Proteins
53BP1 (P53-binding protein 1)	Promotes DSB repair and checkpoint signaling.
Acf1-Snf2h (ATP-dependent chromatin assembly factor complex containing the SWI/SNF related 2h subunit)	Chromatin remodeler
Artemis	Structure-specific endonuclease that promotes DSB repair
ATM (Ataxia telangiectasia mutated)	DNA damage checkpoint kinase.
ATR (Ataxia telangiectasia and Rad3 related)	DNA damage checkpoint kinase.
ATRIP (ATR interacting protein)	Protein that mediates ATR recruitment in response to DSBs
Brca2 (Breast Cancer 2)	Protein that facilitates Rad51 recruitment onto resected DNA
Chd3 (Chromodomain Helicase DNA Binding Protein 3)	Chromatin remodeler.
CtIP (C-terminal binding protein (CtBP)-interacting protein	Protein that promotes resection.
HELLS (Helicase, Lymphoid Specific)	Chromatin remodeler.
HP1 (Heterochromatin protein 1)	Heterochromatin-specific protein associated with H3K9me2/3.
KAP1 (Kruppel-associated box (KRAB)-associated protein 1)	Protein that promotes silencing.
LINC (Linker of nucleoskeleton and cytoskeleton complex)	Complex spanning the nuclear envelope, composed of a SUN protein across the inner membrane and a KASH protein across the outer membrane.
Mdc1 (Mediator of DNA damage checkpoint 1)	Protein that interacts with γH2AX to mediate DSB repair and checkpoint activation.
Mu2 (Mutator 2)	Drosophila homologue of Mdc1.
Rad54 (Radiation-sensitive mutant protein 54)	Protein that promotes Rad51-mediated strand invasion.
Rad6 (Radiation-sensitive mutant protein 6)	E2 ubiquitin-conjugating enzyme that promotes DNA repair progression.
RENi (Rad60-Esc2-NIP45 protein family)	Protein family with SUMO-like domains that work in concert with STUbL for DSB repair.
RPA (Replication Protein A)	Trimeric complex that binds to ssDNA after resection.
SCAI (Suppressor of cancer cell invasion)	Protein that promotes DSB repair.
Smc5/6 (Structural maintenance of chromosomes complex 5/6)	Complex that promotes HR.
SUMO (Small Ubiquitin-like Modifier)	Peptide covalently attached to other proteins to modify their function.
TopBP1 (DNA Topoisomerase II Binding Protein 1)	Protein that promotes ATR activation.
Tosca	Drosophila homologue of the exonuclease Exo1 that contributes to resection.
Unc45 (Uncoordinated mutant protein 45)	Myosin chaperone and activator.
γH2AX/γH2Av	Phosphorylated form of the histone H2A variants H2AX or H2Av. Involved in DSB signaling in mammalian or fly cells, respectively.
Methods
3D-SIM microscopy (3D structured illumination microscopy)	Super resolution microscopy technique.
BrdU (5–bromo–2′–deoxyuridine)	Nucleotide analog.
CLIP tag	Extrinsically fluorescent protein tag that can be labeled with synthetic probes.
CRISPR/Cas9 system (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 system)	Technology that can be used to induce site-specific DSBs by the Cas9 endonuclease directed to a sequence of interest.
Halo tag	Extrinsically fluorescent protein tag that can be labeled with synthetic probes.
Hi-C	Chromatin conformation capture technique used to identify the proximity of genomic regions.
I-SceI (Intron-encoded Saccaromyces cerevisiae endonuclease 1)	Endonuclease used to induce site-specific DSBs.
MiMIC (Minos-mediated integration cassette)	Collection of insertions of transposon for Drosophila genetic manipulation
SNAP tag	Extrinsically fluorescent protein tag that can be labeled with synthetic probes.
STED microscopy (Stimulated emission depletion microscopy)	Super resolution microscopy technique.
TUNEL (Terminal deoxynucleotidyl transferase (TdT) dUTP nick-end labeling)	Assay to detect DNA breaks.