title: DNA break mapping reveals topoisomerase II activity genome-wide.
abstract: Genomic DNA is under constant assault by endogenous and exogenous DNA damaging agents. DNA breakage can represent a major threat to genome integrity but can also be necessary for genome function. Here we present approaches to map DNA double-strand breaks (DSBs) and single-strand breaks (SSBs) at the genome-wide scale by two methods called DSB- and SSB-Seq, respectively. We tested these methods in human colon cancer cells and validated the results using the Topoisomerase II (Top2)-poisoning agent etoposide (ETO). Our results show that the combination of ETO treatment with break-mapping techniques is a powerful method to elaborate the pattern of Top2 enzymatic activity across the genome.
authors: Laboratory of Pathology, NCI/NIH, Bldg 10 Rm 2N106, 10 Center Drive, Bethesda, MD 20892, USA. baranellolf@mail.nih.gov.
authors: Laura
authors: L
authors: Baranello
authors: Laboratory of Pathology, NCI/NIH, Bldg 10 Rm 2N106, 10 Center Drive, Bethesda, MD 20892, USA. kouzinef@mail.nih.gov.
authors: Fedor
authors: F
authors: Kouzine
authors: Computational Biology Branch, NCBI/NLM/NIH, Bldg 38a, 8600 Rockville Pike, Bethesda, MD 20894, USA. wojtowda@mail.nih.gov.
authors: Damian
authors: D
authors: Wojtowicz
authors: Systems Biology Center, NHLBI/NIH, Bldg 10 Rm 7B06A, 10 Center Drive, Bethesda, MD 20892, USA. cuik@mail.nih.gov.
authors: Kairong
authors: K
authors: Cui
authors: Computational Biology Branch, NCBI/NLM/NIH, Bldg 38a, 8600 Rockville Pike, Bethesda, MD 20894, USA. przytyck@mail.nih.gov.
authors: Teresa M
authors: TM
authors: Przytycka
authors: Systems Biology Center, NHLBI/NIH, Bldg 10 Rm 7B06A, 10 Center Drive, Bethesda, MD 20892, USA. zhaok@mail.nih.gov.
authors: Keji
authors: K
authors: Zhao
authors: Laboratory of Pathology, NCI/NIH, Bldg 10 Rm 2N106, 10 Center Drive, Bethesda, MD 20892, USA. levens@helix.nih.gov.
authors: David
authors: D
authors: Levens
mesh_terms: D002874:Chromosome Mapping; D004247:DNA / Q000378:metabolism*; D053903:DNA Breaks, Double-Stranded; D053904:DNA Breaks, Single-Stranded; D004250:DNA Topoisomerases, Type II / Q000378:metabolism*; D045325:HCT116 Cells; D006801:Humans; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA; D004250:DNA Topoisomerases, Type II