Centromeres of human chromosomes

The quantitative architecture of centromeric chromatin

The centromere, responsible for chromosome segregation during mitosis, is epigenetically defined by CENP-A containing chromatin. The amount of centromeric CENP-A has direct implications for both the architecture and epigenetic inheritance of centromeres. Using complementary strategies, we determined that typical human centromeres contain ∼400 molecules of CENP-A, which is controlled by a mass-action mechanism. This number, despite representing only ∼4% of all centromeric nucleosomes, forms a ∼50-fold enrichment to the overall genome. In addition, although pre-assembled CENP-A is randomly segregated during cell division, this amount of CENP-A is sufficient to prevent stochastic loss of centromere function and identity. Finally, we produced a statistical map of CENP-A occupancy at a human neocentromere and identified nucleosome positions that feature CENP-A in a majority of cells. In summary, we present a quantitative view of the centromere that provides a mechanistic framework for both robust epigenetic inheritance of centromeres and the paucity of neocentromere formation.

DOI:http://dx.doi.org/10.7554/eLife.02137.001

The genetic information in a cell is packed into structures called chromosomes. These contain strands of DNA wrapped around proteins called histones, which helps the long DNA chains to fit inside the relatively small nucleus of the cell.

When a cell divides, it is important that both of the new cells contain all of the genetic information found in the parent cell. Therefore, the chromosomes duplicate during cell division, with the two copies held together at a single region of the chromosome called the centromere. The centromere then recruits and coordinates the molecular machinery that separates the two copies into different cells.

Centromeres are inherited in an epigenetic manner. This means that there is no specific DNA sequence that defines the location of this structure on the chromosomes. Rather, a special type of histone, called CENP-A, is involved in defining its location. Bodor et al. use multiple techniques to show that human centromeres normally contain around 400 molecules of CENP-A, and that this number is crucial for ensuring that centromeres form in the right place. Interestingly, only a minority of the CENP-A molecules are located at centromeres; yet this is more than at any other region of the chromosome. This explains why centromeres are only formed at a single position on each chromosome.

When the chromosomes separate, the CENP-A molecules at the centromere are randomly divided between the two copies. In this way memory of the centromere location is maintained. If the number of copies of CENP-A inherited by one of the chromosomes drops below a threshold value, a centromere will not form. However, Bodor et al. found that the number of CENP-A molecules in a centromere is large enough, not only to support the formation of the centromere structure, but also to keep it above the threshold value in nearly all cases. This threshold is also high enough to make it unlikely that a centromere will form in the wrong place because of a random fluctuation in the number of CENP-A molecules. Therefore, the number of CENP-A molecules is crucial for controlling both the formation and the inheritance of the centromere.

DOI:http://dx.doi.org/10.7554/eLife.02137.002

The dynamic nature and evolutionary history of subtelomeric and pericentromeric regions

The organization and evolution of the subtelomeric and pericentromeric regions of human chromosomes exhibit unique characteristics compared to other regions of the genome. As shown in Fig. 1 the functional elements of the centromere and telomere are comprised of highly repetitive DNA sequences, which are responsible for carrying out the main mechanistic duties of these two regions: chromosome segregation and end replication, respectively. The nature of the repeats in these two regions and their function have been reviewed separately and, therefore, will not be discussed in more detail here (Sullivan et al., 1996, 2001; McEachern et al., 2000; Henikoff et al., 2001). Adjacent to these functional element regions, the centromere and telomere regions share an interesting architecture as depicted in Fig. 1. For both pericentromeric and subtelomeric regions, blocks of recent genomic duplications form a zone of shared sequence homologies between certain subsets of human chromosomes. The dynamic nature and evolutionary history of these regions and the unique DNA sequence adjacent to them will be the focus of this review.

Silence of the centromeres – not

Centromeres are a conundrum; although many proteins associated with centomeres are conserved from yeast to humans, the underlying DNA sequence is not. A proposed solution to this problem is that an epigenetic, largely heterochromatic, state be imposed by these proteins. Recent analysis of a human neocentromere and the complete sequence of a rice centromere suggest that this epigenetic state can enable transcription of at least some genes within a centromere.

Mapping the distribution of the interstitial telomeric (TTAGGG)n sequences in eight species of Brazilian marsupials (Didelphidae) by FISH and the correlation with constitutive heterochromatin. Do ITS represent evidence for fusion events in American marsupials?

