Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press ATR acts stage specifically to regulate multiple aspects of mammalian meiotic silencing He´le`ne Royo,1 Haydn Prosser,2 Yaroslava Ruzankina,3 Shantha K. Mahadevaiah,1 Jeffrey M. Cloutier,1 Marek Baumann,4 Tomoyuki Fukuda,5 Christer Ho¨ o¨ g,5 Attila To´ th,4 Dirk G. de Rooij,6 Allan Bradley,2 Eric J. Brown,3 and James M.A. Turner1,7 1Division of Stem Cell Biology and Developmental Genetics, Medical Research Council, National Institute for Medical Research, London NW7 1AA, United Kingdom; 2The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom; 3Abramson Family Cancer Research Institute, Department of Cancer Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA; 4Institute of Physiological Chemistry, Technische Universita¨t Dresden, Dresden 01307, Germany; 5Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden; 6Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands In mammals, homologs that fail to synapse during meiosis are transcriptionally inactivated. This process, meiotic silencing, drives inactivation of the heterologous XY bivalent in male germ cells (meiotic sex chromosome inactivation [MSCI]) and is thought to act as a meiotic surveillance mechanism. The checkpoint protein ATM and Rad3-related (ATR) localizes to unsynapsed chromosomes, but its role in the initiation and maintenance of meiotic silencing is unknown. Here we show that ATR has multiple roles in silencing. ATR first regulates HORMA (Hop1, Rev7, and Mad2) domain protein HORMAD1/2 phosphorylation and localization of breast cancer I (BRCA1) and ATR cofactors ATR-interacting peptide (ATRIP)/topoisomerase 2-binding protein 1 (TOPBP1) at unsynapsed axes. Later, it acts as an adaptor, transducing signaling at unsynapsed axes into surrounding chromatin in a manner that requires interdependence with mediator of DNA damage checkpoint 1 (MDC1) and H2AFX. Finally, ATR catalyzes histone H2AFX phosphorylation, the epigenetic event leading to gene inactivation. Using a novel genetic strategy in which MSCI is used to silence a chosen gene in pachytene, we show that ATR depletion does not disrupt the maintenance of silencing and that silencing comprises two phases: The first is dynamic and reversible, and the second is stable and irreversible. Our work identifies a role for ATR in the epigenetic regulation of gene expression and presents a new technique for ablating gene function in the germline. [Keywords: ATR; meiosis; sex chromosomes] Supplemental material is available for this article. Received April 9, 2013; revised version accepted May 31, 2013. During mammalian meiosis, homologous chromosomes for the rest of meiosis and, in the male, after this time synapse and recombine, generating crossovers that are (Greaves et al. 2006; Namekawa et al. 2006; Turner et al. essential for correct chromosome segregation (Handel 2006). Meiotic silencing has been proposed to cause arrest and Schimenti 2010). In order to prevent the generation by starving germ cells of essential gene products (Burgoyne of aneuploid gametes, meiotic cells exhibiting defects in et al. 2009). Other suggested functions include silencing of synapsis or recombination are eliminated from the germ transposable elements and inhibition of transcription at cell pool by meiotic surveillance mechanisms (Nagaoka sites of meiotic DNA double-strand break (DSB) formation et al. 2012). The molecular pathways that constitute these (Inagaki et al. 2010). During wild-type male meiosis, the surveillance mechanisms are currently not well understood. heterologous X and Y (sex) chromosomes remain largely One proposed mechanism by which unsynapsed chro- unsynapsed, and this triggers meiotic silencing of X- and mosomes trigger germ cell arrest is meiotic silencing Y-linked genes. The resulting phenomenon, known as (Baarends et al. 2005; Turner et al. 2005; Ichijima et al. meiotic sex chromosome inactivation (MSCI) (McKee 2012). At the onset of pachytene, genes located on and Handel 1993; Yan and McCarrey 2009), affects pro- unsynapsed chromosomes are inactivated, remaining so tein-coding but not microRNA genes (Song et al. 2009) and results in the formation of the heterochromatic sex body (Solari 1974). MSCI is essential for male fertility 7Corresponding author E-mail [email protected] (Royo et al. 2010) and represents an ideal paradigm for Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.219477.113. studying the epigenetics of meiotic silencing. 