Table 1.

PQSs selected for biophysical characterization, the coding vs. template strand for the PQSs, their G4 score, and the ChIP-Seq data sets from which the sequences were identified.

Gene	Promoter PQSs Characterized	Coding/ Template Strand	G4 Scorea	G4 ChIP- Seqb	G4-Specific Helicase ChIP-Seqc
BLM	5`-GA GGG A GGGG C GGG A GGG AA	Coding	41	X	X
ERCC8	5`-AA GGG CTAGAA GGG CCA GGGG A GGGG TT	Template		39	X
FAAP24	5`-GT GGGG CTCTGT GGGG CC GGG AATTA GGGG TA	Coding	39	X	X
FANCA	5`-GC GGG CTC GGG CGCA GGG AGCCGCCGCC GGGG CT	Coding	35	X	X
FANCC	5`-TC GGG TCCGT GGGG C GGGG C GGG CG	Template	39	X	X
FEN1	5’-TT GGG CTGAA GGG T GGGG AA GGGGG AA	Template	39		X
GTF2H1	5`-GC GGG AACCCGT GGGGG A GGG A GGG AA	Coding	36	X	X
LIG4	5`-TT GGGGG TCT GGGGG ATCCGGTCGT GGGGG TGTCT GGG AC	Coding	69*		X
MGMT	5`-CC GGGGG C GGGG CC GGGG CGCGC GGGGG CG	Template	60	X
MMS19	5`-AA GGG AGA GGGG CCGGCCT GGGGG C GGGG TT	Template	39	X
NEIL1	5`-CC GGG CCT GGGGG A GGG AAA GGG CC	Template	42		X
NEIL3	5`-TT GGG C GGGG CCT GGG C GGGG CC	Coding	41		X
NTHL1	5`-GT GGG CGC GGG TGA GGG CCC GGG AC	Coding	42		X
PARP3	5`-AA GGG CT GGGG AA GGG CC GGG AC	Coding	41		X
PCNA	5`-CA GGG CGAC GGGGG C GGGG C GGGG CG	Coding	41	X	X
PMS1	5`-CT GGG TGC GGG TGC GGG TGC GGGG TT	Coding	42	X	X
POLB	5`-CT GGG C GGGG C GGGG C GGGG CT	Template	42	X
POLH	5`-CT GGGG CT GGG AGA GGG TGTC GGG AC	Coding	41	X	X
POLL	5’-CC GGG AA GGG CCTCA GGG CCT GGG TT	Template	39		X
POLZ (REV3L)	5`-GA GGG AA GGG C GGG C GGG CG	Template	41	X
PRKDC	5`-TA GGGG CATTTCC GGG TCC GGG CCGAGC GGG CG	Coding	38		X
RAD9A	5`-AT GGGG AGGC GGGGG C GGGG CCGGCA GGGG CG	Coding	59	X
RAD17	5`-CC GGG A GGG ACT GGG CT GGGG CA	Template	40		X
RAD54L	5`-GA GGGG C GGGG C GGGGG C GGGGG TG	Template	62	X
RECQL	5`-CA GGG T GGG AAGCTGAGTC GGG AGAAATGAAGCC GGG AA	Coding	61*		X
REV1	5`-CA GGG C GGGG CC GGGG A GGGG AG	Coding	42	X	X
RPA1	5`-GC GGG CGCT GGG A GGG AGACCA GGG CG	Template	37	X	X
UBE2B	5`-GC GGG TTTAAGA GGG TGA GGG C GGG TA	Template	36	X	X
WRN	5`-GA GGGG A GGG AA GGGG AGGC GGGG AG	Coding	40	X
XAB2	5`-GT GGG TT GGG AGGCT GGG CA GGGG AT	Template	39		X

^aThe G4 scores were calculated with the QGRS mapper algorithm using the default settings,⁵⁸ with the exception of the sequences marked with *, in which the sequence length was increased to 45 nt to accommodate the longer sequences.

^bSequences identified with an X were found in the G4 ChIP-Seq data.³⁰

^cSequences identified with an X were found in the XPB/XPD G4-specific helicase ChIP-Seq data.³¹