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Copyright © 2008, The Rockefeller University Press Article Dynamics of inner kinetochore assembly and maintenance in living cells Leibniz Institute for Age Research, Fritz Lipmann Institute, 07745 Jena, Germany Correspondence to P. Hemmerich: phemmer/at/fli-leibniz.de; or S. Diekmann: diekmann/at/fli-leibniz.de Received October 8, 2007; Accepted February 20, 2008. This article has been cited by other articles in PMC.Abstract To investigate the dynamics of centromere organization, we have assessed the exchange rates of inner centromere proteins (CENPs) by quantitative microscopy throughout the cell cycle in human cells. CENP-A and CENP-I are stable centromere components that are incorporated into centromeres via a “loading-only” mechanism in G1 and S phase, respectively. A subfraction of CENP-H also stays stably bound to centromeres. In contrast, CENP-B, CENP-C, and some CENP-H and hMis12 exhibit distinct and cell cycle–specific centromere binding stabilities, with residence times ranging from seconds to hours. CENP-C and CENP-H are immobilized at centromeres specifically during replication. In mitosis, all inner CENPs become completely immobilized. CENPs are highly mobile throughout bulk chromatin, which is consistent with a binding-diffusion behavior as the mechanism to scan for vacant high-affinity binding sites at centromeres. Our data reveal a wide range of cell cycle–specific assembly plasticity of the centromere that provides both stability through sustained binding of some components and flexibility through dynamic exchange of other components. Introduction Cell division is a highly dynamic process in which the chromosomes are segregated in a coordinated way. The centromere is the genetic locus required for precise and accurate chromosome segregation and provides a platform on which the kinetochore multiprotein complex assembles (Cleveland et al., 2003; Amor et al., 2004; Chan et al., 2005). Accurate chromosome segregation is essential for cell survival and aberrant mitotic segregation can result in aneuploidy, cell death, or cancer (Cimini and Degrassi, 2005; Kops et al., 2005). The six “foundation” centromere/kinetochore proteins centromere protein A (CENP-A), CENP-B, CENP-C, CENP-H, CENP-I, and hMis12 are known as components of the interphase centromeric chromatin. In addition, another set of 11 proteins associated with this complex have been isolated recently (Foltz et al., 2006; Izuta et al., 2006; Okada et al., 2006). Despite the knowledge of the fundamental functions and the essential components of the centromere, its assembly dynamics and mechanisms are still poorly understood (Fukagawa, 2004; Carroll and Straight, 2006; Vos et al., 2006; Schueler and Sullivan, 2006). With the exception of CENP-B, foundation kinetochore proteins are found at all active but not inactive centromeres, including neocentromeres (Saffery et al., 2000). Central to centromere assembly is CENP-A, which replaces histone H3 at the centromeric nucleosome (Palmer et al., 1991; Sullivan et al., 1994). CENP-A proteins, also referred to as cenH3s, are present in all eukaryotes and their depletion leads to the mislocalization of most other centromere proteins. These fundamental and conserved features of CENP-A for centromere organization suggest that it is a key determinant not only for kinetochore assembly but also for epigentic propagation of centromere identity (Dunleavy et al., 2005; Bloom, 2007; for review see Dalal et al., 2007; Morris and Moazed, 2007). Unlike the four core histones, which are assembled just behind the replication fork, CENP-A assembly in human cells occurs uncoupled from DNA replication in early G1 (Shelby et al., 2000; Verreault, 2003; Jansen et al., 2007). CENP-B binds sequence-specifically to the 17-bp CENP-B box within a subset of α-satellite repeats in humans (Masumoto et al., 1989). Although CENP-B is not essential for kinetochore function in mouse cells (Hudson et al., 1998), results obtained with mammalian artificial chromosomes indicate that the CENP-B box interaction plays a crucial role in the assembly of other kinetochore components on the alphoid DNA (Ohzeki et al., 2002). CENP-C is an evolutionarily conserved centromere protein (Tomkiel et al., 1994) that binds to centromeric DNA adjacent to CENP-B in a sequence-independent manner (Sugimoto et al., 