1484 GENES & DEVELOPMENT 27:1484–1494 Ó 2013, Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/13; www.genesdev.org Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press ATR regulates meiotic silencing Meiotic silencing involves two sets of proteins: ‘‘sensors,’’ i.e., for some 8–9 d after the initiation of MSCI (Turner et al. which localize to axial elements (AEs) and sense asynapsis, 2004). This raises the questions of whether meiotic silenc- and ‘‘effectors,’’ which localize to the chromatin loops ing is a dynamic process, involving continuous H2AFX associated with unsynapsed AEs, causing gene silencing phosphorylation, and whether ATR is required for the over a considerable distance. The AE component synapto- maintenance of the inactive state. nemal complex protein 3 (SYCP3) (Kouznetsova et al. To interrogate these points, we generated two forms of 2009), HORMA (Hop1, Rev7, and Mad2) domain proteins conditional Atr mutant mice. The first uses a Cre-recom- HORMAD1 (Daniel et al. 2011) and HORMAD2 (Wojtasz binase-driven approach to delete ATR at the initiation of et al. 2012), and breast cancer I gene BRCA1 (Turner et al. silencing, and the second implements a novel, MSCI- 2004) have been identified as sensors: BRCA1 accumulates driven silencing strategy to deplete ATR levels at later along unsynapsed AEs in an SYCP3-, HORMAD1-, and stages, after silencing has been established. HORMAD2-dependent manner, and mice deficient in any of these four proteins exhibit MSCI defects. In contrast, the mediator of DNA damage checkpoint 1 Results (MDC1) (Ichijima et al. 2011) and histone variant H2AFX ATR ablation causes meiotic arrest and defective (Fernandez-Capetillo et al. 2003) are silencing effectors: H2AFX phosphorylation In MDC1-andH2AFX-nulls, gene silencing within the chromosome loops does not occur. Ser139 phosphorylation To examine the role of Atr in MSCI, we used a previously of H2AFX (gH2AFX) is the key epigenetic event triggering described tamoxifen-inducible Cre-ERT2 approach in which MSCI, with spreading of this modification along chromo- Cre-ERT2 expression is driven from the human ubiquitin C some loops being MDC1-dependent (Ichijima et al. 2011). promoter (Ruzankina et al. 2007). Atr flox/À males treated Ago4À/À mice also exhibit a defect in MSCI, associated with with tamoxifen and killed 3 mo later exhibit spermatogonial defective gH2AFX localization on the XY bivalent and stem cell loss and no germ cells in the seminiferous altered small RNA profiles (Modzelewski et al. 2012). epithelium (Ruzankina et al. 2007). We therefore used H2AFX Ser139 phosphorylation is catalyzed by the a modified strategy in which Atr flox/À males and Atr flox/+ PI3K-like kinases ataxia telangiectasia mutated (ATM), controls received 1 wk of tamoxifen treatment and were ATM and Rad3-related (ATR), and DNA-dependent pro- then killed at earlier time points after treatment cessa- tein kinase (DNA-PK) (Sedelnikova et al. 2003). Which tion (see the Materials and Methods for further details kinase generates gH2AFX on unsynapsed meiotic chromo- on treatment strategy). Here we focus only on the meiotic somes is unclear. H2AFX phosphorylation is preserved on silencing phenotypes. the XY bivalent in DNA-PK and Atm single nulls (Bellani Beginning at 3 d after cessation of tamoxifen treatment, et al. 2005). This implies that either ATR is the responsible we observed abnormal nuclear morphology in spermato- kinase or the PI3K-like kinases act redundantly in this cytes from Atr flox/À males, extending from stages I to VI context in a manner already documented in mitotic cells of the seminiferous cycle, as assayed by testis histology (Stiff et al. 2004). Indeed, both ATR (Turner et al. 2004) and (Fig. 1A). This was associated with meiotic germ cell loss Ser1981-phosphorylated ATM (Hamer et al. 2004) have between stages III and V, corresponding to mid-pachy- been found to localize to the XY bivalent during pachytene. tene. The level of ATR protein, determined by Western Attempts to discriminate between these possibilities have blotting (Fig. 1B) and immunostaining of testis sections been hampered by the fact that Atr ablation causes embry- (Fig. 1C), was globally reduced in Atr flox/À testes 3-d after onic lethality (Brown and Baltimore 2000). treatment cessation relative to Atr flox/+ controls. This A number of other questions concerning the mecha- time point was therefore chosen for further characteriza- nisms underlying meiotic silencing remain unresolved. tion of the Atr-null phenotype. First, it is unclear how sensing of asynapsis at AEs is To assess the degree of ATR depletion in Atr flox/À testes transduced into gene silencing along associated chroma- in greater detail, we performed immunostaining on surface tin loops. Interestingly, ATR exhibits