Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia Taranjit Singh Rai,1,2,3 John J. Cole,1,2,5 David M. Nelson,1,2,5 Dina Dikovskaya,1,2 William J. Faller,1 Maria Grazia Vizioli,1,2 Rachael N. Hewitt,1,2 Orchi Anannya,1 Tony McBryan,1,2 Indrani Manoharan,1,2 John van Tuyn,1,2 Nicholas Morrice,1 Nikolay A. Pchelintsev,1,2 Andre Ivanov,1,2,4 Claire Brock,1,2 Mark E. Drotar,1,2 Colin Nixon,1 William Clark,1 Owen J. Sansom,1 Kurt I. Anderson,1 Ayala King,1 Karen Blyth,1 and Peter D. Adams1,2 1Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; 2Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom; 3Institute of Biomedical and Environmental Health Research, University of West of Scotland, Paisley PA1 2BE, United Kingdom Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Cellular senescence and associated tumor suppression depend on control of chromatin. Histone chaperone HIRA deposits variant histone H3.3 and histone H4 into chromatin in a DNA replication-independent manner. Appropriately for a DNA replication-independent chaperone, HIRA is involved in control of chromatin in nonproliferating senescent cells, although its role is poorly defined. Here, we show that nonproliferating senescent cells express and incorporate histone H3.3 and other canonical core histones into a dynamic chromatin landscape. Expression of canonical histones is linked to alternative mRNA splicing to eliminate signals that confer mRNA instability in non- proliferating cells. Deposition of newly synthesized histones H3.3 and H4 into chromatin of senescent cells depends on HIRA. HIRA and newly deposited H3.3 colocalize at promoters of expressed genes, partially redistributing between proliferating and senescent cells to parallel changes in expression. In senescent cells, but not proliferating cells, promoters of active genes are exceptionally enriched in H4K16ac, and HIRA is required for retention of H4K16ac. HIRA is also required for retention of H4K16ac in vivo and suppression of oncogene- induced neoplasia. These results show that HIRA controls a specialized, dynamic H4K16ac-decorated chromatin landscape in senescent cells and enforces tumor suppression. [Keywords: chromatin; senescence; HIRA; H4K16ac; dynamic; tumor suppression] Supplemental material is available for this article. Received June 15, 2014; revised version accepted November 4, 2014. Cellular senescence is a stable proliferation arrest asso- (Cosme-Blanco et al. 2007; Feldser and Greider 2007). The ciated with an altered proinflammatory secretory path- altered secretory program of senescent cells, comprised of way (Salama et al. 2014). In response to acquisition of an proinflammatory cytokines, chemokines, and matrix pro- activated oncogene, primary human cells enter this pro- teases (the senescence-associated secretory phenotype liferation-arrested senescent state (oncogene-induced se- [SASP]) (Krtolica et al. 2001; Acosta et al. 2008; Kuilman nescence [OIS]). By imposing proliferation arrest, OIS acts et al. 2008), can also contribute to tumor suppression as a tumor suppressor mechanism (Braig et al. 2005; Chen by promoting clearance of some senescent cells by et al. 2005; Collado et al. 2005; Michaloglou et al. 2005). the immune system (Xue et al. 2007; Kang et al. 2011; Even in the absence of an activated oncogene, replicative Lujambio et al. 2013). senescence (RS) places an upper limit on the proliferative Extensive chromatin changes are apparent in senescent capacity of normal cells, also blocking tumor formation cells, most obviously in the form of domains of compacted 4Present address: Barts, The London School of Medicine and Dentistry, Barts Cancer Institute, Queen Mary University of London, London EC1M Ó 2014 Rai et al. This article is distributed exclusively by Cold Spring 6BQ, United Kingdom Harbor Laboratory Press for the first six months after the full-issue 5These authors contributed equally to this work. publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). Corresponding authors: [email protected], taranjitsingh.rai@uws. After six months, it is available under a Creative Commons License ac.uk (Attribution-NonCommercial 4.0 International), as described at http:// Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.247528.114. creativecommons.org/licenses/by-nc/4.0/. 