REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
RPA-pSer33	Bethyl	Cat#A300-246A, RRID:AB_2180847
RPA	Abcam	Cat#Ab2175, RRID:AB_302873
gH2AX	Millipore	Cat#05-636, RRID:AB_309864
ATM-pSer1981	Millipore	Cat#05-740, RRID:AB_309954
ATM	Sigma Aldrich	Cat#A1106, RRID:AB_796190
Chk1	Cell Signaling Technology	Cat#2360, RRID:AB_2080320
Chk1-pSer345	Cell Signaling Technology	Cat#133D3, RRID:AB_331212
Chk2	Millipore	Cat#05-649, RRID:AB_2244941
Cleaved Caspase 3	Cell Signaling Technology	Cat#9661, RRID:AB_2341188
BRCA1	Millipore	Cat#OP107, RRID:AB_213254
BRCA2	Millipore	Cat#OP95, AB_206776
ALC1/CHD1L	Cell Signaling Technology	Cat#13460, RRID:AB_2798225
MBD4	Invitrogen	Cat#PA5-51670, RRID:AB_2643787
SMUG1	Abcam	Cat#ab192240
dUTPase/DUT	Abcam	Cat#ab137097
α-Tubulin	Sigma-Aldrich	Cat#T6199, RRID:AB_477583
UNG	Novus Biologicals	Cat#NBP1-49985, RRID:AB_10012175
PARP1	Cell Signaling Technology	Cat#9542, RRID:AB_216073
UBC13/UBE2N	Cell Signaling Technology	Cat#4919, RRID:AB_2211168
PARP2	Sigma-Aldrich	Cat#MABE18, RRID:AB_10807040
Histone H3	Abcam	Cat#ab10799, RRID:AB_470239
53BP1	Bethyl Laboratories	Cat#A300-272A, RRID:AB_185520
PAR binding reagent	Millipore	Cat#MBE1031
ALC1/CHD1L (mouse)	St John’s laboratory	Cat#STJ116477
53BP1	Novus Biologicals	Cat#NB100-304, RRID:AB_10003037
RAD51	Millipore	Cat#ABE257, RRID:AB_10850319
Beta-Actin (AC-15)	Sigma-Aldrich	Cat#A1978, RRID:AB_476692
BARD1	Abcam	Cat#ab64164, RRID:AB_1924804
SMC1 antibody	Abcam	Cat# ab21583, RRID:AB_2192477
DAPI	Life Technology	Cat#D21490
Goat anti-Mouse Immunoglobulins/HRP	Agilent-Dako	Cat#P0447, RRID:AB_2617137
Swine anti-Rabbit Immunoglobulins/HRP	Agilent-Dako	Cat#P0399, RRID:AB_2617141
Bacterial and Virus Strains
E. coli Rosetta (DE3) Competent Cells	Novagen(Merck)	Cat#0954-3CN
One Shot ccdB Survival 2 T1R Competent Cells	ThermoFisher	Cat#A10460
One Shot Stbl3 Chemically Competent E. coli	ThermoFisher	Cat#C737303
Critical Commercial Assays
CellTiter-Glo	Promega	Cat#G8462
Chemicals, Peptides, and Recombinant Proteins
Doxycycline	Sigma-Aldrich	Cat#M0503-5X2MG
Blasticidin	ThemoFisher Scientific	Cat#A1113903
Hygromycin B	ThemoFisher Scientific	Cat#10687010
Zeocin	ThemoFisher Scientific	Cat#R25005
Puromicin	ThemoFisher Scientific	Cat#A1113803
Lipofectamine 2000	ThemoFisher Scientific	Cat#11668019
EDTA-free Complete protease inhibitor cocktail	Roche	Cat#COEDTAF-RO
PhosSTOP phosphatase inhibitor cocktail	Roche	Cat#PHOSS-RO
4x NuPAGE LDS sample buffer	ThemoFisher Scientific	Cat#NP0008
ProLong Gold antifade with DAPI	Thermo Fisher Scientific	Cat#P36931
Lipofectamine RNAiMAX	Invitrogen	Cat#13778150
QIAquick PCR purification kit	QIAGEN	Cat#28106
QIAquick Gel Extraction Kit	QIAGEN	Cat#28706
QIAprep Spin Miniprep Kit	QIAGEN	Cat# 27106
Veliparib	Selleck Chemicals	Cat#S1004
Olaparib	Selleck Chemicals	Cat#S1060
Talazoparib	Selleck Chemicals	Cat#S7048
Etoposide	Sigma Aldrich	Cat#BP885
Cisplatin	Sigma Aldrich	Cat#C2210000
Aphidicolin	Sigma Aldrich	Cat#A0781-1MG
Hydroxyurea (HU)	Sigma Aldrich	Cat#H8627-5G
Camptothecin	Sigma Aldrich	Cat#C9911
Methyl methanesulfonate (MMS)	Sigma Aldrich	Cat#129925-5G
PARGi	Sigma Aldrich	Cat#PDD00017273
dU	Sigma Aldrich	Cat#D5412
5-FU	Sigma Aldrich	Cat#6627
Formy-dU	Gift from Stephen West	NA
INDOLE-3-ACETIC ACID (IAA)	Sigma-Aldrich	Cat#I2886
Resazurin	Sigma-Aldrich	Cat#R7017
Doxycycline hyclate	Sigma-Aldrich	Cat#D9891
Subcellular Protein Fractionation Kit	Thermo Fisher	Cat# 78840
Clarity Western ECL	Bio-Rad	Cat#1705061
Clarity Max Western ECL	Bio-Rad	Cat#1705062