1994; Politi et al., 2002). The requirement of CENP-A for CENP-C (Howman et al., 2000) and the direct interaction between CENP-C and CENP-B (Suzuki et al., 2004) support a model in which CENP-A, -B, and -C are tightly associated to form centromeric chromatin (Ando et al., 2002). CENP-H was identified as another essential component at vertebrate centromeres (Sugata et al., 2000; Fukagawa et al., 2001). CENP-I is the human orthologue of the Schizosaccharomyces pombe Mis 6 protein, which is required for proper CENP-A localization and mitotic progression (Takahashi et al., 2000; Liu et al., 2003). In vertebrates, reciprocally, CENP-I recruitment to centromeric chromatin is strictly dependent on the presence of CENP-A (and CENP-H; Nishihashi et al., 2002). The human Mis12 protein (hMis12) is also a conserved centromere protein (Goshima et al., 2003). As part of a four-subunit complex, hMis12 seems to play an important role in the assembly of mitotic kinetochores because depletion of each of the components results in misaligned chromosomes and defects in chromosome biorientation (Kline et al., 2006). In recent years, it has been demonstrated that virtually all aspects of nuclear function and organization are dynamic (Houtsmuller et al., 1999; Misteli, 2001a; Hager et al., 2002; Belmont, 2003; Sprague and McNally, 2005). FRAP experiments of GFP-tagged proteins have revealed that nuclear proteins only transiently interact with chromatin, typically with residence times in the order of seconds. This dynamic behavior is thought to play a major role in chromatin organization and plasticity (Phair et al. 2004; Beaudouin et al., 2006). Fluorescence correlation spectroscopy (FCS) is a single-molecule technique that provides more local information and yields a higher temporal resolution. FCS measures fluorescence fluctuations induced by low numbers of diffusing fluorescent molecules within a small confocal volume from which biophysical parameters such as diffusion coefficients and concentrations can be extracted (Weidtkamp-Peters et al., 2008). Because the measuring time scales of FCS are orders of magnitude shorter than with FRAP, combined application allows determination of the full spectrum of the dynamics of a nuclear protein (Schmiedeberg et al., 2004). Using quantitative FRAP and FCS, we have analyzed the mobility of six human inner kinetochore proteins in living cells to obtain insight into the dynamics of centromere assembly and maintenance throughout the cell cycle. Our analyses indicate that centromere integrity is built upon both a rigid core structure comprised of CENP-A, -I, and -H and flexible components such as CENP-B, CENP-C, and hMis12 that exhibit dynamic exchange at the centromere–kinetochore complex. Results Expression of GFP-tagged centromere proteins in living cells For live-cell experiments, GFP-tagged centromere proteins were transiently (CENP-B, -C, -I, and hMis12) or stably (CENP-A and CENP-H) transfected into HEp-2 or HeLa cells. Low-level expressing cells in transient transfections exhibited no obvious abnormalities in chromosome movements and mitotic progression as analyzed by time-lapse microscopy of dividing cells, and stably transfected cells showed growth rates indentical to their parent cell lines (unpublished data). All fusion constructs localized at centromeres during interphase and mitosis and were expressed as full-length proteins (Fig. S1, available at http://www.jcb.org/cgi/content/full/jcb.200710052/DC1). Collectively, these results demonstrated that the GFP-tagged inner kinetochore fusion proteins behaved similarly compared with their endogenous counterparts with regard to full-length expression and constitutive localization at centromeres during the cell cycle. To best represent the native proteins, cells with minimal expression levels of the fusion proteins were generally chosen for live-cell experiments throughout this study (Chen et al., 2005). Cell lines stably expressing GFP-tagged CENP-A and CENP-H yielded protein dynamics identical to those measured in transiently transfected cells (unpublished data). CENP-A is assembled into centromeres exclusively in G1 Using a newly developed live-cell labeling approach, Jansen et al. (2007) have recently demonstrated that CENP-A is assembled into centromeric chromatin of human cells in G1 phase of the cell cycle. To investigate this assembly process in more detail, we used long-term FRAP experiments. GFP–CENP-A–expressing HEp-2 cells were monitored during mitosis and fluorescent centromeres were bleached at late mitosis/early G1 (Fig. 1
