REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
TONSL	Sigma	Cat no. HPA046494; RRID: AB_2679673
CAF1A/p150	Quivy et al., 2004	N/A
MCM2	Bethyl Laboratories	Cat no. A300-122A; RRID: AB_155897
CAF1B/p60	Quivy et al., 2004	N/A
DNAJC9	AbCam	Cat no. ab150394; RRID: AB_2890229
HA	Cell Signaling Technology	Cat no. C29F4 #3724; RRID: AB_1549585
DAXX	Sigma	Cat no. HPA008736; RRID: AB_1078625
HJURP	Sigma	Cat no. HPA008436; RRID: AB_1850757
Flag	Sigma	Cat no. F7425; RRID: AB_439687
H3	Abcam	Cat no. ab1791; RRID: AB_302613
H4	Millipore	Cat no. 05-858; RRID: AB_390138
Tubulin	Abcam	Cat no. ab6160; RRID: AB_305328
BAG2	Abcam	Cat no. ab79406; RRID: AB_1603761
HSC/HSP70	Santa Cruz Biotechnology	Cat no. sc-24; RRID: AB_627760
HSC70	Santa Cruz Biotechnology	Cat no. sc-7298; RRID: AB_627761
Flag	Sigma	Cat no. F3165; RRID: AB_259529
Goat Anti-Mouse-Alexa488	Thermo Scientific	Cat no. A-11029; RRID: AB_138404
Bacterial and virus strains
E.coli: BL21 (DE3)-RIL	Stratagene	Cat no. 230245
Chemicals, peptides, and recombinant proteins
Doxycycline	Clontech	Cat no. 631311
ULP1 protease	Homemade	N/A
TEV protease	Homemade	N/A
3C protease	Homemade	N/A
Drosophila topoisomerase Ι (dTopo Ι)	Homemade	N/A
Micrococcal Nuclease Solution	Thermo Scientific	Cat no. 88216
Benzonase Nuclease	Millipore	Cat no. 70746
RNase A	Sigma	Cat no. R4875
Sequencing Grade Modified Trypsin	Promega	Cat no. V5113
Trypsin, Proteomics Grade	Sigma	Cat no. T6567
Critical commercial assays
MinElute PCR Purification Kit	QIAGEN	Cat no. 28004
MinElute Reaction Cleanup Kit	QIAGEN	Cat no. 28204
truChIP Chromatin Shearing Kit	Covaris	Cat no. 520127
KAPA Hyperprep Kit	Kappa Biosystems, Roche	Cat no. KK8504
Deposited data
Structure of the DNAJC9 αB–H3.3–H4–MCM2 HBD quaternary complex	This study	PDB: 7CIZ
Structure of the DNAJC9 ΗΒΔ–H3.3–H4–MCM2 HBD quaternary complex	This study	PDB: 7CJ0
ChIP-seq Data	This study	GEO: GSE154445
Raw Mass Spectrometry Data Sets	This study	PRIDE: PXD020268
Raw Data for Western Blots, Gel-based Assays and ITC	This study	Mendeley Data: https://doi.org/10.17632/y9mgyw9r59.1
Experimental models: Cell lines
U-2-OS FRT/TO Flp-In T-REX	Malecki et al., 2006	N/A
U-2-OS FRT/TO Flp-In T-REX FlagHA-MCM2-WT	Huang et al., 2015	N/A
U-2-OS FRT/TO Flp-In T-REX FlagHA-MCM2-Y81A-Y90A	Huang et al., 2015	N/A
U-2-OS FRT/TO Flp-In T-REX U-2-OS eGFP-TONSL-WT	Saredi et al., 2016	N/A
U-2-OS FRT/TO Flp-In T-REX U-2-OS eGFP-TONSL-N571A	Saredi et al., 2016	N/A
HeLa S3	ATCC	Cat no. CCL-2.2; RRID: CVCL_0058
HeLa S3 pTetOne Puro H3.1-FlagHA	This study	N/A
HeLa S3 pTetOne Puro H3.2-FlagHA	This study	N/A
HeLa S3 pTetOne Puro H3.3-FlagHA	This study	N/A
HeLa S3 pTetOne Puro H4-FlagHA	This study	N/A
HeLa S3 pTetOne Puro CENPA-FlagHA	This study	N/A
HeLa S3 pTetOne Puro H3.1T-FlagHA	This study	N/A
HeLa S3 pTetOne Puro H3.1-E105A-D106A-FlagHA	This study	N/A
U-2-OS FRT/TO Flp-In T-REX DNAJC9-MYC-Flag (WT)	This study	N/A
U-2-OS FRT/TO Flp-In T-REX DNAJC9-H43Q-D45N-MYC-Flag (J)	This study	N/A
U-2-OS FRT/TO Flp-In T-REX DNAJC9-Q224A-R227A-M238A-Y242A-MYC-Flag (4A)	This study	N/A
U-2-OS FRT/TO Flp-In T-REX DNAJC9-H43Q-D45N-Q224A-R227A-M238A-Y242A-MYC-Flag (4AJ)	This study	N/A
