REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-SKIV2L	Proteintech group	Cat#11462-1-AP; RRID:AB_2187472
Rabbit polyclonal anti-TTC37	Novus Biologicals	Cat#NBP1-93640; RRID:AB_11030277
Rabbit polyclonal anti-WDR61	Sigma-Aldrich	Cat#SAB1401852; RRID:AB_10609719
Rabbit polyclonal anti-WDR61	Thermo Fisher Scientific	Cat#PA5-40079; RRID:AB_2605542
Mouse monoclonal anti-human RNASEH1 (Clone 5D10)	Abnova	Cat#H00246243-M01; RRID:AB_530236
Rabbit polyclonal anti-GFP	Abcam	Cat#ab290
Mouse monoclonal anti-beta-Actin	Abcam	Cat#ab8226; RRID:AB_306371
Mouse monoclonal anti-Histone H3	Abcam	Cat#ab10799; RRID:AB_470239
Mouse monoclonal anti-alpha-Tubulin	Sigma-Aldrich	Cat#T6199
Rabbit polyclonal anti-TRF2	Novus Biologicals	Cat#NB110-57130; RRID:AB_844199
Mouse monoclonal anti-TRF2 (Clone 4A794)	Millipore	Cat#05-521; RRID:AB_2303145
Mouse monoclonal anti-TRF1	Santa Cruz Biotechnology	Cat#sc-56807; RRID:AB_793407
Mouse monoclonal anti-TIN2	Sigma-Aldrich	Cat#SAB4200108; RRID:AB_10624591)
Mouse monoclonal anti-DNA-RNA Hybrid	Kerafast	Cat#ENH001, RRID:AB_2687463
Mouse monoclonal anti-Phospho-ATM (Ser1981) (10H11.E12)	Cell Signaling	Cat#4526
Rabbit polyclonal anti-53BP1	Novus Biologicals	Cat#NB 100-304, RRID:AB_350221
Mouse monoclonal anti-Cyclin A (At10.2)	Santa Cruz biotechnology	Cat#sc-53227; RRID:AB_782329
Goat anti-rabbit Alexa Fluor 594	Thermo Fisher Scientific	Cat#A-11037
Goat anti-mouse Alexa Fluor 594	Thermo Fisher Scientific	Cat#A-11005
Donkey anti-rabbit Alexa Fluor 488	Thermo Fisher Scientific	Cat#A-21206
Donkey anti-mouse Alexa Fluor 488	Thermo Fisher Scientific	Cat#R37114
goat anti-rabbit Alexa Fluor 488	Thermo Fisher Scientific	Cat#A11008
Goat anti-Mouse Ig/HRP	Agilent	Cat#P0447, RRID:AB_2617137
Swine anti-rabbit Ig/HRP	Agilent	Cat#P0217, RRID:AB_2728719
anti-DIG-alkaline phosphatase	Roche	Cat#11093274910
Bacterial and virus strains
E. coli: Stable Competent cells	New England BioLabs	Cat#C3040H
Chemicals, peptides, and recombinant proteins
Aphidicolin	Sigma-Aldrich	Cat#A0781
Thymidine	Sigma-Aldrich	Cat#T1895
Nocodazole	Sigma-Aldrich	Cat#M1404
Phosphatase inhibitor	Sigma-Aldrich	Cat#P0044
RNase III	Thermo Fisher Scientific	Cat#AM2290
Colcemid	Roche	Cat#10295892001
RNase H	New England BioLabs	Cat#M029L
RNase A	Roche	Cat#10109169001
EdU	Thermo Fisher Scientific	Cat#E10415
7-Amino-Actinomycin D	BD Biosciences	Cat#559925
Propidium Iodide	Sigma-Aldrich	Cat#P4864
ProLong gold antifade Mountant with DAPI	Invitrogen	Cat#P36935
Benzonase	Sigma-Aldrich	Cat#E1014-25KU
cOmplete, EDTA-free Protease Inhibitor Cocktail	Roche	Cat#11873580001
Protease inhibitor cocktail	Sigma-Aldrich	Cat# P8340
DNase I	Qiagen	Cat#79254
DNase I	Roche	Cat#4716728001
SuperScript III Reverse Transcriptase	Thermo Fisher Scientific	Cat#18080093
Fetal Bovine Serum	Sigma-Aldrich	Cat#F2442
Insect-XPRESS medium	Lonza	Cat#BELN12-730Q
Lipofectamine RNAiMax	ThermoScientific	Cat#13778150
Normal Donkey serum	Jackson ImmunoResearch	Cat#017-000-121
Normal Goat serum	Jackson ImmunoResearch	Cat#005-000-121
Blocking Reagent	Roche	Cat#11096176001
Dynabeads Protein A	Invitrogen	Cat#10001D
Dynabeads Protein G	Invitrogen	Cat#10004D
CDP-Star ready-to-use	Roche	Cat#12041677001
BsrGI-HF	New England Biolabs	Cat#R3575S
EcoRI-HF	New England Biolabs	Cat#R3101S
HindIII-HF	New England Biolabs	Cat#R3104S
SspI-HF	New England Biolabs	Cat#R3132L
XhoI	New England Biolabs	Cat#R0146L
Glycogen	Thermo Fisher Scientific	Cat#R0561
Ni-NTA agarose	Qiagen	Cat#30210
Bio-Rad Protein Assay Dye Reagent Concentrate	Bio-Rad	Cat#500-0006
Trypsin Gold, Mass Spectrometry Grade	Promega	Cat#V5280
UltraHyb-Oligo solution	Thermo Fisher Scientific	Cat#AM8663
Critical commercial assays
3’ end labelling kit	Roche	Cat#03353575910
RNeasy Mini Kit	Qiagen	Cat#74104
iTaq Universal SYBR Green Supermix	Bio-Rad	Cat#1725124