Mononucleosomes	EpiCypher	Cat No. 16-0006
Recombinant human PARG protein	Lambrecht et al., 2015	N/A
Recombinant human PARP1 protein	Gibbs-Seymour et al., 2016	N/A
Recombinant human ALC1 macro domain a.a 585-897	This paper	N/A
HiLoad 16/600 Superdex 200 pg	Sigma-Aldrich	GE28-9893-35
Benzonase Nuclease	Millipore-Merck	E1014
Ni-NTA Agarose	QIAGEN	30230
QuikChange Lightning Site-Directed Mutagenesis Kit	Agilent	210519
NAD+[32P]	Perkinelmer	NEG023X500UC
IPTG	Sigma-Aldrich	I6758-5G
Lysozyme	Sigma-Aldrich	62971-10G-F
Olaparib	Enzo Life Sciences	LKT-O4402-M005
Q5 Site-Directed Mutagenesis Kit	New England BioLabs	Cat#E0554
Diethylnitrosamine	Sigma-Aldrich	N0756
Deposited Data
Code	GitHub	https://github.com/saphir746/ALC1-HR-survival
Mendeley Data	Mendeley	https://doi.org/10.17632/xhw58f995c.1
Experimental Models: Cell Lines
Mouse: ALC1 +/+ MEFs #18	This Paper	N/A
Mouse: ALC1 +/+ MEFs #19	This Paper	N/A
Mouse: ALC1 −/− MEFs #11	This Paper	N/A
Mouse: ALC1 −/− MEFs #14	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 (Non-targeting gRNA LentiGuide Hygro)	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11(ALC1 EX2 gRNA LentiGuide Hygro)	This Paper	N/A
Human: U2OS Flp-In T-Rex HOST	Durocher lab	N/A
Human: ALC1 −/− U2OS Flp-In T-REx	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 Non-targeting gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 Non-targeting gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 PARP1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 PARP1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 PARP2 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 PARP2 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 53BP1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 53BP1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 pLenti CMV Puro (control)	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 pLenti CMV Puro (control)	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 pLenti CMV ALC1 CRISPR-resistant Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 pLenti CMV ALC1 G750E CRISPR-resistant Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 pLenti CMV ALC1 K77R CRISPR-resistant Puro	This Paper	N/A
Human: eHAP iCAS9 #3 Non-targeting gRNA LentiGuide Hygro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1 EX2 gRNA LentiGuide Hygro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 POLQ gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 POLQ gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 POLB gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 POLB gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 FEN1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 FEN1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 EXO1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 EXO1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 LIG4 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 LIG4 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 LIG1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 LIG1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 LIG3 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 LIG3 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 HPF1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 HPF1 gRNA LentiGuide Puro	This Paper	N/A
Human: DLD-1 ALC1 NT LentiCRISPR Puro	This Paper	N/A
Human: DLD-1 BRCA2−/− NT LentiCRISPR Puro	This Paper	N/A
Human: DLD-1 ALC1 EX2 LentiCRISPR Puro	This Paper	N/A
