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Note: Gamma-H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin (doi: 10.1093/nar/gkn550) Three PI3KK can phosphorylate H2Ax; ATM, ATR and DNA-PK – each requires partner to recognize the break differently. MRN-ATM (heterochromatin region, S/G2-phase), ATRIP-ATR (stalled replication fork or bulk-damage entering to S-phase) and KU70/80-DNA-PK (occur throughout cell cycle). Scoring gH2Ax requires attention since it is not solely represented DSB. Remaining of gH2Ax foci does not mean the DSB has not been fixed. It may remain there to signal the HR to do more additional repair after seal with NHEJ, or the phosphatase system might be malfunction. The further condensation of the 30nm fiber as well as higher levels of chromatin condensation, which culminate with the 10 000-fold compaction of the stretched DNA fiber in the 700nm metaphase chromosomes, are less well understood, but are facilitated by the linker histone H1 and condensins. By ...

Note: DNA Damage Foci: Meaning and Significance (doi: 10.1002/em.21944) Basically, it can reflect DNA damage response but it cannot be solely related to DSB. (ionizing) radiation-induced foci (IRIF or RIF) or DNA repair foci. the histone variant H2AX which gets phosphorylated at its C-terminal Ser-139 residue by the DNA damage-activated kinases ATM, ATR, and DNA-PK, to form gH2AX. gH2AX then acts as a docking station for other DNA damage signaling factors such as MDC1 and 53BP1 which accumulate to form foci in a histone-modification-dependent manner. Foci can also be analysed using fluorescent protein fusion constructs, enabling foci formation and loss  to be monitored in live cells. As scoring is severely influenced by staining quality and imaging characteristics, it is good practice to include positive and negative reference samples which help confirm the validity and reproducibility of the results obtained in a particular experiment. Intensity-based approaches suc...