| Antibodies |
| Rabbit polyclonal anti-G3BP1 |
Proteintech |
Cat# 13057-2-AP, RRID:AB_2232034 |
| Rabbit polyclonal anti-HA |
Abcam |
Cat# ab9110, RRID:AB_307019 |
| Mouse monoclonal anti-FLAG |
Sigma-Aldrich |
Cat# F3165, RRID:AB_259529 |
| Rat monoclonal anti-FLAG |
Invitrogen |
Cat# MA1-142, RRID:AB_2536846 |
| HRP conjugated anti-FLAG |
Invitrogen |
Cat# MA1-91878-HRP, RRID:AB_2537626 |
| Rabbit polyclonal anti-GAPDH |
Invitrogen |
Cat# PA1-16777, RRID:AB_568552 |
| Mouse monoclonal anti-GFP |
Santa Cruz |
Cat# sc-996, RRID:AB_2187785 |
| Mouse anti-puromycin, clone 12D10, Alexa Fluor 488 conjugated antibody |
Sigma-Aldrich |
Cat# MABE343-AF488, RRID:AB_2736875 |
| Goat anti-mouse IgG (H&L) (HRP) |
Abcam |
Cat# ab6789, RRID:AB_955439 |
| Mouse monoclonal anti-ATP5A |
Abcam |
Cat# ab14748, RRID:AB_301447 |
| Goat anti-Mouse IgG H&L (Alex Fluor® 647) |
Abcam |
Cat# ab150115, RRID:AB_2687948 |
| Goat anti-Rabbit IgG H&L (Alexa Fluor® 594) |
Abcam |
Cat# ab150080, RRID:AB_2650602 |
| Goat anti-Mouse IgG H&L (Alexa Fluor® 488) |
Abcam |
Cat# ab150113, RRID:AB_2576208 |
| Goat Anti-Rat IgG H&L (Alexa Fluor® 488) |
Abcam |
Cat# ab150157, RRID:AB_2722511 |
| Mouse monoclonal anti-DDX3 |
Abcam |
Cat# ab196032 |
| Rabbit polyclonal anti-DDX3Y |
Invitrogen |
Cat# PA5-90055, RRID:AB_2805908 |
| Bacterial and Virus Strains |
| One Shot™ TOP10 Chemically Competent E. coli
|
Invitrogen |
Cat# 404003 |
| BL21(DE3)-RIL Competent E. coli
|
Agilent |
Cat# 230204 |
| Chemicals, Peptides, and Recombinant Proteins |
| Streptavidin-HRP |
Cell Signaling Technology |
Cat# 3999, RRID:AB_10830897 |
| DDX3X-mCherry recombinant protein |
This paper |
N/A |
| DDX3Y-mCherry recombinant protein |
This paper |
N/A |
| MBP-DDX3X recombinant protein |
This paper |
N/A |
| MBP-DDX3Y recombinant protein |
This paper |
N/A |
| N-Lauroylsarcosine sodium salt solution |
Sigma-Aldrich |
Cat# L7414-10ML |
| SUPERase·In™ RNase Inhibitor |
Invitrogen |
Cat# AM2694 |
| Proteinase K solution (20 mg/mL) |
Life Technologies |
Cat# AM2548 |
| Lipofectamine 2000 |
Thermo Fisher |
Cat# 11668019 |
| Pierce streptavidin magnetic beads |
Thermo Fisher |
Cat# 88816 |
| Agencourt AMPure XP |
Beckman Coulter |
Cat# A63881 |
| TRIzol |
Invitrogen |
Cat# 15596026 |
| IPTG |
Thermo Fisher |
Cat# 34060 |
| DAPI |
Sigma-Aldrich |
Cat# D9542 |
| Fisher BioReagents™ Bovine Serum Albumin, Heat Shock Treated |
Fisher Scientific |
