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First published online July 18, 2002; 10.1105/tpc.003079
American Society of Plant Biologists Functional Rice Centromeres Are Marked by a Satellite Repeat and a Centromere-Specific Retrotransposon
a Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706 1 To whom correspondence should be addressed. E-mail jjiang1{at}facstaff.wisc.edu; fax 608-262-4743
The centromere of eukaryotic chromosomes is essential for the faithful segregation and inheritance of genetic information. In the majority of eukaryotic species, centromeres are associated with highly repetitive DNA, and as a consequence, the boundary for a functional centromere is difficult to define. In this study, we demonstrate that the centers of rice centromeres are occupied by a 155-bp satellite repeat, CentO, and a centromere-specific retrotransposon, CRR. The CentO satellite is located within the chromosomal regions to which the spindle fibers attach. CentO is quantitatively variable among the 12 rice centromeres, ranging from 65 kb to 2 Mb, and is interrupted irregularly by CRR elements. The break points of 14 rice centromere misdivision events were mapped to the middle of the CentO arrays, suggesting that the CentO satellite is located within the functional domain of rice centromeres. Our results demonstrate that the CentO satellite may be a key DNA element for rice centromere function.
The centromere is the most characteristic landmark of chromosomes in higher eukaryotic species and appears cytologically as a distinct primary constriction on condensed metaphase chromosomes. The centromere is responsible for sister chromatid cohesion and is the site for kinetochore assembly and spindle fiber attachment, allowing for the faithful pairing and segregation of sister chromatids during cell division. Determining the precise DNA boundary of a centromere has proven to be a difficult task. In the majority of eukaryotic species, centromeres are embedded within megabases of highly repetitive DNA that cannot be sequenced precisely by even the most tenacious genome-sequencing projects (Arabidopsis Genome Initiative, 2000  ; International Human Genome Sequencing Consortium, 2001).
The budding yeast Saccharomyces cerevisiae is the most striking exception to the rule of DNA sequence complexity in eukaryotic centromeres. Each of the "point" centromeres in S. cerevisiae consists of only
The
The centromeres of the model plant Arabidopsis have been defined genetically (Copenhaver et al., 1999
The centromeres of supernumerary B chromosomes of maize have been well studied. A repetitive element specific to the B centromere was isolated (Alfenito and Birchler, 1993
Several centromeric repetitive DNA elements have been reported in rice (Dong et al., 1998 In this study, we conducted high-resolution cytological mapping of the CentO satellite repeat in the rice genome. The distribution and organization of the CentO satellite, together with the centromere-specific retrotransposon CRR, in the 12 rice centromeres are illustrated using a combination of cytological and molecular methods. Quantification of the CentO repeat in normal and telocentric rice chromosomes revealed that the break points of centromere misdivisions always are located within the CentO loci, suggesting that the CentO satellite is a key component of functional rice centromeres.
The CentO Satellite Is Located in Cytologically Defined Rice Centromeres The CentO satellite was identified originally in the clone pRCS2, which contains four tandemly arranged monomers with units between 154 and 165 bp and maps to the centromeric regions of somatic metaphase chromosomes of rice (Dong et al., 1998 ). Because of the low mapping resolution using somatic metaphase chromosomes, it is not known if the CentO satellite is associated with the primary constrictions. However, meiotic pachytene chromosomes of rice are >10 times the length of somatic metaphase chromosomes and provide superior resolution for fluorescence in situ hybridization (FISH) mapping (Cheng et al., 2001b). Pachytene FISH analysis using pRCS2 revealed a single CentO locus on each of the 12 rice chromosomes (Figures 1A to 1C) . The pRCS2 FISH signals clearly were associated with the primary constriction in pachytene cells, in which the morphology of the chromosomes was well preserved after the FISH procedure. Noncentromeric signals were not observed on pachytene chromosomes, even under conditions of low hybridization stringency (30% formamide at 37°C), indicating that the CentO satellite is highly specific to the centromeres. On meiotic metaphase I chromosomes, the FISH signals are located consistently on the tips (the most poleward positions) of the bivalent chromosomes (Figures 1D to 1F), suggesting that the chromosomal regions containing the CentO satellite are associated with the kinetochore protein complex.