Cell cycle–dependent chromatin-binding stability of centromere proteins Using the same approach as for CENP-A (Fig. 1
Fast exchange of hMis12 and a fraction of CENP-B and CENP-C at centromeres The fast recovery kinetics of CENP-B (in G1 and S) and CENP-C (in G1 and G2) within the first 10 min of long-term FRAP analysis indicated the existence of protein pools with higher exchange rates (Fig. 2, B and C CENP-C stability at centromeres sharply increases during mid and late but not early S phase To further dissect the immobilization timing of CENP-C at centromeres during replication, FRAP was performed in HEp-2 cells coexpressing mRFP-PCNA. Early S phase cells are characterized by the presence of hundreds of replication foci scattered throughout euchromatin (Weidtkamp-Peters et al., 2006). FRAP of kinetochore-bound GFP–CENP-C in such cells revealed fast and complete recovery (Fig. 4 A
A loading-only mechanism for CENP-A and CENP-I assembly Maximum FRAP recovery of CENP-A and CENP-I was <50% even after 6 h of observation time (Fig. 2, A and I Stable chromatin binding of centromere proteins during mitosis We next determined the exchange dynamics of centromere proteins at kinetochores during mitosis. Metaphase cells were bleached in spots containing several kinetochores and fluorescence recovery in the bleached area was monitored over time by sequential imaging scans for 100 s (Fig. 6
Mechanism of stable CENP-B and CENP-C binding to kinetochores To address the molecular basis for stable CENP-B and CENP-C binding to kinetochores, we performed FRAP on GFP-tagged truncation variants. These analyses demonstrated that the centromere localization domains of CENP-B and CENP-C are each necessary but not sufficient for stable centromere binding (Fig. S2, available at http://www.jcb.org/cgi/content/full/jcb.200710052/DC1). We conclude that CENP-B and CENP-C exhibit multiple protein–DNA and protein–protein contacts to establish a stable binding to centromeres, and proper binding requires the full-length proteins. Centromere protein mobility outside the centromere is governed by anomalous diffusion FRAP methods failed to assess the kinetics of the low abundant centromere protein pools in the nucleoplasm. We therefore applied FCS. In FCS, a low-intensity laser beam is directed though a confocal setup into a defined measuring volume (Fig. 7 A
Discussion Understanding centromere assembly and function requires detailed knowledge of its components, interactions, and dynamic coordination to form a functional unit. In this study, the intranuclear dynamics and chromatin binding stabilities of six centromere proteins were assessed in living human cells. These analyses revealed unexpectedly complex and dynamic changes within the centromere throughout cell cycle progression (Fig. 8
CENP-A assembly into centromeres: a loading-only mechanism during G1 CENP-A replaces histone H3 at centromeric nucleosomes, where it has unique properties essential for centromere function (for review see Dalal et al., 2007). Unlike the replicative variants H3.1 and H3.2, which are incorporated into chromatin exclusively during S phase of the cell cycle (for review see Loyola and Almouzni, 2007), CENP-A loading into centromeric chromatin occurs exclusively during the early hours of G1 in human cells (Fig. 1 Increased kinetochore stability of CENP-B in G2 CENP-B specifically binds to a 17-bp DNA motif known as the CENP-B box, which is present in human α-satellite DNA (Masumoto et al., 1989). The presence of two CENP-B populations with different residence times indicates two modes of retention of CENP-B in G1 and S phase cells: one probably directly at the high-affinity CENP-B box and the other probably at adjacent centromeric DNA after saturation of the CENP-B boxes. In G2 and M phase, the majority of CENP-B is stably incorporated into the centromere complex (Fig. 8 Immobilization of CENP-C at kinetochores during centromere DNA replication CENP-C is downstream of CENP-A but is required for the assembly of most other centromere components (Kwon et al., 2007). This function may be performed by the fast-exchanging CENP-C population during G1 and G2, which could act as a mediator to attract