Cat# BP1600-100 |
| Polyuridylic acid potassium salt |
Sigma-Aldrich |
Cat# P9528-10MG |
| Sodium arsenite |
Spectrum Chemical |
Cat# S-222 |
| Sorbitol solution |
Spectrum Chemical |
Cat# S-1525 |
| Thapsigargin |
ACROS Organics |
Cat# AC328570010 |
| CCCP |
Alfa Aesar |
Cat# AAL06932MC |
| Puromycin |
Takara Bio USA |
Cat# 631305 |
| MG132 |
Sigma-Aldrich |
Cat# 474790-1 MG |
| Hydrogen peroxide solution |
Sigma-Aldrich |
Cat# H1009 |
| Biotin-phenol |
Iris Biotech |
Cat# LS-3500.1000 |
| Sodium azide |
Sigma-Aldrich |
Cat# S2002 |
| Sodium ascorbate |
Sigma-Aldrich |
Cat# A7631 |
| Trolox |
Sigma-Aldrich |
Cat# 238813 |
| Cycloheximide |
Sigma-Aldrich |
Cat# C7698 |
| Critical Commercial Assays |
| Malachite Green Phosphate Assay Kit |
Sigma-Aldrich |
Cat# MAK307-1KT |
| Flexi® Rabbit Reticulocyte Lysate System |
Promega |
Cat# L4540 |
| Luna® Universal One-Step RT-qPCR Kit |
NEB |
Cat# M3005L |
| Truseq Stranded mRNA Library Prep |
Illumina |
Cat# 20020594 |
| Dynabeads™ mRNA Purification Kit (for mRNA purification from total RNA preps) |
Invitrogen |
Cat# 61006 |
| EnzChek™ Phosphate Assay Kit |
Thermo Fisher |
Cat# E6646 |
| RNA Clean and Concentrator-5 |
Zymo Research |
Cat# R1016 |
| Deposited Data |
| APEX-seq with stress treatment |
This paper |
GEO: GSE171792
|
| APEX-seq without stress treatment |
This paper |
GEO: GSE193783
|
| Raw data |
This paper; Mendeley Data |
https://dx.doi.org/10.17632/9hs5d4fvgd.1
|
| Experimental Models: Cell Lines |
| Human: HeLa |
ATCC |
CCL-2, RRID:CVCL_0030 |
| Human: HEK 293T |
ATCC |
CRL-3216, RRID:CVCL_0063 |
| Mouse: N2a |
ATCC |
CCL-131, RRID:CVCL_0470 |
| Oligonucleotides |
| Primers for all the recombinant DNA |
This paper |
Table S3
|
| Recombinant DNA |
| pPB DDX3X |
This paper |
N/A |
| pPB DDX3Y |
This paper |
N/A |
| pPB DDX3X-IDR1 |
This paper |
N/A |
| pPB DDX3Y-IDR1 |
This paper |
N/A |
| pPB DDX3X-Helicae |
This paper |
N/A |
| pPB DDX3Y-Helicae |
This paper |
N/A |
| pPB DDX3X-IDR2 |
This paper |
N/A |
| pPB DDX3Y-IDR2 |
This paper |
N/A |
| pPB DDX3X-ΔIDR1 |
This paper |
N/A |
| pPB DDX3Y-ΔIDR1 |
This paper |
N/A |
| pPB DDX3X-ΔIDR2 |
This paper |
N/A |
| pPB DDX3Y-ΔIDR2 |
This paper |
N/A |
| pPB DDX3X-ΔHelicase |
This paper |
N/A |
| pPB DDX3Y-ΔHelicase |
This paper |
N/A |
| pPB DDX3XIDR1-DDX3YHelicae-DDX3YIDR2
|
This paper |
N/A |
| pPB DDX3YIDR1-DDX3XHelicae-DDX3XIDR2
|
This paper |
N/A |
| pPB DDX3XIDR1-DDX3Xhelicae-DDX3YIDR2