The C-band pattern and the distribution of the (TTAGGG)(n) sequence after fluorescence in situ hybridization (FISH), were studied in eight species of Didelphidae marsupials: four species with 2n = 14 (Marmosops parvidens, Marmosops incanus, Marmosa murina and Metachirus nudicaudatus), two species with 2n = 18 (Monodelphis domestica and M. americana), and two with 2n = 22 (Didelphis marsupialis and Lutreolina crassicaudata). The hybridization signals were observed at both termini telomeres of all chromosomes. In addition, interstitial sequences were detected in the pericentromeric region of all chromosomes of Marmosops parvidens, in five chromosome pairs of M. incanus, and in the first pair of Monodelphis domestica. These sites always occur in the region of constitutive heterochromatin, even though C-band positive regions do not always present interstitial telomeric sequences (ITS). We suggest that the interstitial (TTAGGG)(n) sequences are associated with satellite DNA and do not necessarily arise through chromosomal rearrangements.

Mammalian artificial chromosomes as vectors: progress and prospects

Artificial chromosomes have long been touted as the ideal vector for gene therapy and biotechnology purposes based on the idea that such a chromosome would mimic the natural state of DNA in the cell. This, it is argued, would mean that essentially unlimited amounts of DNA could be incorporated into such a vector enabling either large genes or whole metabolic pathways to be provided to the recipient cell or organism. Additionally, such a vector would not integrate into the genome of the host cell and so would not cause mutagenesis by insertion and could perhaps be withdrawn from the cell or organism when no longer required. A number of preconditions are implicit in these claims. First, the chromosome should have a segregation efficiency approaching 100% in order to be useful in a cell population undergoing multiple rounds of cell divisions. Second, the chromosome should have a defined structure for regulatory and practical reasons. A defined structure is needed to maximize the control of expression of the genes that it contains. Third, the chromosome should not be so large that delivery becomes a problem. Finally, chromosomal effects such as centromeric or telomeric silencing should not dominate the expression of genes contained in an artificial chromosome. In this article, we discuss our own and others' efforts to achieve these aims using a variety of nonviral approaches to the problem.

CENP-B is not critical for meiotic chromosome segregation in male mice

Centromere protein B (CENP-B) is a constitutive protein that binds to a highly conserved 17bp motif located at most mammalian centromeres. To determine whether disruption of this gene affects chromosome segregation in male germ cells, we evaluated the frequencies of disomic and diploid sperm in CENP-B heterozygous and homozygous null mice using the mouse epididymal sperm aneuploidy (m-ESA) assay, a multicolor FISH method with probes for chromosomes X, Y and 8. The specificity and sensitivity of the m-ESA assay was demonstrated using Robertsonian (2.8) translocation heterozygotes as positive controls for sperm aneuploidy. Our results show that the frequencies of disomic and diploid sperm did not differ significantly between CENP-B heterozygous and homozygous null mice (P> or = 0.5) or from 129/Swiss isogenic mice (P> or = 0.5) and B6C3F1 mice (P> or = 0.2). These findings indicate that CENP-B does not have an essential role during chromosome segregation in male meiosis.

Small marker chromosome identification in metaphase and interphase using centromeric multiplex fish (CM-FISH)

Multicolor karyotyping procedures, such as multiplex fluorescence in situ hybridization (M-FISH), spectral karyotyping, or color-changing karyotyping, can be used to detect chromosomal rearrangements and marker chromosomes in prenatal diagnosis, peripheral blood cultures, leukemia, and solid tumors, especially in cases where G-banding is not sufficient. A regular M-FISH analysis requires relatively large amounts of labeled DNA (microgram quantities), is not informative in interphase nuclei, hybridization can take up to 2 to 3 days, and unlabeled human chromosome-painting probes are not available commercially. Unique probes (plasmids, PAC), specific for centromeric or subtelomeric chromosomal regions, can replace the painting probes in M-FISH to address specific issues, such as the identification of marker chromosomes and aneuploidies. A set of plasmid probes carrying repetitive sequences specific for the alpha-satellite region of all human chromosomes were combined in a metaphase assay and an interphase assay, allowing identification of aneuploidies in one hybridization step, on a single cytogenetic slide. The fluorophore-dUTP and the labeled antibodies required to label and detect the DNA probes can be prepared in any laboratory. All DNA probes can be easily isolated and labeled using common molecular cytogenetic procedures. Because of the repetitive nature of the probes, hybridization time is short, usually less than 1 hour, and the analysis can be performed with nonspecialized image-processing software.

