REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
SUMO2/3 (IPs)	Abcam	Cat# ab81371; RRID: AB_1658424
SUMO2/3 (Immunoblots)	MBL	Cat# M114-3; RRID: AB_592769
SUMO1	Abcam	Cat# ab32058; RRID: AB_778173
Ubc9	Abcam	Cat# ab75854; RRID: AB_1310787
Dppa2	Millipore	Cat# MAB4356; RRID: AB_1977389
Dppa4	R&D systems	Cat# AF3730; RRID: AB_2094166
Hnrnpc	Abcam	Cat# ab133607; RRID: AB_2860560
HA-probe	Santa Cruz	Cat# sc-805; RRID: AB_631618
Sae1	Abcam	Cat# ab185949; RRID: AB_2827735
Uba2	Abcam	Cat# ab185955; RRID: AB_2827736
Pias1	Cell signaling	Cat# 3550; RRID: AB_1904090
Pias2	Novus Biologicals	Cat# NBP2-19819; RRID: AB_2827737
Pias3	Santa Cruz	Cat# sc-46682; RRID: AB_628128
Pias4	Cell signaling	Cat# 4392; RRID: AB_10547884
Znf451	Sigma	Cat# SAB2108741; RRID: AB_2827738
Ranbp2	Santa Cruz	Cat# sc-74518; RRID: AB_2176784
Senp1	Santa Cruz	Cat# sc-271360; RRID: AB_10611042
Senp2	Santa Cruz	Cat# sc-67075; RRID: AB_2198251
Senp3	Cell signaling	Cat# 5591; RRID: AB_10694546
Senp5	Abcam	Cat# ab47631; RRID: AB_882488
Senp6	Thermo Fisher Scientific	Cat# PA5-69704; RRID: AB_2689788
Senp7	Thermo Fisher Scientific	Cat# PA5-36089; RRID: AB_2827739
H3	Abcam	Cat# ab24834; RRID: AB_2553364
Smchd1	Abcam	Cat# ab31865; RRID: AB_777986
Chemicals, Peptides, and Recombinant Proteins
ML-792	Takeda Oncology	N/A
Trypsin-EDTA	GIBCO	Cat# 25300-054
FBS	Eurobio	Cat# CVFSVF00-01
GlutaMAX	GIBCO	Cat# 35050-038
NEM-NEAA	GIBCO	Cat# 11140-050
LIF	Miltenyi Biotec	Cat# 130-099-895
KSR	Invitrogen	Cat# 10828028
2-mercaptoethanol	GIBCO	Cat# 21985-023
TRIzol	Life Technologies	Cat# 15596018
PfuTurbo polymerase	Agilent	Cat# 600255
HIS-Select® Nickel Affinity Gel	Sigma Aldrich	Cat# P6611
Lysyl Endopeptidase, Mass Spectrometry Grade (Lys-C)	Wako	Cat# 125-05061
Protein G Agarose beads	Roche	Cat# 11243233001
Endoproteinase Asp-N Sequencing Grade	Roche	Cat# 11420488001
Critical Commercial Assays
Affymetrix Mouse Gene 2.0 ST array	Thermo Fisher	Cat# 902119
RNA 6000 Nano kit	Agilent	Cat# 5067-1511
Lipofectamine 2000	Thermo Scientific	Cat# 301705
Q5® Site-Directed mutagenesis kit	New England Biolabs	Cat# E0554S
Gateway BP™ Clonase™ II Enzyme mix	Thermo Scientific	Cat# 11789020
Gateway LR™ Clonase II™ Enzyme mix	Thermo Scientific	Cat# 11791020
Sep-Pak C8 3 cc Vac Cartridge	Waters	Cat# WAT036780
Empore SPE Disks	Sigma Aldrich	Cat# 66883-U
ReproSil-Pur 120 C18-AQ, 1.9 μm	Dr. Maisch	Cat# r119.aq.
Deposited Data
Micro-array dataset	This study	NCBI GEO: GSE144881
Raw MS data (SUMOylome)	This study	ProteomeXchange: PXD017697
Raw MS data (total proteome)	This study	ProteomeXchange: PXD020287
Experimental Models: Cell Lines
R1 mouse ES cells	Cossec et al., 2018	N/A
MERVL::tdTomato Dppa4 KO ES cells	Laboratory of W.Reik	N/A
MERVL::tdTomato Dppa2 KO ES cells	Laboratory of W.Reik	N/A
MERVL::tdTomato Dppa2/4 double KO ES cells	Laboratory of W.Reik	N/A
Mouse embryonic fibroblasts	This study	N/A
Experimental Models: Organisms/Strains
Mouse: C57BL/6J	Institut Pasteur	N/A
Oligonucleotides and plasmids
Mutagenesis primers	Eurofins	See Method Details for sequences
pCMV6-entry Dppa2 WT plasmid	Origene	Cat# MR224204
pCMV6-entry Dppa2 K31R plasmid	This study	N/A
MGC Mouse Dppa4 cDNA	Horizon	Cat# MMM1013-202805602
pCMV Dppa4 WT plasmid	This study	N/A
pCMV K141R/K143R plasmid	This study	N/A
pDONR221 plasmid	Laboratory of Wolf Reik	N/A
pDEST eGFP plasmid	Laboratory of Wolf Reik	N/A
pDEST Dppa2 WT-eGFP plasmid	This study	N/A
pDEST Dppa2 K31R-eGFP plasmid	This study	N/A
pDEST Dppa4 WT-eGFP plasmid	This study	N/A
pDEST Dppa4 K141R/K143R-eGFP plasmid	This study	N/A
siRNA	Horizon Discovery	Table S6
RT-qPCR primers	Eurofins	Table S6
Software and Algorithms
STRING 11.0	Szklarczyk et al., 2019	N/A
FlowJo software	N/A	https://www.flowjo.com/
Graphpad – Prism software	N/A	https://www.graphpad.com/
Cytoscape software	Shannon et al., 2003	https://cytoscape.org/
MaxQuant version 1.5.3.30	Cox et al., 2011	https://www.maxquant.org/
Perseus	Tyanova et al., 2016	https://maxquant.net/perseus/
Other
MEF and ESC RNA-seq data	Cossec et al., 2018	NCBI GEO: GSE99009