Histone acetylation is regulated by the concerted action of histone acetyltransferases and histone deacetylases that add or remove, re spectively, acetyl groups from lysine residues. There are 18 known HDACs in human cells falling into four classes. Class I is related to budding yeast Rpd3 and includes the Rucaparib supplier proteins HDAC1, HDAC2, HDAC3 and HDAC8 that are ubiquitously expressed and mainly loca lized in the nucleus. Class II HDACs are related to yeast Hda1 and includes the proteins HDAC4 7, HDAC9 and HDAC10. they are not ubiquitously expressed and are mainly localized in the cytoplasm. Class III HDACs known as sirtuins, are related to yeast Sir2 and includes the proteins SIRT1 7 that can be nuclear or cytoplasmic. Class IV HDACs consists of only HDAC11.
Trichostatin A is an aliphatic, hydroxamic acid based compound, which exhibits strong inhibi tory activity on both class I and class II HDACs. Its mode of inhibition is thought to be through chela tion of the zinc ion at the catalytic site of HDAC, which prevents the multiprotein complex from removing the acetyl group from the lysine residues of histones. Treatment of cells with TSA provokes histone acetylation and chromatin relaxation, but also cell cycle arrest. The levels of chromatin acetylation or changes in chromatin acetylation have widely different and pos sibly context dependent effects on DNA repair. In murine cells histone hypoacetylation results in defective recruitment of DNA repair factors and compromises DSB repair, while hyperacetylation mediated by treat ment with HDAC inhibitors allows efficient recruitment of HRR proteins.
On the other hand, treatment with HDAC inhibitors suppresses D NHEJ factor ex pression and causes cell radiosensitization to killing. Also, a delaying effect of HDAC inhibitors on both HRR and NHEJ has been observed. While it is thought that nucleosome unfolding and re laxation facilitates D NHEJ, chromatin compactness may also contribute to efficient NHEJ by keeping the two DNA ends of a DSB close together. Thus, chro matin conformation can be either a facilitator or an im pediment of DSB repair. Indeed, chromatin compactness contributes to the efficient and correct rejoining of IR induced DSBs in centromeric DNA. On the other hand, access of D NHEJ factors to DSBs in transcrip tionally active genomic regions enhances repair.
Re cent work also shows that DSB repair within heterochromatic regions is facilitated by modulations Carfilzomib in chromatin compactness, suggesting that transient con formational alterations are integrated in DSB repair pathways more than previously thought. How the chromatin state or changes in chromatin conformation affect B NHEJ remains unknown, although effects such as the marked reduction in B NHEJ effi ciency in non cycling cells point to chromatin conform ation as a candidate parameter.