Essay on the nucleoli survey by the alpha- and beta-satellite DNA probes of the acrocentric chromosomes in mitogen-stimulated human lymphocytes

The two constitutive heterochromatin (alpha- and beta-satellite DNA) probes of human acrocentric chromosomes were assayed separately to label the nucleoli in the phytohemagglutinin (PHA)-stimulated human lymphocytes. Fluorescent in situ hybridisation (FISH) results have shown that: a) whole (100%) signal-nucleoli overlapping was obtained with both heterochromatin probes in maximally activated nuclei (MANs); b) partial overlapping was observed in non-activated or slightly activated nuclei; c) random signal-nucleolus overlapping (background level) was found to be approximately 6% by the NOR-irrelevant euchromatic probe (D5S23); d) Yq-nucleolus association in the MANs was found to be approximately 97% without the subtraction of the background level. We concluded that: a) acrocentric alpha- or beta-satellite DNA probes may be used as nucleolar markers only in the MANs and not in slightly activated or non-activated nuclei; b) the distances between rDNA loci and alpha-/beta-satellite DNA on human acrocentrics are short enough to permit their observation on the same nucleolus.

Taxol-induced meiotic maturation delay, spindle defects, and aneuploidy in mouse oocytes and zygotes

To increase our understanding about the potential risks of chemically-induced aneuploidy, more information about the various mechanisms of aneuploidy induction is needed, particularly in germ cells. Most chemicals that induce aneuploidy inhibit microtubule polymerization. However, taxol alters microtubule dynamics by enhancing polymerization and stabilizing the polymer fraction. We tested the hypothesis that taxol induces meiotic delay, spindle defects, and aneuploidy in mouse oocytes and zygotes. Super-ovulated ICR mice received 0 (control), 2.5, 5.0, and 7.5 mg/kg taxol intraperitoneally immediately after HCG. Females were paired (1:1) with males for 17 h after taxol treatment. Mated females were given colchicine 25 h after taxol and their one-cell zygotes were collected 16 h later. Ovulated oocytes from non-mated females were collected 17 h after taxol. Chromosomes were C-banded for cytogenetic analyses. Oocytes were also collected from another group of similarly treated females for in situ chromatin and microtubule analyses. Taxol significantly (p<0.01) enhanced the proportion of oocytes exhibiting parthenogenetic activation, chromosomes displaced from the meiotic spindle, and sister-chromatid separation. Moreover, 7.5 mg/kg taxol significantly (p<0.01) increased the proportions of metaphase I and diploid oocytes and polyploid zygotes. A significant (p<0.01) dose response for taxol-induced hyperploidy in oocytes and zygotes was found. These results support the hypothesis that taxol-induced meiotic delay and spindle defects contribute to aneuploid mouse oocytes and zygotes.

Nucleotide specificity at the boundary and size requirement of the target sites recognized by human centromere protein B (CENP-B) in vitro

Human centromere protein B (CENP-B) has a sequence-specific DNA binding activity. We previously reported several CENP-B binding motifs by analysing synthetic oligonucleotides as well as alphoid DNA isolated from the human genomic library. Here, we examined the size requirement and nucleotide specificity of human CENP-B binding sequences in vitro. We synthesized three sets of mixed oligonucleotides containing diverged authentic binding sites (CTTCGTTGGAAACGGGA) in which certain pairs of nucleotides (underlined) were degenerated. Each oligonucleotide with a defined sequence was separately introduced into a plasmid and mixed with GST-fused recombinant CENP-B. The DNA-protein complex formed was affinity purified with glutathione Sepharose. Any nucleotide substitutions at the positions 1, 2 and 17 did not significantly influence the recovery, while the substitutions at positions 3, 4 and 16 did, suggesting that the internal 14-bp motif (TCGTTGGAAACGGG) constituted the minimum requirement. However, it showed a lower affinity to CENP-B, compared with the authentic motif. The inclusion of T at the 5' end greatly increased the affinity, and the further addition of A or T at the 3' end (TTCGTTGGAAACGGGA/T) offered affinity similar to the authentic motif. The first nucleotide of the 17-bp authentic binding motif may not be essential for CENP-B binding.