We also observed a unique FISH hybridization pattern in some mitotic metaphase cells. The centromeric regions of the chromosomes in these cells were stretched out (Figure 1G), possibly as a result of the attachment of spindle fibers and the mechanical stretching of the spindle fibers imposed by the crushing in the cytological preparation. Interestingly, the FISH signals derived from the CentO satellite always colocalized with the stretched centromeric regions (Figures 1H and 1I). This unique FISH signal pattern indicates that the CentO satellite is located within the chromosomal regions that are the sites of kinetochore formation and spindle fiber attachment.
Complex Composition of the CentO Satellite
The 62-kb insert of 17p22 consists of two uninterrupted CentO arrays of 9 and 39.5 kb that are separated by a single retrotransposon insertion and flanked on one side by a complex arrangement of additional retrotransposon sequences (Figure 2A). All CentO monomers are arranged in the same orientation, but their organization and polymorphism are surprisingly complex. There are two distinct subfamilies, with consensus lengths of 155 bp (252 copies) and 164 bp (61 copies), which differ principally as a result of a single 10-bp insertion in the larger family (Figure 3) . All 164-bp monomers are flanked on both sides by the 155-bp monomers.
Within each subfamily, there are many variants, consisting mainly of single base changes and/or single base insertions/deletions relative to the consensus. There are a limited number of common polymorphisms, although all monomers are >90% identical to the relevant consensus. Few bases are conserved absolutely, and there are no simple universal consensus motifs present. Two variants have internal deletions (11 and 35 bp), and the deletions are centered on the same consensus position, yet otherwise these variants appear unrelated by polymorphism at other positions (Figure 3). The majority of variants occur only once, but some (including the 35-bp deletion) are repeated moderately (6 to 14 copies). Repeated variants generally are dispersed widely throughout the clone, and there are no simple tandem arrays of identical units.
Sequence Similarity between the CentO Satellite and the Maize Centromeric Repeat CentC The central CentC deletion appears to have been balanced by a degenerate duplication of the terminal 25 bp (shown in Figure 3 as a 3' extension relative to CentO), such that the length of both satellite families remains similar, suggesting that this may have functional importance. Interestingly, the conserved 3' region is predicted to have significant potential to direct bending, based on the criteria of the bend.it server (http://www2.icgeb.trieste.it/~dna/bend_it.html; see Methods), whereas both deletions found in the CentO variants have occurred at this point, suggesting that it may be susceptible to breakage. Therefore, it is likely that structural constraints play a role in the pattern of sequence conservation observed between CentC and CentO.
Quantification of the CentO Satellite in Individual Rice Centromeres
The 10 best cells in which all 12 pachytene bivalents were identified unambiguously were selected for measurements. The intensity of the FISH signal derived from centromere 8 was calibrated as 1, and the relative intensities of the signals derived from other centromeres were calculated and are summarized in Table 1. A BAC clone, RC8-1, was found to be closely linked to the CentO locus of chromosome 8. Using RC8-1 as a reference marker, we were able to determine the length of the CentO locus of chromosome 8 (CentO-8) using fiber-FISH (Figure 4A) . The sizes of the CentO-8 in Nipponbare and Zhongxian 3037 were measured as 64 and 81 kb, respectively, by fiber-FISH analysis (Figure 4A, Table 1). The amount of the CentO satellite in other centromeres was calculated based on relative fluorescence intensities compared with centromere 8 (Table 1). We also identified DNA markers that are closely linked to the CentO locus on chromosome 11 (CentO-11). Using a strategy similar to that demonstrated in Figure 4A, we measured the sizes of the CentO-11 in Nipponbare and Zhongxian 3037 to be 1.64 and 0.64 Mb, respectively, based on five fiber-FISH signals from each rice variety (data not shown). These measurements are similar to the estimated sizes of CentO-11 (1.90 and 0.42 Mb) based on relative fluorescence intensities (Table 1). These results demonstrated an appreciable accuracy of the quantification method based on measurements of FISH signal intensities.