293FT	Thermo Scientific	Cat no. R70007; RRID: CVCL_6911
Drosophila S2-DRSC cells	Drosophila Genomics Resource Center; Stock No. 181	RRID: CVCL_Z992
Oligonucleotides
NGS indexed PentAdapters	PentaBase	Cat no. SKU 310
Silencer® Select siDNAJC9	Thermo Scientific	Cat no. s23354
Silencer® Select siBAG2	Thermo Scientific	Cat no. s18295
Silencer® Select siHSPA8 (siHSP7C)	Thermo Scientific	Cat no. s6987
Silencer® Select Negative Control No. 1	Thermo Scientific	Cat no. 4390843
Recombinant DNA
ΦX174 RF I DNA	NEB	Cat no. N3021S
pTetOne Puro H3.1-FlagHA	This study	N/A
pTetOne Puro H3.2-FlagHA	This study	N/A
pTetOne Puro H3.3-FlagHA	This study	N/A
pTetOne Puro H4-FlagHA	This study	N/A
pTetOne Puro CENPA-FlagHA	This study	N/A
pTetOne Puro H3.1T-FlagHA	This study	N/A
pTetOne Puro H3.1-E105A-D106A-FlagHA	This study	N/A
pCMV6-DNAJC9-siRNA-resistent-Myc-Flag (WT)	This study	N/A
pCMV6-DNAJC9-siRNA-resistent-L216A-I220A-Myc-Flag	This study	N/A
pCMV6-DNAJC9-siRNA-resistent-Q224A-R227A-Myc-Flag	This study	N/A
pCMV6-DNAJC9-siRNA-resistent-M238A-Y242A-MycFlag	This study	N/A
pCMV6-DNAJC9-siRNA-resistent-E195A-E199A- MycFlag	This study	N/A
pcDNA5-DNAJC9-siRNA-resistent-Myc-Flag (WT)	This study	N/A
pcDNA5-DNAJC9-siRNA-resistent-Q224A-R227A-M238A-Y242A-Myc-Flag (4A)	This study	N/A
pcDNA5-DNAJC9-siRNA-resistent-H43Q-D45N-Myc-Flag (J)	This study	N/A
pcDNA5-DNAJC9-siRNA-resistent-H43Q-D45N-Q224A-R227A-M238A-Y242A-Myc-Flag (4AJ)	This study	N/A
Software and algorithms
HKL-3000	Minor et al., 2006	https://www.hkl-xray.com/hkl-3000
Xia2	Winter, 2010	https://xia2.github.io/
Phenix	Adams et al., 2010	https://www.phenix-online.org/
PyMOL	The PyMOL Molecular Graphics System, Version 1.7, Schrodinger, LLC	https://www.pymol.org/2/
MaxQuant 1.6.3.4	Cox and Mann, 2008; Cox et al., 2011	https://maxquant.net/maxquant/
Perseus 1.6.2.3	Tyanova et al., 2016	https://maxquant.net/perseus/
GraphPad Prism v8.4	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
R 3.6.2	The R Foundation	https://cran.r-project.org/
Cytoscape 3.8.0	Shannon et al., 2003	https://cytoscape.org/
stringApp 1.5.1	Doncheva et al., 2019	http://apps.cytoscape.org/
Omics Visualizer app 1.3.0	Legeay et al., 2020	http://apps.cytoscape.org/
Trim Galore!	Babraham Bioinformatics	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Bowtie2	Langmead and Salzberg, 2012	https://github.com/BenLangmead/bowtie2
SeqMonk	Babraham Bioinformatics	https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
Galaxy	Afgan et al., 2016	RRID: SCR_006281; https://galaxyproject.org/
MACS	Zhang et al., 2008	https://github.com/macs3-project/MACS
Other
Glutathione Sepharose 4B beads	GE Healthcare	Cat no. 17-0756-04
IMAC Sepharose 6 Fast Flow	GE Healthcare	Cat no. 17-0921-09
HiTrap Heparin HP (5 mL)	GE Healthcare	Cat no. 17-0407-03
HiLoad 16/600 Superdex 200 pg	GE Healthcare	Cat no. 28-9893-35
GFP-Trap® Magnetic Agarose	Chromatek	Cat no. GTMA-20
ANTI-FLAG M2 Affinity Gel	Sigma	Cat no. A2220
Pierce Anti-HA Agarose	Thermo Scientific	Cat no. 26181
Pierce Anti-HA Magnetic Beads	Thermo Scientific	Cat no. 88836
Dynabeads Protein G for Immunoprecipitation	Thermo Scientific	Cat no. 10003D
Agencourt AMPure XP beads	Beckman Coulter	Cat no. A63881