freely diffusing downstream components to the centromere. A remarkable finding was the observed immobilization of CENP-C specifically through mid to late S phase (Fig. 8 Stable kinetochore incorporation of CENP-H Although cell cycle–dependent amounts of CENP-H slowly exchanged at centromeres with a residence time of ~75 min, at least 20% of the CENP-H population was stably bound throughout the complete cell cycle (Fig. 8 CENP-I carries features of an epigenetic centromere mark It came as a surprise that GFP–CENP-I did not show any FRAP during G1 and G2 phase (Fig. 8 Immobilization of hMis12 during mitosis FRAP of hMis12 revealed high turnover at centromeres during interphase (residence time, 7.3 ± 1.9 s) with no immobile fraction supporting the recent notion that this protein is probably not constitutively associated with centromeres (Liu et al., 2006). During metaphase, hMis12 showed no FRAP at centromeres, which suggests stable interactions with other kinetochore- or microtubule-interacting proteins, or both. A previous study proposed that Mis12 regulates the rate and extent of outer kinetochore assembly because it was not strictly required to form stable kinetochore–microtubule attachments (Cheeseman et al., 2004). In hMis12-depleted human cells, however, the chromosomes do not align anymore at the metaphase plate, a mitotic phenotype consistent with impairment of the kinetochore–microtubule connection (Goshima et al., 2003). Combined with our observation of stable association of hMis12 at metaphase kinetochores, we suggest a more structural role for Mis12 in human cells that may physically contribute to the mechanical stability between kinetochores and microtubules. Distinct diffusional behaviors of inner kinetochore proteins outside centromeres The nucleoplasmic pools of the GFP-tagged CENPs and hMis12 showed protein-specific anomalous diffusion characteristics. In agreement with previous analyses (Banks and Fradin, 2005), we find an anomaly parameter of α = 0.73 for GFP alone in the nucleus, although the anomalous diffusion parameters determined for GFP-tagged centromere proteins were well below this value. Although our data were fitted perfectly using one diffusion and one triplet term, and hence not of a quality to allow an additional binding term, these observations strongly indicated transient binding events throughout the chromatin area. We would like to point out that (a) consistent results were obtained at different x, y, and z positions and hence throughout different parts of chromatin and (b) that examination of the centromere itself led to a strong bleaching indicative of immobile proteins (unpublished data). Because this was not observed throughout the chromatin space devoid of centromeres, the respective CENP proteins still have a high enough mobility to escape bleaching. In addition, the diffusion coefficients of centromere proteins ranging between 0.08 ± 0.04 μm2/s for CENP-C and 3.19 ± 0.18 μm2/s for CENP-H were too slow to account only for diffusion barriers based on the size of the fusion proteins in comparison to GFP. Our data therefore clearly indicate an obstructed, diffusional behavior of centromere proteins outside centromeres that allows these proteins to “scan” the nucleus in search of their appropriate binding sites at the centromere without the need for directional transport. A dynamic centromere throughout the cell cycle A “prekinetochore” complex consisting of CENP-A, -B, -C, and the CENP-H–CENP-I complex is believed to provide the platform for recruiting other kinetochore proteins (Ando et al., 2002; Schueler and Sullivan, 2006; Alonso et al., 2007). This view is supported by these proteins' ability to directly associate with centromeric DNA and by our FRET analyses, which reveal distinct interactions between specific CENPs in living cells (Orthaus et al., 2007). This model predicts tight mutual and cooperative interactions of the component parts involving multiple binding contacts to form a stable unit. This assumption is supported by our observation that full-length CENP-B and CENP-C proteins are necessary to convey centromere binding stability (Fig. S2). At the same time, this stability is achieved although CENP-B, CENP-C, and subpopulations of CENP-H dynamically exchange at centromeres in a cell cycle–dependent manner (Fig. 8 Implications for the concept of nuclear dynamics