The total amounts of the CentO satellite are
The Break Points of Rice Centromere Misdivisions Are Located in the Middle of the CentO Arrays
Somatic metaphase chromosomes prepared from the telotrisomic stocks were hybridized to the CentO satellite probe pRCS2. Chromosome arm–specific BAC clones (Cheng et al., 2001a ) also were included in FISH analysis to unambiguously detect the telocentric chromosome and its corresponding normal chromosome (Figures 5A to 5C) . The relative fluorescence intensities of the telocentric chromosomes and the two normal chromosomes were measured using IPLab software (Table 2). Quantitative FISH results demonstrated that the telocentric chromosomes always contain a lower amount of the CentO satellite than their respective normal centromeres in all 14 telotrisomic stocks. The centromeres of telocentric chromosomes contain an average of 65% (ranging from 48 to 84%) of the CentO satellite compared with the normal centromeres. These results demonstrate that the break points of all of the centromere misdivisions are located within the CentO arrays.
Distribution and Organization of the Centromere-Specific Retrotransposon in the Rice Genome We previously demonstrated that the centromeres of grass species, including rice, contain a Ty3/gypsy-class retrotransposon family (Miller et al., 1998a ; Langdon et al., 2000). This centromere-specific family in rice is referred to as CRR (Centromeric Retrotransposon of Rice). The insert of BAC 17p22 contains two regions, 4.4 and 9.2 kb, respectively, that are derived from the CRR family (Figure 2A).
The 4.4-kb region represents an insertion of a nonautonomous element into the CentO satellite array. This insertion has occurred relatively recently, as judged by the lack of divergence of its long terminal repeat (LTR) sequences. As with other members of the nonautonomous subfamily of CRR elements, an open reading frame that has homology with the gag gene of full-length elements is fused to a reading frame of unknown function (Langdon et al., 2000
The 9.2-kb region is derived from three CRR elements, each of which is truncated differently (Figure 2A). The most 5' element is a nonautonomous element whose upstream sequences have been lost in cloning that has inserted into the integrase region of a full-length element. The 5' LTR of the full-length element is recombined exactly with the 3' LTR of a second full-length element, generating two tandem overlapping elements. The second full-length element has lost almost all upstream sequences, apparently as a consequence of a deletion event that extended into the CentO array. This deletion may have occurred during propagation of the BAC clone, because we found recently that many BAC clones containing tandem repeats are not stable in Escherichia coli (Song et al., 2001
To investigate the distribution of CRR elements in the rice genome, we screened a Nipponbare BAC library (http://www.genome.clemson.edu/orders/Product.html) using the CentO satellite pRCS2 probe and the pRCS1 probe derived from the integrase domain of CRR (Miller et al., 1998a All of the CentO- and CRR-positive clones were used to search the BAC fingerprint database developed by Clemson University (http://www.genome.clemson.edu/projects/rice/fpc/). Among the 569 clones associated with the CentO repeat, 267 clones are singletons and the other 302 clones are distributed in 26 different contigs. Among the 712 clones associated with CRR, 604 clones are distributed on 70 contigs and 98 clones are singletons. These results suggest that the CentO satellite is organized into long arrays with few disruptions by other sequences, whereas the CRR elements are dispersed in a wider range of chromosomal regions than the CentO satellite. In addition, many of the BACs containing the CentO satellite may not produce distinct restriction patterns; thus, they appear as singletons. To gain a cytological view of the distribution of the CRR elements, we conducted FISH analysis by pooling the six plasmid clones derived from different parts of the CRR element as a single probe (Figure 2A; referred to as CRR probe hereafter). FISH signals derived from the CRR probe were highly enriched in the centromeric regions on both somatic metaphase and meiotic pachytene chromosomes (Figure 6A) . However, cross-hybridization of the CRR probe to other chromosomal regions was observed. The noncentromeric signals were not consistent among different cells and generally were much weaker than the signals detected in the centromeres. We could not determine whether such signals were derived from noncentromeric members of the CRR family or from cross-hybridization with other retrotransposon sequences. Based on the size and intensity of the FISH signals, the copy number of the CRR element varied significantly among the 12 rice centromeres. The CRR elements were distributed in a much wider range of the centromeric regions than the CentO satellite (Figures 6B to 6E), which is consistent the BAC library screening results.
