The common stress responsive transcription factor ATF3 binds genomic sites enriched with p300 and H3K27ac for transcriptional regulation

Zhao et al. BMC Genomics (2016) 17:335 DOI 10.1186/s12864-016-2664-8 RESEARCH ARTICLE Open Access The common stress responsive transcription factor ATF3 binds genomic sites enriched with p300 and H3K27ac for transcriptional regulation Jonathan Zhao1†, Xingyao Li2†, Mingxiong Guo4, Jindan Yu1* and Chunhong Yan2,3,4* Abstract Background: Dysregulation of the common stress responsive transcription factor ATF3 has been causally linked to many important human diseases such as cancer, atherosclerosis, infections, and hypospadias. Although it is believed that the ATF3 transcription activity is central to its cellular functions, how ATF3 regulates gene expression remains largely unknown. Here, we employed ATF3 wild-type and knockout isogenic cell lines to carry out the first comprehensive analysis of global ATF3-binding profiles in the human genome under basal and stressed (DNA damage) conditions. Results: Although expressed at a low basal level, ATF3 was found to bind a large number of genomic sites that are often associated with genes involved in cellular stress responses. Interestingly, ATF3 appears to bind a large portion of genomic sites distal to transcription start sites and enriched with p300 and H3K27ac. Global gene expression profiling analysis indicates that genes proximal to these genomic sites were often regulated by ATF3. While DNA damage elicited by camptothecin dramatically altered the ATF3 binding profile, most of the genes regulated by ATF3 upon DNA damage were pre-bound by ATF3 before the stress. Moreover, we demonstrated that ATF3 was co-localized with the major stress responder p53 at genomic sites, thereby collaborating with p53 to regulate p53 target gene expression upon DNA damage. Conclusions: These results suggest that ATF3 likely bookmarks genomic sites and interacts with other transcription regulators to control gene expression. Keywords: ATF3, ChIP-seq, Enhancer, p300, H3K27ac, p53 Background The development of human diseases is often accompanied by changes in the gene expression landscape. Regulated mainly at the transcription level, gene expression is tightly controlled by transcription factors (TF) that bind not only promoters proximal to transcription start sites (TSS), but also distal cis-regulatory elements (i.e., enhancers) that are far removed from TSS [1, 2]. Genome-wide profiling studies using chromatin immunoprecipitation coupled with * Correspondence: ; † Equal contributors 1 Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA 2 Georgia Cancer Center, Augusta University, Augusta, GA, USA Full list of author information is available at the end of the article sequencing (ChIP-seq) have identified thousands of functional/active enhancers that are either bound by the transcriptional co-activator p300, or characterized by their association with high levels of H3 K27 acetylation (H3K27ac) [3–5]. These enhancers often carry binding sites for more than one TF, which interact with the basal transcription machinery associated with core promoters to regulate gene transcription [2]. Very often, TFs also recruit chromatin-modifying enzymes to convert the chromatin to a state permissive for transcription. Pioneer transcription factors (e.g., FoxA1, PU.1), for example, are often the first to engage in a regulatory chromatin region upon stimulation, and enhance transcription by remodeling the local chromatin to make it competent for other TFs to bind [6]. © 2016 Zhao et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Zhao et al. BMC Genomics (2016) 17:335 While global profiling of genomic sites competent for TF binding is imperative for the understanding of TF functions, such work has also become increasingly important for defining disease etiologies, as mutations in cis-regulatory elements are frequently found to be associated with human diseases (e.g., cancer) by wholegenome sequencing studies [7]. Activating transcription factor 3 (ATF3) is a member of the ATF/CREB family of transcription factors involving in many important human diseases including cancer [8–11], atherosclerosis [12], infections [13], cardiac hypertrophy [14], and hypospadias [15]. The contributions of ATF3 to these diseases are often owing to its rapid induction by a wide-range of cellular stresses (e.g., DNA damage, oxidative stress, and endoplasmic reticulum (ER) stress), leading to activation of cellular signaling required for the maintenance of cell homeostasis. Indeed, while it binds and activates the tumor suppressor p53 in response to oncogenic challenges (e.g., DNA damage and Pten inactivation) [11, 16], ATF3 also engages in the immune response by interacting with NF-κB and repressing expression of proinflammatory cytokines induced by the toll-like receptor 4 [17]. Similarly, ATF3 induced by reactive oxygen species causes high susceptibility to secondary infections by repressing interleukin 6 (IL-6) expression during sepsis-associated immunosuppression [13]. Like other ATF/CREB transcription factors, ATF3 regulates transcription by binding the canonical ATF/CRE cis-regulatory element (5’-TGACGTCA-3’) or the similar AP-1 site (5’-TGA(C/G)TCA-3’) via its basic region-leucine zipper domain (bZip) [18]. Although an over-simplified model suggests that ATF3 homodimers and heterodimers (with other bZip proteins) repress and induce gene expression, respectively [19], the mechanism by which ATF3 regulates transcription remains largely unknown. Interestingly, although the structures of the bZip domains are highly similar allowing the largely diversified ATF/ CREB proteins to bind the same cis-regulatory elements, the genes regulated by ATF3 are distinct from those controlled by its family members. ATF3 and ATF6, for instance, regulate expression of proapoptotic genes and genes involved in protein folding and ER quality control upon ER stress, respectively [20]. As recent evidence supports that ATF3 engages in a complex protein-protein interaction network involving many TFs and transcription co-regulators [16, 21, 22], it is likely that the interactions with other nuclear proteins define the genomic sites where ATF3 binds and the transcription programs that ATF3 regulates. Characterization of genome-wide ATF3 binding sites would thus lead to further elucidation of the ATF3 interaction network and a better understanding of how ATF3 regulates expression of disease- (...truncated)