RT Journal
A1 van Eijk, Patrick
A1 Nandi, Shuvro Prokash
A1 Yu, Shirong
A1 Bennett, Mark
A1 Leadbitter, Matthew
A1 Teng, Yumin
A1 Reed, Simon H.
T1 Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
JF Genome Research 
JO Genome Research 
YR 2019 
FD January 01 
VO 29 
IS 1 
SP 74 
OP 84 
DO 10.1101/gr.237198.118 
UL http://genome.cshlp.org/content/29/1/74.abstract 
AB Repair of UV-induced DNA damage requires chromatin remodeling. How repair is initiated in chromatin remains largely unknown. We recently demonstrated that global genome–nucleotide excision repair (GG-NER) in chromatin is organized into domains in relation to open reading frames. Here, we define these domains, identifying the genomic locations from which repair is initiated. By examining DNA damage–induced changes in the linear structure of nucleosomes at these sites, we demonstrate how chromatin remodeling is initiated during GG-NER. In undamaged cells, we show that the GG-NER complex occupies chromatin, establishing the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBSs). We demonstrate that these sites are frequently located at genomic boundaries that delineate chromosomally interacting domains (CIDs). These boundaries define domains of higher-order nucleosome–nucleosome interaction. We demonstrate that initiation of GG-NER in chromatin is accompanied by the disruption of dynamic nucleosomes that flank GCBSs by the GG-NER complex.