Histone and Chromatin Dynamics Facilitating DNA repair

Abstract

Our nuclear genomes are complexed with histone proteins to form nucleosomes, the repeating units of chromatin which function to package and limit unscheduled access to the genome. In response to helix-distorting DNA lesions and DNA double-strand breaks, chromatin is disassembled around the DNA lesion to facilitate DNA repair and it is reassembled after repair is complete to reestablish the epigenetic landscape and regulating access to the genome. DNA damage also triggers decondensation of the local chromatin structure, incorporation of histone variants and dramatic transient increases in chromatin mobility to facilitate the homology search during homologous recombination. Here we review the current state of knowledge of these changes in histone and chromatin dynamics in response to DNA damage, the molecular mechanisms mediating these dynamics, as well as their functional contributions to the maintenance of genome integrity to prevent human diseases including cancer.

Keywords: Chromatin; DNA end resection; Homologous recombination; Non-homologous End Joining.

Fig 1.

Generic overview of stepwise chromatin assembly and disassembly processes to form and dismantle, respectively, nucleosomes. The magnification on the left shows the nucleosome structure determined by Karolin Luger by X-ray crystallography. The zoom out on the right indicates that nucleosomes are the repeating unit of chromatin within the nucleus.

Fig 2.

Model for chromatin dynamics during Nucleotide Excision Repair: Upon UVC damage, DDB2 and associated protein ubiquitinate the histones in the vicinity of the DNA lesion, resulting in removal of parental histones from the chromatin in the vicinity of the DNA lesion, triggering chromatin opening which facilitates access for the DNA repair machinery to the DNA lesion. HIRA assembles H3.3 into the chromatin, followed by CAF-1/ASF1-mediated assembly of newly-synthesized H3.1/H4 and FACT-mediated assembly of H2A/H2B onto the repaired DNA. Parental histones also return to the repaired DNA.

Fig 3.

Chromatin disassembly and assembly during DSB repair in mammalian cells. During NHEJ the DSB triggers ATM and INO80-dependent disassembly of ~8 nucleosomes around the break, to allow NHEJ. After NHEJ is complete, HIRA, CAF-1 and ASF1 assemble histones onto repaired DNA. During HR, DNA-PK phosphorylates ASF1 which increases its interaction with CAF-1 and histones. ASF1, CAF-1 and the histone interaction in turn are required for recruitment of the RAD51 loader MMS22L/TONSL to the DSB, resulting in the replacement of RPA with RAD51 on ssDNA. TONSL recruitment is via binding to newly-synthesized histones bearing H4K20me0. After Rad51 loading, H3.3 incorporation promotes extended repair synthesis and sister exchange. By analogy to the situation in yeast, it is likely that CAF-1 and ASF1 also assemble new H3/H4 after DNA repair but this has not yet been shown in mammalian cells. Exactly when chromatin compaction occurs during / after DNA repair is unclear.

Fig 4.

Histone degradation and chromatin movement during HR in yeast. In response to DSBs, histones are ubiquitinated by ubiquitin ligases and histones are evicted from the DNA in a manner dependent on the INO80 complex. These evicted histones are degraded by the proteasome. The resulting loss of histones causes chromatin decompaction which assists in a faster homology search during HR.

Fig 5.

Types of chromatin dynamics during DSB repair in metazoan cells: Clustering of DSBs occurs where DSBs on different chromosomes cluster. 53BP1 accumulates over mega base lengths of DNA along with γH2A.X to form repair foci in the form of liquid droplets acting as a scaffold to recruit other repair factors. Loop extrusion in TADs and spreading of γH2A.X to mega base regions in the TAD occurs during DSB repair. DSBs in repetitive heterochromatin move to the nuclear periphery to facilitate HR with the sister chromatid, away from all the other repeats.