Chromatin-binding proteins are highly dynamic, they roam the nucleus in an energy-independent manner in search for high-affinity binding sites (Misteli, 2001a), and their residence times on chromatin are typically on the order of several seconds (Phair et al., 2004; Beaudouin et al., 2006). This dynamic behavior is thought to play a major role in generating combinatorial protein complexes on chromatin, providing a mechanism to finely regulate transcription, chromatin organization, and genomic plasticity. Our FCS data demonstrate that centromere components share these high mobility properties with chromatin-binding proteins within the nuclear compartment outside centromeres but not at the centromere. Some component parts of the centromere do not rapidly exchange with soluble pools but are extremely stable. Other rare examples of stable chromatin binding include core histones and cohesins (Kimura and Cook, 2001; Gerlich et al., 2006). Binding of CENP-A, CENP-I, and a subpopulation of CENP-H to centromeres is so tight that it likely persists into the next cell cycle, a phenomenon that has so far only been reported for components of the nuclear pore complex and the nucleosome (Kimura and Cook, 2001; Rabut et al., 2004). Thus, although dynamic interaction appears to be a general property of chromatin-binding proteins, it is certainly not universal. Conceptually, centromeres could acquire overall stability from dynamic parts based on self-organization (Misteli, 2001b). Obviously, however, the functional and epigenetic demands of chromosome maintenance and segregation required the establishment of a structurally rigid entity at the centromeres on human chromosomes. Materials and methods Plasmids The plasmid pGFP–AF8–CENP-A vector encoding a GFP–CENP-A fusion protein (Wieland et al., 2004) was a gift of K. Sugimoto (Osaka University, Osaka, Japan). Full-length hMis12 cDNA was amplified by PCR (Expand High FidelityPLUS PCR System; Roche) from plasmid IRAUp969C0611D6-pOTB7 (imaGenes). The PCR fragment was subcloned into the EcoRI–PspOMI sites of a pGFP-C3 vector (Clontech Laboratories, Inc.). Full-length CENP-B was amplified by PCR from pT7.7/CENP-B (a gift from W. Earnshaw, University of Edinburgh, Edinburgh, UK) and cloned into the EcoRI–SalI sites of the pGFP-C2 vector. Plasmid pCBS56T encoding GFP tagged to the DNA-binding domain of CENP-B was a gift of K.F. Sullivan (National University of Ireland, Galway, Ireland). Full-length CENP-C (aa 1–943) and three subfragments (aa 1–315, aa 315–635, and aa 635–943) were amplified by PCR from pTCATG recombinant plasmid (provided by W. Earnshaw) containing the entire human CENP-C–coding region. The PCR fragments were subcloned into the XhoI–PspOMI sites of pGFP-C2 vector. Full-length CENP-I was obtained from T. Yen and S. Tao (Fox Chase Cancer Center, Philadelphia, PA), amplified by PCR, and subcloned as a Xho–PspOMI fragment into pGFP-C2. All plasmids were verified by sequencing (MWG Biotech). The vector pEN–mRFP–PCNA-2 encoding a functional PCNA-RFP fusion (Sporbert et al., 2005) was a gift of C. Cardoso (Max Delbrück Center for Molecular Medicine, Berlin, Germany). Western blots Whole cell extracts were produced from transiently or stably transfected cell lines, electrophoresed on SDS-PAGE, and transferred to a Protran nitrocellulose membrane (Whatman). Membrane was incubated strip-wise with primary antibodies (in PBS-T) and developed with a peroxidase-conjugated secondary species-specific antibody (Jackson ImmunoResearch Laboratories). Signal was detected using the ECL reagent (GE Healthcare) on imaging film (Biomax; Kodak). Anti-GFP antibody was from obtained from Santa Cruz Biotechnology, Inc. Cell culture and transfection HEp-2 cells obtained from the American Type Culture Collection were cultured in DME supplemented with 10% fetal calf serum in a 10% CO2 atmosphere at 37°C. For live-cell imaging experiments, cells were seeded on 42-mm glass dishes (Helmut Saur Laborbedarf) and transfected with plasmid DNA 1–2 d before observation using FuGENE 6 transfection reagent (Roche) according to the manufacturer's instructions. Stable cell lines were seeded similarly without transfection. A HeLa cell line stably expressing YFP–CENP-H was a gift of I. Cheeseman (University of California, San Diego, La Jolla, CA). Immunocytochemistry and microscopy HeLa or HEp-2 cells grown on 15-mm-diameter