The FISH signals derived from the CRR probe were not distributed uniformly in the majority of the centromeres. In several centromeres, the signals from the CRR probe were clearly enriched on both sides of the CentO locus (Figures 6C to 6E). In some chromosomes, the CRR signal on one side of the centromere was significantly stronger than the signal on the other side of the centromere. The FISH results also indicated that the majority of the CRR elements flank the CentO arrays rather than insert into the CentO arrays.
The CRR and CentO probes were used for FISH analysis on extended DNA fibers prepared from Nipponbare. Insertions of the CRR elements into the CentO arrays were visualized (Figure 4B). The density of the CRR elements inserted in the CentO arrays varied significantly among different fiber- FISH signals (Figure 4B). We observed CentO arrays as long as 500 kb without disruptions by CRR elements (Figure 4B). Another interesting observation is the nesting of the CRR elements in some centromeric regions. Most of the fiber-FISH signals derived from the CRR probe consisted of two to four fluorescent spots, representing
DNA sequences associated with centromeric regions have been reported in numerous plant species (Alfenito and Birchler, 1993 ; Harrison and Heslop-Harrison, 1995; Aragon-Alcaide et al., 1996; Jiang et al., 1996; Brandes et al., 1997; Miller et al., 1998b; Nagaki et al., 1998; Francki, 2001; Gindullis et al., 2001; Hudakova et al., 2001; Page et al., 2001; Saunders and Houben, 2001). However, large-scale sequencing and organization studies of centromeric DNA have been documented in only a few plant species. The most abundant DNA element in Arabidopsis centromeres is the 180-bp satellite repeat pAL1. The pAL1 arrays may be interrupted by the 106B repeat, a diverged copy of the LTR of the Athila retrotransposon (Fransz et al., 2000), but complete Athila elements, the most dominant retrotransposon family in Arabidopsis, are highly enriched in the pericentromeric region rather than in functional centromeres (Fransz et al., 2000). Satellite repeats and retrotransposons also are the major component of centromeric DNA in barley (Hudakova et al., 2001) and Beta species (Gindullis et al., 2001).
In this study, we demonstrate that the centers of rice centromeres are occupied by the CentO satellite repeat sequence. Cytological mapping revealed that the CentO satellite is located within the chromosomal regions at which the kinetochore is formed and the spindle fibers are attached (Figures 1D to 1F and 1G to 1I). A Ty3/gypsy-class retrotransposon family, CRR, is colocalized with the CentO satellite within rice centromeres. CRR is highly specific to the centromeres, and its homologous sequences have been found in the centromeric regions of all grass chromosomes (Ananiev et al., 1998
Despite its centromeric specificity, the copy number and density of CRR elements within and outside of the CentO arrays are highly variable among the 12 rice centromeres. In addition, a majority of the CRR elements flank the CentO arrays rather than insert into the CentO satellite sequences. Frequent and drastic nesting of the CRR element was detected (Figure 4B). It will be interesting to determine if this retrotransposon has any direct or indirect role in rice centromere function. Other retroelements that are not specific to the centromeres have been identified in rice centromeric regions (Nonomura and Kurata, 2001
The mechanism of centromere function is an intriguing puzzle for biologists. The functional role of the centromere in cell division, including both meiosis and mitosis, is highly conserved in all eukaryotic species. Several proteins involved in centromeric function have been found to be conserved in highly divergent eukaryotic species, including S. cerevisiae, Caenorhabditis elegans, D. melanogaster, human, and plants (for reviews, see Dobie et al., 1999
Satellite repeats often are the major component of complex eukaryotic centromeres (Csink and Henikoff, 1998
Although satellite repeats are the most common feature of eukaryotic centromeres and have been proposed to be the key centromeric DNA component in many species, their true functional role is difficult to verify. Human We have obtained several lines of evidence that indicate that the CentO satellite is the key component of functional rice centromeres. First, the CentO satellite is cytologically located at the tip of the bivalent chromosomes at metaphase I of meiosis, indicating that the CentO satellite is located within the chromosomal regions at which the kinetochore forms and the spindle fibers attach. Second, sequence comparison revealed that the CentO satellite repeats share significant similarity with the maize centromeric satellite repeat CentC. Both the localization of these two satellites and the features that appear to have been conserved during their divergence since a common origin support a functional role for these sequences. Third, and most importantly, we have demonstrated that the break points of all 14 centromere misdivision events are located in the middle of the CentO loci, suggesting that the CentO satellite occupies the center of functional rice centromeres.