Human: DLD-1 BRCA2−/− ALC1 EX2 NT LentiCRISPR Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 UBC13 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 UBC13 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 ATM gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 ATM gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 DUT gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 DUT gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 SMUG1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 SMUG1 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 UNG gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 UNG gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 MBD4 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 MBD4 gRNA LentiGuide Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 pLenti CMV Puro (control) #2	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 pLenti CMV ALC1 Puro	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 SMUG1 −/−	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 SMUG1 −/−	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1+/+ #1 APEX1 −/−	This Paper	N/A
Human: eHAP iCAS9 #3 ALC1−/− #11 APEX1 −/−	This Paper	N/A
Human: HCT116 BARD1AID/AID	Nakamura et al., 2019	https://doi.org/10.1038/s41556-019-0282-9
Human: HCT116 53BP1−/− BARD1AID/AID	Becker et al., 2020 (bioRxiv)	https://doi.org/10.1101/2020.06.01.127951
Experimental Models: Organisms/Strains
Mouse: Chd1lGt(E305F08)Wrst	This Paper	MGI:3910467
Oligonucleotides
ALC1 G750E F: GGGCAGAGGTGAGTTATTTACAGCTC	This Paper	NA
ALC1 G750E R: CAGTGGCCAGAGTCATCT	This Paper	NA
ALC1 EX2 CRISPR-R F:ATTAGAAGGCGGAGT AAACTGGCTCGCC	This Paper	NA
ALC1 EX2 CRISPR-R R:TGATAGCTCCTTAG GTGAATCCCTGTCAGC	This Paper	NA
BRCA1 siGENOME smart-pool	Dharmacon	M-003461-02
BRCA2 siGENOME smart-pool	Dharmacon	M-003462-01
MPG ON-TARGETplus	Dharmacon	L-005146-00-0005
Non-targeting ON-TARGETplus	Dharmacon	D-001810-10
ALC1KO-3, TTTCTGCCAGGTGGATTAGG; ALC1KO-4, ATACCCTGCTTGCCATGAAA; ALC1KO-5, ATTCTGGCAATGGAAGCACT	This paper	N/A
CRISPR Guides	This Paper	Table S1
Sequencing Barcodes	This Paper	Table S2
Recombinant DNA
pLenti CMV Puro DEST (w118-1)	Addgene	#17452
ALC1 CRISPR-R CMV Puro DEST	This Paper	NA
ALC1 G750E CRISPR-R CMV Puro DEST	This Paper	NA
ALC1 K77R CRISPR-R CMV Puro DEST	This Paper	NA
ALC1wt CMV Puro DEST	This Paper	NA
BFP/GFP Cas9 reporter	Addgene	#67980
px459v2	Addgene	#62988
LentiCRISPRv2	Addgene	#52961
Lenti-sgRNA-Hygro	Addgene	#104991
Lenti-sgRNA-Puro	Addgene	#104990
pX458	Addgene	#48138
Edit-R inducible lentiviral Cas9	Horizon Discovery	#CAS11229
CRISPR Guides	This Paper	Table S1
pNIC-CTHF-ALC1 585-897	This paper	N/A
pNIC-CTHF-ALC1 585-897(D723A)	This paper	N/A
Software and Algorithms
Fiji	NIH	https://imagej.net/Fiji/Downloads
Image Lab 5.2.1	Bio-Rad Laboratories	http://www.bio-rad.com/en-uk/product/image-lab- software?ID = KRE6P5E8Z
Adobe Illustrator 23.11	Adobe	https://www.adobe.com/uk/products/illustrator.html
Adobe Photoshop 20.0.08	Adobe	https://www.adobe.com/uk/products/photoshop.html
Prism 8	GraphPad Software	https://www.graphpad.com/
BWA	Li and Durbin, 2009	0.5.9-r16
MAGeck	Li et al., 2014	0.5.7
R	https://www.r-project.org	3.6.3 (2020-02-29) “Holding the Windsock”
QuPath-0.2.3	https://doi.org/10.1038/s41598-017-17204-5	https://qupath.github.io/
Other
High fat diet	Teklad	TD.06414
Uncropped Data	Mendeley	https://data.mendeley.com/datasets/xhw58f995c/draft?a=f322441d-e12e-4a47-b15b-95d388b35ea1