Power SYBR Green PCR Master Mix	Applied Biosystems	Cat#4368708
Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay kit	Thermo Fisher Scientific	Cat#C10634
Click-iT Edu Alexa Fluor 647 Imaging Kit	hermo Fisher Scientific	Cat#C10640
Click-iT EdU Alexa Fluor 488 Imaging kit	Thermo Fisher Scientific	Cat#C10337
Duolink PLA Red Starter Kit	Sigma-Aldrich	Cat#DUO92101
Nucleofector kit R	Lonza	Cat#VVCA-1001
Nucleofector Kit V	Lonza	Cat#VVCA-1003
QuickChange Lightning Multi Site-Directed Mutagenesis Kit	Aligent Technologies	Cat##210513
Deposited data
FACS data for cell cycle synchronisation and analysis HeLa1.3 cells	This paper, FLOWRepository	FR-FCM-Z6UL (http://flowrepository.org/id/RvFrbTWARY1y21uJW9H6F6kRo6g2gxddtnRXZHYLwP0vvYBl5OSEapEbgElyn0rp)
FACS data for cell cycle analysis of HeLa1.3 shCtr or SKIV2L depleted treated with DMSO or APH	This paper, FLOWRepository	FR-FCM-Z6UR (http://flowrepository.org/id/RvFrjD1JJzAVyuLfZU1I3VYSQjN1gkLsX1swjnyfnv80eupejavnlAbSdgWHB7Ws)
FACS data for cell cycle analysis HEK293 cells	This paper, FLOWRepository	FR-FCM-Z6UX (http://flowrepository.org/id/RvFr42D68NSnAwxaQDdBbxD7uq9CmVKK6QxqtXNKvuT0Qw0sJk18HtoHxnbaVhIM)
Raw and underlying data	This paper, Zenodo	https://doi.org/10.5281/zenodo.10015203
PICh mass spectrometry data	This paper, ProteomeXchange	https://www.proteomexchange.org/Accession number: PXD046955
Experimental models: Cell lines
Spodoptera frugiperda: Sf9 insect cells	Laboratory of P. Cejka	N/A
Human: HeLa1.3 cells	Laboratory of T. De Lange. https://doi.org/10.1074/jbc.M109.038026	N/A
Human: HT1080-ST cells	Laboratory of J. Lingner. https://doi.org/10.1038/sj.emboj.7600952	N/A
Human: HEK293FT cells	ATCC	N/A
Human: U2OS cells	ATCC	Cat#HTB-96
Human: IMR90 cells	Coriell Institute	Cat#I90-83
Oligonucleotides
ON-TARGETplus Non-targeting Pool siRNA	Dharmacon	Cat#D-001810-10-20
SMARTpool: ON-TARGETplus SKIV2L siRNA	Dharmacon	Cat#L-013435-01-0010
SMARTpool: ON-TARGETplus TTC37 siRNA	Dharmacon	Cat#L-020959-02-0020
Set of 4: ON-TARGETplus WDR61 siRNA	Dharmacon	Cat#LQ-014614-01-0002
Primers for qPCR, see Table S3	This paper, Feretzaki et al.70, Sagie et al.11, Porro et al.8	N/A
Oligonucleotides used for EMSA assays, see Table S2	This paper	N/A
Tel-Cy3-O-O-(CCCTAA)3 probe for FISH	PNA bio	Cat#F1002
Telomeric C-rich probe: TAA(CCCTAA)4	This paper	N/A
Telomeric G-rich probe: ATT(GGGATT)4	This paper	N/A
Recombinant DNA
pLKO.1 SKIV2L shRNA	Dharmacon	RNAi Consortium TRCN0000051816
pEGFP	Laboratory of RJ. Crouch, Cerritelli et al.71	N/A
pEGFP-M27-H1	Laboratory of RJ. Crouch, Cerritelli et al.71	N/A
pcDNA3.1(+)-GFP	GenScript	N/A
pcDNA3.1(+)-SKIV2L	GenScript	N/A
pcDNA3.1(+)-SKIV2L (siRes)	This paper	N/A
pcDNA3.1(+)-SKIV2L-V341G	This paper	N/A
pcDNA3.1(+)-SKIV2L-K338R	This paper	N/A
pcDNA3.1(+)-SKIV2L-D243R	This paper	N/A
pFastbac1	GenScript	N/A
pFB-SKIV2L	This paper	N/A
pFB-His-Flag-TTC37	This paper	N/A
pFB-WDR61	This paper	N/A
pFB-MBP-SKIV2L	This paper	N/A
Software and algorithms
Fiji	https://doi.org/10.1038/nmeth.2019	https://imagej.net/software/fiji/
ImageJ macro code used for quantification of S9.6 signal intensity per nucleus	This paper, Zenodo	https://zenodo.org/doi:10.5281/zenodo.10015203
Image Studio Lite 5.0	LICORbio	https://www.licor.com/bio/image-studio/
ImageQuant	Cytiva	https://info.cytivalifesciences.com/image-analysis-software.html
PyMOL	Schrödinger	https://www.pymol.org/
ChimeraX	UCSF Resource for Biocomputing, Visualization, and Informatics, Pettersen et al.72	https://www.cgl.ucsf.edu/chimerax/
MaxQuant software platform (v1.5.8.3)	Max Planck Institute of Biochemistry	https://www.maxquant.org/
GraphPad Prism 9.1.0	Dotmatics	https://www.graphpad.com/
Carl ZEISS ZEN 2 software (blue edition) version 2.0.0.0	ZEISS	https://www.micro-shop.zeiss.com/