title: An epigenomic role of Fe65 in the cellular response to DNA damage.
abstract: Previous findings describe Fe65 as a key protein in the cellular response to genotoxic stress. However, the precise molecular mechanism by which Fe65 contributes to DNA damage signaling remains unclear. In this study, we hypothesized that the transcriptional activity of Fe65 may contribute to DNA damage pathways by regulating gene expression patterns activated in response to genotoxic stress. To address this hypothesis, we mapped the global binding profile of Fe65 by chromatin immunoprecipitation (ChIP)-sequencing in the SK-N-SH cells exposed to genotoxic stress. Unexpectedly, the genome-wide location analysis showed a substantial enrichment of Fe65 in the promoter regions of coding genes linked to DNA damage signaling pathways. To further investigate the role of Fe65 in the transcriptional regulation of putative coding target genes identified by ChIP-seq, we performed microarray assays using wild-type (WT) or Fe65 deficient mouse embryonic fibroblasts (MEFs) exposed to oxidative stress with multiple recovery times. Gene ontology analysis of the Fe65-depedent transcriptome suggested that Fe65 modulates the expression of genes critical for DNA damage response. Motif enrichment analysis of regulatory regions occupied by Fe65 revealed a strong correlation with key transcription factors involved in DNA damage signaling pathways, including E2F1, p53, and Jun. Comparison of ChIP-sequencing results with microarray results ultimately identified 248 Fe65-depedent target genes, the majority of which were known regulators of cell cycle, cell death, and DNA replication and repair pathways. We validated the target genes identified by in silico analysis by qPCR experiments. Collectively, our results provide strong evidence that Fe65 plays a role in DNA damage response and cell viability by epigenomic regulation of specific transcriptional programs activated upon genotoxic stress.
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Seungjin
authors.initials: S
authors.lastname: Ryu
authors.affiliation: Howard Hughes Medical Institute and Graduate Program in Biomedical Sciences, University of California at San Diego, School of Medicine, La Jolla, CA 92093, USA.
authors.forename: Francesca
authors.initials: F
authors.lastname: Teles
authors.affiliation: Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Napoli, Italy.
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Minopoli
authors.affiliation: Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Napoli, Italy.
authors.forename: Tommaso
authors.initials: T
authors.lastname: Russo
authors.affiliation: Howard Hughes Medical Institute and Graduate Program in Biomedical Sciences, University of California at San Diego, School of Medicine, La Jolla, CA 92093, USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Rosenfeld
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Institute of Aging Research, Guangdong Medical College, Dongguan, China. Electronic address: yousin.suh@einstein.yu.edu.
authors.forename: Yousin
authors.initials: Y
authors.lastname: Suh
mesh_terms: D000818:Animals; D002460:Cell Line; D004249:DNA Damage; D004260:DNA Repair / Q000502:physiology*; D004622:Embryo, Mammalian / Q000378:metabolism; D044127:Epigenesis, Genetic; D005347:Fibroblasts / Q000378:metabolism; D020869:Gene Expression Profiling; D051379:Mice; D018345:Mice, Knockout; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism*; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: C486243:Apbb1 protein, mouse; D009419:Nerve Tissue Proteins; D009687:Nuclear Proteins; D014157:Transcription Factors
keywords: Chromatin immunoprecipitation-sequencing; DNA damage response; Fe65 transcription; Microarray