Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin

Abstract

The rates at which lesions are removed by DNA repair can vary widely throughout the genome, with important implications for genomic stability. To study this, we measured the distribution of nucleotide excision repair (NER) rates for UV-induced lesions throughout the budding yeast genome. By plotting these repair rates in relation to genes and their associated flanking sequences, we reveal that, in normal cells, genomic repair rates display a distinctive pattern, suggesting that DNA repair is highly organized within the genome. Furthermore, by comparing genome-wide DNA repair rates in wild-type cells and cells defective in the global genome-NER (GG-NER) subpathway, we establish how this alters the distribution of NER rates throughout the genome. We also examined the genomic locations of GG-NER factor binding to chromatin before and after UV irradiation, revealing that GG-NER is organized and initiated from specific genomic locations. At these sites, chromatin occupancy of the histone acetyl-transferase Gcn5 is controlled by the GG-NER complex, which regulates histone H3 acetylation and chromatin structure, thereby promoting efficient DNA repair of UV-induced lesions. Chromatin remodeling during the GG-NER process is therefore organized into these genomic domains. Importantly, loss of Gcn5 significantly alters the genomic distribution of NER rates; this has implications for the effects of chromatin modifiers on the distribution of mutations that arise throughout the genome.

Nucleosome remodelling at origins of Global Genome-Nucleotide Excision Repair occurs at the boundaries of higher-order chromatin structure

“…This enabled us to accurately map the nucleosome structure at positions of GG-NER complex binding in a similar fashion to that shown in Figure 2A. In agreement with our previously published Abf1 ChIP-chip data (Yu et al 2016), we found ~4,000 Abf1 binding sites detected by MACS2 (data not shown). It is well established that Abf1 exists in the cell in large excess over the other GG-NER components (Rad7 and Rad16), and has a wide range of different functions outside of GG-NER (Yarragudi et al 2007;Schlecht et al 2008;Ganapathi et al 2011;Zhang et al 2012).…”

“…The Venn-diagram in Figure 3A enables us to identify various subcategories of Abf1 binding sites. We then used our previously published Rad16 ChIP-chip genome-wide occupancy data (Yu et al 2016) to refine this list by identifying the genomic positions enriched for GG-NER complex binding. This yielded 3,600 Abf1 binding sites that are enriched for Rad16.…”

“…We recently demonstrated that the GG-NER complex binds to promoter-proximal regions (Yu et al 2016), but how its components bind to chromatin in relation to the nucleosome structure that exists at these genomic features is unknown. Therefore, we used the list of annotated TSSs described above and plotted GG-NER complex chromatin occupancy at those features to describe in more detail the GG-NER complex binding at these sites.…”

“…We've developed genomic tools for the analysis of DNA damage and repair (Teng et al 2011;Powell et al 2015) (Yu et al 2016). We showed that enhanced DNA repair rates occur within open reading frames; a result of the concerted action of both the TC-NER and GG-NER pathways in these regions.…”

“…We showed that enhanced DNA repair rates occur within open reading frames; a result of the concerted action of both the TC-NER and GG-NER pathways in these regions. Inactivation of the GG-NER complex by deletion of the RAD7 or RAD16 genes, resulted in a striking alteration to the genomic distribution of DNA repair rates (Yu et al 2016), suggesting the presence of repair domains. In the present study, we examined these domains in greater detail to define them, and to determine how chromatin structure is altered by the GG-NER pathway to promote DNA repair at the level the nucleosome, its primary structural unit.…”