AGS	Aicardi–Goutières syndrome
BER	base excision repair
Bis-DRIP	bisulfite DNA:RNA immunoprecipitation
cpDNA	chloroplast DNA
CPDs	cyclobutane pyrimidine dimers
dNMP	deoxyribonucleoside monophosphate
dNTP	deoxyribonucleoside triphosphate
DRIP	DNA:RNA immunoprecipitation sequencing
DRIPc	DNA:RNA Immunoprecipitation followed by cDNA conversion
DSB	double-strand break
emRiboSeq	embedded ribonucleotide sequencing
GFP	green fluorescent protein
HBD	hybrid binding domain
HydEn-seq	hydrolytic end sequencing
mtDNA	mitochondrial DNA
NER	nucleotide excision repair
NHEJ	nonhomologous end-joining
OKFs	Okazaki fragments
PRR	post-replication repair
Pu-seq	polymerase usage sequencing
R-ChIP	R-loop chromatin immunoprecipitation
RADAR-seq	rare damage and repair sequencing
rDNA	ribosomal DNA
RED	ribonucleotide excision defective
RER	ribonucleotide excision repair
RITOLS	ribonucleotide incorporation throughout the lagging strand
RNAi	RNA initiator
RNAPs	RNA polymerases
RNase H	ribonuclease H
rNMP	ribonucleoside monophosphate
RNR	ribonucleotide reductase
rNTP	ribonucleoside triphosphate
S1-DRIP	S1 nuclease DNA:RNA immunoprecipitation
SLE	systemic lupus erythematosus
ssDNA	single-strand DNA
ssDRIP	ssDNA ligation-based library construction from DRIP
TdT	terminal deoxynucleotidyl transferase
TLS	translesion DNA synthesis