Genes Possessing the Most Frequent DNA DSBs Are Highly Associated with Development and Cancers, and Essentially Overlap with the rDNA-Contacting Genes

Abstract

Double-strand DNA breakes (DSBs) are the most deleterious and widespread examples of DNA damage. They inevitably originate from endogenous mechanisms in the course of transcription, replication, and recombination, as well as from different exogenous factors. If not properly repaired, DSBs result in cell death or diseases. Genome-wide analysis of DSBs has revealed the numerous endogenous DSBs in human chromosomes. However, until now, it has not been clear what kind of genes are preferentially subjected to breakage. We performed a genetic and epigenetic analysis of the most frequent DSBs in HEK293T cells. Here, we show that they predominantly occur in the active genes controlling differentiation, development, and morphogenesis. These genes are highly associated with cancers and other diseases. About one-third of the genes possessing frequent DSBs correspond to rDNA-contacting genes. Our data suggest that a specific set of active genes controlling morphogenesis are the main targets of DNA breakage in human cells, although there is a specific set of silent genes controlling metabolism that also are enriched in DSBs. We detected this enrichment by different activators and repressors of transcription at DSB target sites, as well breakage at promoters. We propose that both active transcription and silencing of genes give a propensity for DNA breakage. These results have implications for medicine and gene therapy.

Genome-Wide Study of Colocalization between Genomic Stretches: A Method and Applications to the Regulation of Gene Expression

“…In the work [ 32 ], we noticed that the DNA double-strand breaks (DSBs) profile around TSSs for the EPD database (which contains only experimentally validated promoters and TSSs) is quite similar to transcription factor occupancy profile around TSSs [ 33 ]. Replacement of canonical histones by histone variants, in particular, the replacement of H2A by H2A.Z (isoform H2AFZ) over promoters [ 34 , 35 , 36 ], plays an important role in chromatin dynamics during transcription and other DNA-templated activities.…”

Induction of the Erythroid Differentiation of K562 Cells Is Coupled with Changes in the Inter-Chromosomal Contacts of rDNA Clusters

“…The sizes of these domains more or less overlapped with the postulated sizes of nuclear condensates (approximately 0.3–0.4 μm), corresponding to a 30-nm-like fiber structure of 50 kb DNA stretches [ 35 , 36 ]. Third, the analysis of rDNA-contacting regions in genome browsers revealed that these regions very often corresponded to long stretches of up to 50 kb, decorated with H3K27ac marks, which are known as super-enhancer sites that can shape condensates [ 10 , 13 , 16 , 37 ]. Nucleoli, as the largest membrane-less organelles in nuclei, are good candidates for the organization of condensates, possessing either set of activators or repressors of transcription.…”

“…The DNA samples used for 4C experiments were isolated according to the procedures previously described [ 16 ]. The cells were then fixed in 1.5% formaldehyde, and the nuclei were isolated.…”

“…rDNA clusters often shape numerous contacts in chromosomal regions possessing the long stretches of H3K27ac marks that are associated with super-enhancers and active chromatin regions [ 9 , 12 , 13 ]. However, it has been observed that rDNA contact sites can exactly correspond to repressed chromatin areas [ 14 ] and that rDNA contacts are enriched in segments of closed, repressed, late-replicating chromatin, CTCF-binding sites, and with the regions possessing the most frequent DNA DSBs inside active and silenced genes [ 15 , 16 ]. Taken together, these facts support the view on the role of rDNA genes in the global epigenetic regulation of gene expression by the shaping of physiological 3D chromosomal structures [ 17 , 18 ].…”