|
This paper |
N/A |
| pPB DDX3YIDR1-DDX3Yhelicae-DDX3XIDR2
|
This paper |
N/A |
| pPB DDX3XIDR1-DDX3Yhelicae-DDX3XIDR2
|
This paper |
N/A |
| pPB DDX3YIDR1-DDX3Xhelicae-DDX3YIDR2
|
This paper |
N/A |
| pcDNA3 mito-APEX2 |
This paper |
N/A |
| pPB DDX3X-EGFP |
This paper |
N/A |
| pPB DDX3Y-EGFP |
This paper |
N/A |
| pcDNA3 FLAG-DDX3X |
This paper |
N/A |
| pcDNA3 FLAG-DDX3Y |
This paper |
N/A |
| pcDNA3 HA-DDX3X |
This paper |
N/A |
| pcDNA3 HA-DDX3Y |
This paper |
N/A |
| pET-MCN_His-TEV_V5-DDX3X-mCherry |
(Hondele et al., 2019) |
N/A |
| pET-MCN_His-TEV_V5-DDX3Y-mCherry |
This paper |
N/A |
| pET-MCN_His-TEV_V5-DDX3XIDR1-DDX3YHelicae-DDX3YIDR2-mCherry |
This paper |
N/A |
| pET-MCN_His-TEV_V5-DDX3YIDR1-DDX3XHelicae-DDX3XIDR2-mCherry |
This paper |
N/A |
| pET-MCN_His-TEV_V5-DDX3XIDR1-DDX3Xhelicae-DDX3YIDR2-mCherry |
This paper |
N/A |
| pET-MCN_His-TEV_V5-DDX3YIDR1-DDX3Yhelicae-DDX3XIDR2-mCherry |
This paper |
N/A |
| pET-MCN_His-TEV_V5-DDX3XIDR1-DDX3Yhelicae-DDX3XIDR2-mCherry |
This paper |
N/A |
| pET-MCN_His-TEV_V5-DDX3YIDR1-DDX3Xhelicae-DDX3YIDR2-mCherry |
This paper |
N/A |
| pMAL-c2X |
(Walker et al., 2010) |
Addgene Plasmid #75286, RRID:Addgene_75286 |
| pMAL-c2X-DDX3X |
This paper |
N/A |
| pMAL-c2X-DDX3Y |
This paper |
N/A |
| pcDNA5/FRT/TO APEX2-GFP |
(Padron et al., 2019) |
Addgene Plasmid #129640, RRID:Addgene_129640 |
| pJ4M/TDP-43 |
(Hallegger et al., 2021) |
Addgene plasmid #104480, RRID:Addgene_104480 |
| pPB APEX2-DDX3X |
This paper |
N/A |
| pPB APEX2-DDX3Y |
This paper |
N/A |
| pPB APEX2-EGFP |
This paper |
N/A |
| Software and Algorithms |
| HISAT2 |
(Kim et al., 2015) |
https://ccb.jhu.edu/software/hisat2/index.shtml, RRID:SCR_015530 |
| DESeq2 |
(Love et al., 2014) |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html, RRID:SCR_015687 |
| featureCounts |
(Liao et al., 2014) |
http://bioinf.wehi.edu.au/featureCounts/, RRID:SCR_012919 |
| trimmomatic |
(Bolger et al., 2014) |
http://www.usadellab.org/cms/index.php?page=trimmomatic, RRID:SCR_011848 |
| R |
https://www.r-project.org
|
https://www.r-project.org, RRID:SCR_000036 |
| Fiji |
(Schindelin et al., 2012) |
https://imagej.net/Fiji, RRID:SCR_002285 |
| GraphPad Prism |
GraphPad Software |
https://graphpad.com/scientificsoft, RRID:SCR_002798 |
| Other |
| 384-well microscopy plates |
Brooks Life Sciences |
Cat#4ti-0203 |
| Amicon ultra-15 |
EMD Millipore |
Cat# UFC901024 |
