Doxorubicin Enhances Nucleosome Turnover around Promoters

Abstract

Summary Doxorubicin is an anthracycline DNA intercalator that is among the most commonly used anti-cancer drugs [1]. Doxorubicin causes DNA double-strand breaks in rapidly dividing cells, although whether it also affects general chromatin properties is unknown. Here, we use a metabolic labeling strategy to directly measure nucleosome turnover [2] to examine the effect of doxorubicin on chromatin dynamics in squamous cell carcinoma cell lines derived from genetically defined mice. We find that doxorubicin enhances nucleosome turnover around gene promoters, and turnover correlates with gene expression level. Consistent with a direct action of doxorubicin, enhancement of nucleosome turnover around promoters gradually increases with time of exposure to the drug. Interestingly, enhancement occurs both in wild-type cells and in cells lacking either the p53 tumor suppressor gene or the master regulator of the DNA damage response, Atm, suggesting that doxorubicin action on nucleosome dynamics is independent of the DNA damage checkpoint. In addition, another anthracycline drug, aclarubicin, shows similar effects on enhancing nucleosome turnover around promoters. Our results suggest that anthracycline intercalation promotes nucleosome turnover around promoters by its effect on DNA topology, with possible implications for mechanisms of cell killing during cancer chemotherapy.

Genome-Wide Identification and Characterization of Novel Factors Conferring Resistance to Topoisomerase II Poisons in Cancer

“…3,4,30). To establish which of these mechanisms are affected by Keap1, the SWI/SNF complex, and C9orf82, we treated the respective knockdown or knockout cell lines with either the different Topo II poisons daunorubicin (an anthracycline with a structure and activity similar to doxorubicin) or etoposide (a Topo II poison structurally unrelated to doxorubicin and incapable of evicting histones), or with aclarubicin (an anthracycline family member that evicts histones, induces ROS and inhibits Topo II but does not induce DNA damage; ref.…”

“…Anthracyclines, with doxorubicin as their prominent example, constitute an especially effective class of anticancer drugs, as they intercalate into the DNA and evict histones from the chromatin, concomitant to inhibiting Topo II after the formation of a DNA DSB (3,4). As a result, the DNA damage response is attenuated and the epigenome becomes deregulated at defined regions in the genome (3,5).…”

Local Depletion of DNA Methylation Identifies a Repressive p53 Regulatory Region in the NEK2 Promoter

“…Both doxo and 5aza-dC have been shown to alter chromatin structure, including causing eviction or turnover of nucleosomes (35,38). To determine whether drug treatment causes changes in nucleosome occupancy at the NEK2 promoter, nuclei from HCT116 cells treated with or without 5aza-dC or doxo were digested with MNase and analyzed by qPCR using convergent primers spanning the p53-binding region (Fig.…”

Topoisomerase-mediated chromosomal break repair: an emerging player in many games

“…For example, anthracyclines induce cytotoxicity by trapping TOP2cc on DNA and/or by the generation of free radicals 41 . Anthracyclines have also been shown to promote nucleo some eviction at the promoter of active genes, causing promoter fragility and potentially attenuating the DNA repair response 42,43 .…”