsLGALS3BP-STOP3-HA This study N/A
pCIneo-HsLGALS3BP-STOP30-HA This study N/A
pCIneo-HsLGALS3BP-STOP60-HA This study N/A
pCIneo-R-LUC-HsLGALS3BP 3′ UTR This study N/A
pCIneo-Hs SPLGALS3BP-R-LUC This study N/A
pCIneo-Hs SPNPTX1-R-LUC This study N/A
pCIneo-R-LUC Pillai et al., 2004 N/A
pSpCas9(BB)-2A-Puro (PX459) Ran et al., 2013 Addgene 48139
pSUPERpuro-BglII-scrambled Jonas et al., 2013 N/A
pSUPERpuro-BglII-HsUPF1-t2 Paillusson et al., 2005 N/A
pSUPERpuro-BglII-HsUPF1-t4 Paillusson et al., 2005 N/A
Software and Algorithms
Adobe Illustrator Adobe https://www.adobe.com/uk/creativecloud.html
Integrative Genomics Viewer Robinson et al., 2011; Thorvaldsdóttir et al., 2013 https://software.broadinstitute.org/software/igv/
ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/
Bowtie 2 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
TopHat 2 Kim et al., 2013 https://ccb.jhu.edu/software/tophat/index.shtml
RiboTaper Calviello et al., 2016 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
QuasR Gaidatzis et al., 2015 https://bioconductor.org/packages/release/bioc/html/QuasR.html
edgeR McCarthy et al., 2012; Robinson et al., 2010 https://bioconductor.org/packages/release/bioc/html/edgeR.html
RiboDiff Zhong et al., 2017 https://github.com/ratschlab/RiboDiff
goseq Young et al., 2010 https://bioconductor.org/packages/release/bioc/html/goseq.html
CHOPCHOP Labun et al., 2016, 2019; Montague et al., 2014 http://chopchop.cbu.uib.no