53BP1	p53 Binding Protein 1
AGS	Aicardi-Goutières Syndrome
AID	Activation-Induced Deaminase
ALS4	Amyotrophic Lateral Sclerosis type 4
ALT	Alternative Lengthening of Telomeres
AOA2	Ataxia with Oculomotor Apraxia type 2
ASF1	Anti-silencing function 1 protein
ATM	Ataxia Telangectasia Mutated
ATR	Ataxia Telangectasia and Rad3-related protein
BAF	BRG1-associated factor
BAMBI	BMP and Activin Membrane-Bound Inhibitor
BAP1	BRCA1-associated protein 1
BER	Base Excision Repair
CAF-1	Chromatin assembly factor-1
cBAF	Canonical BAF
CBP	cAMP-response element binding protein
CD	Co-directional
CFSs	Common Fragile Sites
CPEO	Chronic Progressive External Ophthalmoplegia
CSB	Cockayne syndrome group B
CSR	Class-Switch Recombination
DIP-seq	DNA immunoprecipitation sequencing
DRIP-Seq	DNA–RNA Immuno-Precipitation sequencing
DRIPc-Seq	DNA-RNA Immuno-Precipitation followed by cDNA conversion coupled to high-throughput sequencing
DSB	Double-strand break
ERFSs	Early Replicating Fragile Sites
ESCs	Mouse embryonic stem cells
FA	Fanconi Anemia
FACT	Facilitates chromatin transcription
G4	G-quadruplex
GLP	G9a-like protein
HAT	Histone acetyltransferase
HBD	Hybrid binding domain
HO	Head-on
HP1	Heterochromatin protein 1
HR	Homologous Recombination
ICLs	Inter-strand crosslinks
Ig	Immunoglobulin
iPSCs	induced pluripotent stem cells
m6A	N6-methyladenosine
MEFs	Mouse Embryonic Fibroblasts
METTL3	Methyltransferase-like protein 3
miRNA	microRNA
MMEJ	Micro-homology-Mediated End Joining
MMR	Mismatch Repair
MRN	Mre11-Rad50-Nbs1
mRNP	messenger ribonucleoprotein
ncBAF	Non-canonical BAF
NHEJ	Non-Homologous End-Joining
PAF-1	RNAPII-Associated Factor 1
PCNA	Proliferating cell nuclear antigen
PRC	Polycomb Repressor Complex
PTMs	Post-translational modifications
RBPs	RNA-Binding Proteins
rDNA	ribosomal DNA
REZ	R-loop Elongation Zones
RFSs	Rare Fragile Sites
RIZ	R-loop Initiation Zones
RLFS	R-loop Forming Sequence
RNAPII	RNA polymerase II
RNF168	Ring Finger protein 168
rNMPs	ribonucleotide monophosphates
R-T	Replication-Transcription
SETX	Senataxin
SWI/SNF	SWItch/Sucrose Non-Fermentable
TA-HRR	Transcription-Associated Homologous Recombination Repair
TAM	Transcription-associated mutagenesis
TAR	Transcription-associated recombination
TC-NER	Transcription-Coupled Nucleotide Excision Repair
TDRD3	Tudor domain-containing protein 3 complex
TERRA	Telomeric-Repeat-containing RNA
TGFβ	Transforming growth factor beta
TonEBP	Tonicity-responsive enhancer binding protein
TOP1	DNA topoisomerase 1
TOP2A	DNA topoisomerase 2-alpha
TOP2B	DNA topoisomerase 2-beta
TOP3B	DNA topoisomerase 3 Beta
UFBs	Ultra-fine anaphase bridges
XPG	Xeroderma Pigmentosum group G
Xrn2	5′-3′ exoribonuclease 2