The human and Arabidopsis genomes have been sequenced using a clone-by-clone approach (Arabidopsis Genome Initiative, 2000 Rice provides an excellent model for functional and evolutionary studies of centromeres. Several rice centromeres contain only a limited amount of satellite repeat compared with human and Arabidopsis centromeres. It should be technically feasible to construct BAC contigs that span the entire centromeres of such chromosomes. The BAC contigs would provide an unprecedented resource for centromere sequencing.
It has been demonstrated in several eukaryotic species that a centromeric motif would have to be reiterated over hundreds of kilobases to achieve the minimum size of fully functional centromeres. In humans, a minimum of 100 kb of
Materials Rice (Oryza sativa subsp japonica var Nipponbare and Wuyujing 8 and O. sativa subsp indica var Zhongxian 3037) was used for cytological studies. The telotrisomic stocks used in this study were developed from Zhongxian 3037 (Cheng et al., 2001c ). All BAC clones used for fluorescence in situ hybridization (FISH) analysis were selected from a BAC library developed from Nipponbare by Clemson University (http://www.genome.clemson.edu/orders/Product.html). The rice chromosome-specific BAC markers and rice centromeric DNA probes, including pRCS1, pRCS2, pRCH1, pRCH2, pRCH3, pRCE1, and pRCE2, were described previously (Dong et al., 1998; Cheng et al., 2001a).
FISH and Fiber-FISH
Cytological Measurements and Analysis
DNA Sequencing and Analysis
Unique sequences (vector and nonsatellite) were readily assembled as described previously (Blattner et al., 1997
Sequence alignments were refined manually and displayed using GeneDoc (http://www.psc.edu/biomed/genedoc). DNA bending predictions were made using the bend.it server (http://www2.icgeb.trieste.it/~dna/bend_it.html). This server predicts DNA curvature from DNA sequences, calculated as a vector sum of dinucleotide geometries (roll, tilt, and twist angles) using the BEND algorithm of Godsell and Dickerson and expressed as degrees per helical turn (Munteanu et al., 1998 Upon request, all novel materials described in this article will be made available in a timely manner for noncommercial research purposes. No restrictions or conditions will be placed on the use of any materials described in this article that would limit their use for noncommercial research purposes.
Accession Number
This research was supported by a grant from the Consortium for Plant Biotechnology Research, Novartis Seeds, and Dow AgroSciences, by Department of Energy Grant DE-FG02-01ER15266, and by funds from the Graduate School of the University of Wisconsin-Madison to J.J. This work also was partially supported by Chinese Project 973 Grant G1999011601 to Z.C. and M.G. Funding support to C.R.B. included U.S. Department of Agriculture Grant 99-35317-8275, National Science Foundation Grant DBI998282, and Department of Energy Grants DE-FG02-99ER20357 and DE-FG01-01ER15265.
Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.003079. Received March 13, 2002; accepted May 6, 2002.
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Abstract
INTRODUCTION
125 bp of unique sequence (Clarke, 1990
satellite located in human centromeres. 