The distribution of binding sites for centromere protein B (CENP-B) is partly conserved among diverged higher order repeating units of human chromosome 6-specific alphoid DNA

We previously reported the isolation of alphoid satellite clones from a human genomic library using a DNA immunoprecipitation with centromere protein B (CENP-B). Here, we have characterized the distribution of CENP-B-binding sites on the 3-kb BamHI repeats of the cos2 clone. Using in situ hybridization, this alphoid satellite was located primarily at the centromeric region of chromosome 6. The functional binding sites were mapped by precipitating the restriction fragments with recombinant CENP-B in vitro. One repeat (2B3-11) consisted of 19 copies of alphoid monomer, eight of which possessed the binding sites, while another (2B3-9) consisted of 18 copies of the monomer, seven of which possessed the binding sites. The distribution of the sites was well conserved between them, except for the terminus. A similar analysis with the remaining 6-kb region suggested the presence of a continuous 1-kb region with regular spacing of EcoRI sites and the CENP-B-binding sites. When the nucleotide sequence of 2B3-11 was compared with that of another chromosome 6-specific alphoid repeat (p308) that had been described previously, this 1-kb region was highly conserved between them. The distribution of the CENP-B binding sites and the order of alphoid monomers might define the folding of alphoid repeats in the centromeric region.

Aneuploidy in germ cells: disruption of chromosome mover components

The task of the Workgroup on "Disruption of Chromosome Mover Components" was to establish what cellular structures are involved in chromosome segregation and how disruption of these could occur. Recent research on the mechanism of action of the cellular components that segregate chromosomes accurately during mitosis or meiosis has served to highlight the number of potential targets for disruption. The process of chromosome segregation represents an orchestrated chain of events centered on the activities of cellular motors, kinesins and dyneins. These motors are involved in arranging chromosomes at the metaphase plate, providing the spindle tension necessary for progression, and the actual segregation of the chromosomes to the poles. The Workgroup determined that there is a lack of information on the effects of chemical exposure to cell motors and other chromosome mover components, and that there is a clear need for further research. This article describes the discussions of the Workgroup and highlights areas of future research into chromosome movement, particularly in human meiotic and mitotic cells. The Workgroup emphasized that obtaining mechanistic data on the induction of aneuploidy will allow for extrapolation of the dose response curves for chemical exposures below the level of observation and for using aneuploidy data for quantitative risk assessment for adverse health effects.

Aneuploidy in germ cells: etiologies and risk factors

A 2 1/2-day workshop on germ cell aneuploidy was convened September 11-13, 1995 at the National Institute of Environmental Health Sciences in Research Triangle Park, North Carolina to discuss current understandings of the etiology and origin of human aneuploidy, especially in regard to potential environmental causes, and to identify gaps in our research knowledge. The workshop was designed to facilitate interactions among research experts conducting studies on the fundamental biology of chromosomal movement and segregation, on aneuploidy as a human clinical problem, and on toxicological aspects of aneuploidy induction. Overview presentations provided perspectives on aneuploidy as a human clinical problem, the genetics of aneuploidy, and the issues of concern in toxicological testing and regulatory risk assessment. The four chairs introduced the topics for each of their workgroups, setting the stage for subsequent, in-depth discussions on (1) chromosome mover components, (2) altered recombination, (3) parental age effects, and (4) differential chromosome susceptibility. From these discussions, gaps in our research knowledge related to the role of the environment in the etiology of aneuploidy and associated molecular, cellular, and genetic processes involved were identified, and will be used to establish a research agenda for filling those gaps.

Chromosomal differences in susceptibility to meiotic aneuploidy

A basic question concerning the origins of germ cell aneuploidy is whether the same mechanisms operate for all chromosomes, or whether there are chromosome-specific factors influencing the susceptibility to nondisjunction. Although selective loss of some trisomies in early gestation may contribute to the observed differences in trisomy frequency, data from spontaneous abortions, early embryos and gametes strongly suggest that there are real differences in the frequency with which different trisomies arise. In particular the preponderance of trisomy 16 and acrocentric trisomy appears to be present at conception. Maternal and paternal age relationships also differ among trisomies, as do the extent of maternal and paternal contributions, and the relative frequency of meiosis I and meiosis II errors. Recombination patterns associated with nondisjunction also show chromosomal differences. Chromosomal differences in length, centromere position, pericentromeric and other repetitive sequences, recombination patterns and chromatin characteristics might all be related to a differential susceptibility to aneuploidy, but no current explanation accounts for the excess of maternally derived trisomy 16. The existence of chromosome-specific factors makes extrapolation from observations on one chromosome to all aneuploidy unwise, both for investigations into the causes of aneuploidy, and for surveillance of aneuploidy frequency.