RESEARCH ARTICLE Dynamics of chromatin accessibility and epigenetic state in response to UV damage Sandra Schick*, David Fournier*, Sudhir Thakurela, Sanjeeb Kumar Sahu, Angela Garding and Vijay K. Tiwari ‡ ABSTRACT Epigenetic mechanisms determine the access of regulatory factors to DNA during events such as transcription and the DNA damage response. However, the global response of histone modifications and chromatin accessibility to UV exposure remains poorly understood. Here, we report that UV exposure results in a genome-wide reduction in chromatin accessibility, while the distribution of the active regulatory mark H3K27ac undergoes massive reorganization. Genomic loci subjected to epigenetic reprogramming upon UV exposure represent target sites for sequence-specific transcription factors. Most of these are distal regulatory regions, highlighting their importance in the cellular response to UV exposure. Furthermore, UV exposure results in an extensive reorganization of super-enhancers, accompanied by expression changes of associated genes, which may in part contribute to the stress response. Taken together, our study provides the first comprehensive resource for genome-wide chromatin changes upon UV irradiation in relation to gene expression and elucidates new aspects of this relationship. KEY WORDS: Chromatin, Transcription, UV, Epigenetic state INTRODUCTION Maintenance of genome integrity is essential for cell survival and reproduction as DNA is continuously challenged, for example, by environmental factors like solar UV light. UV light primarily induces DNA lesions, such as cyclobutane pyrimidine dimers (CPDs), pyrimidine 6-4 pyrimidone photoproducts (6-4PPs) and their Dewar isomers, but it can also cause DNA double-strand breaks (Rastogi et al., 2010). Many DNA repair pathways have evolved to correct these diverse types of damages in order to prevent DNA lesions causing pathologies such as skin cancer (Iyama and Wilson, 2013; Lo and Fisher, 2014). The DNA damage response involves recognition of damaged sites and transduction of the signal to effector molecules, which further regulate transcriptional changes, DNA repair, cell cycle arrest or, if the damage is too severe, cell death (Zhou and Elledge, 2000). Consequences of DNA lesions, either as a result of UV irradiation or other genotoxic agents, to cell physiology are widely governed by changes in gene expression regulated on various levels (Andrade- Lima et al., 2015; Bowden et al., 2015; Dawes et al., 2014; Sesto et al., 2002). UVB has been shown to inhibit initiation of transcription by impeding the binding of RNA polymerase II to the promoters of many transcribed genes (Gyenis et al., 2014). UV can further modulate the action of polymerases through activation of transcription factors such as the tumor suppressor protein TP53 and activator protein 1 (AP1) resulting in gene expression changes (Engelberg et al., 1994; Laptenko and Prives, 2006). Recent studies have revealed that epigenetic mechanisms also play a role in the transcriptional response following UV irradiation. For example, the components of the ATP-dependent SWI–SNF chromatin remodeling complex BRG1 and BRM (also known as SMARCA4 and SMARCA2, respectively) have been implicated in the transcriptional regulation of UV-induced genes (Hassan et al., 2014; Zhang et al., 2014). Furthermore, many posttranslational histone modifications have been shown to be modulated during the cellular response to DNA damage (Corpet and Almouzni, 2009; Kumar et al., 2012; Li et al., 2014; Tjeertes et al., 2009). For example, following UV exposure, the histone acetyltransferase p300 (also known as EP300) is recruited close to the MMP-1 promoter, regulating MMP-1 transcription by its catalytic activity (Kim et al., 2009). UV exposure induces phosphorylation of histone H3 serine 28 (H3S28p) at promoters of stress-response genes and causes dissociation of histone deacetylase (HDAC) co-repressor complexes that further accompanies enhanced levels of histone acetylation and transcriptional induction of these genes (Keum et al., 2013; Sawicka et al., 2014). H3S28 phosphorylation is furthermore involved in the regulation of RNA-polymerase-III- dependent transcription (Zhang et al., 2011). Given that many long non-coding RNAs (lncRNAs) are deregulated upon X-ray irradiation and doxorubicin treatment in mammalian fibroblasts (Rashi-Elkeles et al., 2014; Younger et al., 2015), and several lncRNAs have been implicated in the DNA damage response (Huarte et al., 2010; Liu and Lu, 2012; Negishi et al., 2014; Wan et al., 2013), it is likely that lncRNAs also play a crucial role in modulating gene expression upon UV irradiation. In addition to promoters, the importance of distal regulatory regions in regulating gene expression is increasingly being appreciated. Enhancers are among such distal regulatory regions that function to augment the transcription of associated genes (Shlyueva et al., 2014). Their active state is characterized by high levels of histone 3 acetylated at lysine 27 (H3K27ac) and chromatin accessibility (Creyghton et al., 2010; Rada-Iglesias et al., 2011; Wang et al., 2008b). Recent findings suggest that enhancer regions might also play an essential role in the DNA damage response by recruiting factors such as TP53 (Younger et al., 2015). Recently, clusters of putative enhancers (named ‘super-enhancers’) have been shown to regulate the expression of genes defining cell identity (Whyte et al., 2013). They have also been found to be deregulated in diseases such as cancer and inflammation (Brown et al., 2014; Chapuy et al., 2013; Hnisz et al., 2013; Mansour et al., 2014; Schmidt et al., 2015; Vahedi et al., 2015), but have not yet been studied in context of UV exposure. Chromatin dynamics constitute a crucial part of the DNA damage response and many studies have shown recruitment of several ATP-dependent chromatin-remodeling complexes as well as histone- modifying enzymes to damage sites (Corpet and Almouzni, 2009; Received 28 April 2015; Accepted 29 September 2015 Institute of Molecular Biology (IMB), Mainz, Germany. *These authors contributed equally to this work ‡ Author for correspondence (v.tiwari@imb-mainz.de) 4380 © 2015. Published by The Company of Biologists Ltd | Journal of Cell Science (2015) 128, 4380-4394 doi:10.1242/jcs.173633 Journal of Cell Science