coverslips were fixed with 4% formaldehyde for 10 min and permeabilized with 0.25% Triton X-100 for 3 min. A monoclonal antibody against CENP-A (MBL International) or a guinea pig serum against the CENP-C (a gift of K. Yoda, Nagoya University, Nagoya, Japan) was incubated with the cells for 45 min. After washing steps with PBS, the secondary antibody against mouse IgG coupled to rhodamine (Jackson ImmunoResearch Laboratories) was incubated with the cells for 45 min followed by a DNA-staining step using ToPro3 (Invitrogen) for 10 min and mounting with Prolong Gold antifade mounting medium (Invitrogen). For microscopy, a laser scanning confocal microscope (LSM 510 Meta; Carl Zeiss, Inc.) was used as described previously (Weidtkamp-Peters et al., 2006). FCS measurements FCS measurements were performed at 37°C on an LSM 510 Meta/Confocor2 combi system (Carl Zeiss, Inc.) using a C-Apochromat infinity-corrected 1.2 NA 40× water objective (Carl Zeiss, Inc.). With this setup, a spot on a previously scanned image of a cell can be selected for the FCS measurement. GFP-tagged proteins were illuminated with the 488-nm line of a 20-mW argon laser (Carl Zeiss, Inc.) with 4.3-A tube current attenuated by an acousto-optcal tunable filter to 0.1%. The detection pinhole had a diameter of 70 μm and emission was recorded through a 505-nm-long path filter. For the measurements, 10 × 30 time series of 10 s each were recorded with a time resolution of 1 μs and then superimposed for fitting to an anomalous diffusion model in three dimensions with triplet function (Schwille et al., 1999; Saxton, 2001) using Origin software (OriginLab). The diffusions coefficients and anomaly parameters were extracted from fit curves as described previously (Schmiedeberg et al., 2004). FRAP FRAP experiments were performed on a confocal microscope (LSM 510 Meta; Carl Zeiss, Inc.) using a C-Apochromat infinity-corrected 1.2 NA 40× water objective and the 488-nm laser line for GFP. 5 or 10 images were taken before the bleach pulse and 50–200 images after bleaching of two to four centromeres of a nucleus with an image acquisition frequency of 0.5–1 frame/s at 0.05% laser transmission to avoid additional bleaching. During short-term FRAP experiments, the pinhole was completely opened to increase low fluorescence intensities and ensure total bleaching of centromeric spots in the nucleus. In long-term FRAP experiments, the pinhole was adjusted to 1 airy unit and image stacks were taken at time intervals as indicated. Quantitation of relative fluorescence intensities was done according to Schmiedeberg et al. (2004) using Excel (Microsoft) and Origin software. Recovery half-times and residence times were determined from FRAP data as described previously (Bulinski et al., 2001; Schmiedeberg et al., 2004). Online supplemental material Fig. S1 shows the characterization of GFP-tagged centromere proteins in HEp-2 cells. Fig. S2 shows that the centromere-targeting domains of CENP-B and CENP-C are necessary but not sufficient for stable binding to centromeres in living cells. Fig. S3 shows the dynamics of CENP-B, -C, -H, and -I at the centromere during interphase. Online supplemental material is available at http://www.jcb.org/cgi/content/full/jcb.200710052/DC1. [Supplemental Material Index]
Acknowledgments We thank H. Kimura for comments on the manuscript and S. Ohndorf and M. Koch for expert technical assistance. We are grateful to E. Birch-Hirschfeld for DNA synthesis and C. Cardoso, K. Sugimoto, T. Yen, S. Tao, W.C. Earnshaw, K. Yoda, and I. Cheeseman for the kind gifts of antibodies, plasmids, or stable cell lines. I. Erliandri obtained a fellowship from the Deutscher Akademischer Austauschdienst (grant No. A/02/32415). This work was supported by a grant from the Deutsche Forschungsgemeinschaft to P. Hemmerich (HE 2484/3-1). Notes P. Hemmerich and S. Weidtkamp-Peters contributed equally to this paper. S. Weidtkamp-Peters' present address is Institut für Physikalische Chemie II, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany. L. Schmiedeberg's present address is Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland. Abbreviations used in this paper: CENP, centromere protein; FCS, fluorescence correlation spectroscopy; mRFP, monomeric red fluorescent protein; PCNA, proliferating cell nuclear antigen. References
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