2712 GENES & DEVELOPMENT 28:2712–2725 Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/14; www.genesdev.org Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press HIRA mediates tumor suppression heterochromatin called senescence-associated hetero- is required for deposition of histone H3.3 at active and chromatin foci (SAHF) (Narita et al. 2003, 2006; Braig poised genes and enhancers (Goldberg et al. 2010; Ray- et al. 2005; Zhang et al. 2005; O’Sullivan et al. 2010; Gallet et al. 2011; Pchelintsev et al. 2013). Accordingly, Chandra et al. 2012; Cruickshanks et al. 2013; De Cecco HIRA is required for gene activation in some contexts et al. 2013; Sadaie et al. 2013; Shah et al. 2013). These and (Placek et al. 2009; Dutta et al. 2010; Yang et al. 2011) as other chromatin changes are thought to contribute to the well as recruitment and function of polycomb complexes onset and maintenance of viable senescence-associated at gene promoters and dynamic restoration of chromatin proliferation arrest (Braig et al. 2005; Narita et al. 2006; after DNA damage repair (Adam et al. 2013; Banaszynski Di Micco et al. 2011; Benhamed et al. 2012; Cruickshanks et al. 2013). On the other hand, the HIRA complex and its et al. 2013; Martin et al. 2013). Chromatin changes likely orthologs, together with histone H3.3, are also involved also contribute to activation of the SASP in senescent in chromatin silencing (Sherwood et al. 1993; van der cells (Shah et al. 2013). Subunits of the SWI/SNF ATP- Heijden et al. 2007). Importantly, several recent studies dependent chromatin remodeling complex are targets of have shown histone H3.3 to be a target of recurrent mutation and inactivation in cancer (Wilson and Roberts missense mutations in human cancer, and transcription- 2011), and SWI/SNF is thought to contribute to tumor coupled methylation of histone H3.3 is also thought to be suppression in part through induction of senescence tumor-suppressive (Schwartzentruber et al. 2012; Wu (Chai et al. 2005). In sum, several lines of evidence et al. 2012; Wen et al. 2014; Zhu et al. 2014). Appropri- indicate that chromatin of senescent cells contributes ately for a DNA replication-independent chaperone, to tumor suppression (Braig et al. 2005; Narita et al. HIRA is also involved in control of chromatin in non- 2006). However, the molecular basis of this is poorly proliferating senescent cells (Zhang et al. 2005; Ye et al. understood. 2007; Banumathy et al. 2009; Rai et al. 2011; Duarte et al. Specifically, SAHF have been suggested to contribute to 2014). However, HIRA’s function in senescent cells is stable repression of proliferation genes and/or suppres- poorly defined, and there is currently no direct evidence sion of DNA damage signaling in senescent cells (Narita for a role in tumor suppression. et al. 2003; Zhang et al. 2007; Di Micco et al. 2011). Either Here we set out to better understand dynamic chroma- way, the apparent heterochromatinization of senescent tin regulation in nonproliferating senescent cells and the cells intuitively suggests that their compacted, stable role of HIRA in this process. We reveal chromatin in chromatin contributes to a senescence-mediated barrier senescent cells to be a dynamic landscape linked to to tumor progression. In line with this view of relatively noncanonical regulation of histone mRNAs and excep- static chromatin in senescent cells, compared with pro- tional marking by H4K16ac. The histone chaperone liferating cells, senescent cells synthesize less total HIRA is required for regulation of this landscape and also histone H3 and H4 (O’Sullivan et al. 2010). In fact, in for suppression of oncogene-induced neoplasia in a mouse mammalian cells, the canonical DNA replication-depen- model. This study points to shared roles of HIRA, histone dent histones—H2A, H2B, H3 (H3.1 and H3.2), and H4— H3.3, and H4K16ac in both cellular senescence and tumor are each coded for by 10–15 genes located mostly in suppression. clusters on chromosomes 1 and 6, and the corresponding mRNAs are typically unstable in nonproliferating cells Results (Marzluff et al. 2008). This is again consistent with the view that chromatin in nonproliferating senescent cells The mRNAs encoding the canonical DNA replication- is a relatively fixed entity, intuitively suggestive of an dependent histones are generally regarded as unstable in immobile barrier to tumor progression. However, the nonproliferating cells (Marzluff et al. 2008). Moreover, extent of chromatin dynamics in senescent cells has not compared with proliferating cells, senescent cells synthe- been properly investigated. size less total histone H3 and H4 (O’Sullivan et al. 2010). Histone variant H3.3 contributes to nucleosome de- We were surprised, therefore, when gene expression stabilization (Jin and Felsenfeld 2007) and so is thought to microarray revealed that a subset of histone mRNAs facilitate nucleosome dynamics associated with tran- was apparently up-regulated in RS cells (senescence scription activation and ongoing transcription. Histone confirmed by standard markers of senescence) (Fig. 1A; H3.3 is enriched at nucleosomes at transcription start Supplemental Data Set 1; Supplemental Fig. 1A,B). Close sites (TSSs) of genes and at enhancers and gene bodies of examination showed that these are typically canonical actively transcribed genes (Ahmad and Henikoff 2002; Jin DNA replication-dependent histones from the HIST1 et al. 2009; Goldberg et al.