Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage

Abstract

The addition of poly(ADP-ribose) (PAR) chains along the chromatin fiber due to PARP1 activity regulates the recruitment of multiple factors to sites of DNA damage. In this manuscript, we investigated how, besides direct binding to PAR, early chromatin unfolding events controlled by PAR signaling contribute to recruitment to DNA lesions. We observed that different DNA-binding, but not histone-binding, domains accumulate at damaged chromatin in a PAR-dependent manner, and that this recruitment correlates with their affinity for DNA. Our findings indicate that this recruitment is promoted by early PAR-dependent chromatin remodeling rather than direct interaction with PAR. Moreover, recruitment is not the consequence of reduced molecular crowding at unfolded damaged chromatin but instead originates from facilitated binding to more exposed DNA. These findings are further substantiated by the observation that PAR-dependent chromatin remodeling at DNA lesions underlies increased DNAse hypersensitivity. Finally, the relevance of this new mode of PAR-dependent recruitment to DNA lesions is demonstrated by the observation that reducing the affinity for DNA of both CHD4 and HP1α, two proteins shown to be involved in the DNA-damage response, strongly impairs their recruitment to DNA lesions.

A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice: Impact of Sex and Age

“…However, it was also shown that PARylation of histones and the respective damage sites results in chromatin remodelling and relaxation of the chromatin structure. Resulting from this, accessibility of the damage site is improved and binding of DNA repair factors enhanced upon PARylation [ 33 , 57 ]. Thus, the negative relationship we observed could also reflect a repair facilitating effect of PARylation concomitant with decreasing DNA damage levels.…”

“…Design of oligonucleotides was based on a previously suggested base sequence harbouring the DNA lesion 8-oxodG [ 12 ]. In addition, this base sequence was shown to be suitable for investigation of incision activity towards an AP site analogue (tetrahydrofuran (THF) derivate) [ 57 ]. THF is commonly applied to mimic an AP site in oligonucleotides [ 63 ].…”

Ewing sarcoma protein promotes dissociation of poly( ADP ‐ribose) polymerase 1 from chromatin

“…To confirm that PARP1 is trapped on DNA upon Ews siRNA depletion, we stably expressed GFP‐PARP1 in U2OS cells and precisely monitored the kinetics of GFP‐PARP1 after micro‐irradiation (Smith et al , 2019). We found that while GFP‐PARP1 equally accumulated on micro‐irradiated sites both in WT and Ews −/− cells, it persisted longer when EWS was depleted (Fig 2C).…”

In Situ Analysis of DNA-Protein Complex Formation upon Radiation-Induced DNA Damage

“…For instance, they have been used to discriminate the recruitment of DNA repair proteins at damaged sites in heterochromatin vs. euchromatin regions: light-stimulated production of oxidatively generated DNA lesions was obtained with Killer Red protein fused to transcription repressor, or activator cassettes integrated into distinct genomic loci [87]. Lastly, the chromatin unfolding effect induced by PARP-1 on the accessibility of DNA-binding vs. histone binding domains to DNA damage sites has been investigated by live-cell imaging and fluorescence lifetime measurements [88].…”