Comparative chromosome painting discloses homologous segments in distantly related mammals

Zoo-FISH delineates conserved chromosomal segments in horse and man

Human chromosome specific libraries (CSLs) were individually applied to equine metaphase chromosomes using the fluorescence in situ hybridization (FISH) technique. All CSLs, except Y, showed painting signals on one or several horse chromosomes. In total 43 conserved chromosomal segments were painted. Homoeology could not, however, be detected for some segments of the equine genome. This is most likely related to the very weak signals displayed by some libraries, rather than to the absence of similarity with the human genome. In spite of divergence from the human genome, dated 70-80 million years ago, a fairly high degree of synteny conservation was observed. In seven cases, whole chromosome synteny was detected between the two species. The comparative painting results agreed completely with the limited gene mapping data available in horses, and also enabled us provisionally to assign one linkage group (U2) and one syntenic group (NP, MPI, IDH2) to specific equine chromosomes. Chromosomal assignments of three other syntenic groups are also proposed. The findings of this study will be of significant use in the expansion of the hitherto poorly developed equine gene map.

Comparative FISH mapping of bovine cosmids to reindeer chromosomes demonstrates conservation of the X-chromosome

Three X chromosome-specific bovine cosmids were used for fluorescence in situ hybridization mapping on reindeer (Rangifer tarandus) chromosomes, to test whether such large genomic clones could be used for comparative mapping across distantly related species. All three cosmids showed distinct unique hybridization sites on the reindeer X. Comparative map locations of these cosmids, together with the relative C-banding and genome size data on the X chromosomes of the two species, provide preliminary indications that the short and long arms of bovine X correspond, respectively, to the long and short arms of the reindeer X. The study also demonstrates that cosmid clones can be used successfully for comparative mapping across species that diverged 35 million years ago.

Assignment of 19 porcine type I loci by somatic cell hybrid analysis detects new regions of conserved synteny between human and pig

Nineteen so-called type I-loci, including ACO2, ADRA2, CAST, CCK, CHAT, IGKC, IGLV, IL4, IL6, INHA, LIF, MX1, PTH, RBP2, TCRA, TCRB, TGFB2, TGFB3, and UOX have been mapped in the pig with an informative somatic cell hybrid panel. By analyzing these new assignments in the knowledge of heterologous chromosome painting (Zoo-FISH) data for the porcine genome, it is possible to predict subchromosomal locations for most of these loci. Previously defined regions of conserved synteny were confirmed, and the extent of six of these regions was refined. These improvements in the porcine gene map facilitate the transfer of gene mapping data from "map-rich" species such as humans and mice.

Homologous and heterologous FISH painting with PARM-PCR chromosome-specific probes in mammals

Numerous loci can be amplified by PARM-PCR on 300 sorted chromosomes in low-stringency conditions (annealing at 30 degrees C during the two first cycles) to produce a probe that can be used in FISH painting experiments. We demonstrate that, depending on the primer chosen for the amplification, patterns of different quality can be obtained. In order to design a primer that allows amplification of coding sequences, we have shown that motifs of at least seven glutamic acid repeats (GAG or GAA codons) are present in human proteins more frequently than expected. Moreover, these repeats do not correspond to triplet expansion and can be conserved between species. Using probes prepared from sorted chromosomes with (GAG)7 primer, we were able to achieve homologous FISH painting on human, porcine, ovine, and bovine species, and bidirectional heterologous FISH painting between human and porcine species. As an example, using probes for human Chromosome (Chr) 19 and porcine Chrs 1 and 6, we clearly defined the regional homologies existing between those chromosomes.

Chromosome-specific paints from a high-resolution flow karyotype of the dog

Using peripheral blood lymphocyte cultures and dual-laser flow cytometry, we have routinely obtained high-resolution bivariate flow karyotypes of the dog in which 32 peaks are resolved. To allow the identification of the chromosome types in each peak, chromosomes were flow sorted, amplified and labelled by polymerase chain reaction with partially degenerate primers and hybridized onto metaphase spreads of a male dog. The chromosome paints from 22 of the 32 peaks each hybridized to single homologue pairs and eight peaks each hybridized to two pairs. Paints from the remaining two peaks hybridized to only one homologue each in the male metaphase spread, thus corresponding to the sex chromosomes X and Y. All of the 38 pairs of autosomes and the two sex chromosomes of the dog could be accounted for in these painting experiments. The positions of chromosomes 1-21 were assigned to the flow karyotype (only chromosomes 1-21 have as yet been officially designated). The high-resolution flow karyotype and the chromosome paints will facilitate further standardization of the dog karyotype. The ability to sort sufficient quantities of dog chromosomes for the production of chromosome-specific DNA libraries has the potential to accelerate the physical and genetic mapping of the dog genome.

Chromosome 'painting' in plants - a feasible technique?

It is shown that chromosome painting is as yet not possible for plants with very complex genomes, neither intra- nor interspecific. The reasons are inefficient blocking of dispersed repetitive sequences and insufficient signal intensity of short unique sequences. Future perspective are indicated.

The application of FISH techniques for physical mapping in the dog (Canis familiaris)

The abundance of CA/GT repeats in the DNA of the dog (Canis familiaris) has established the importance of polymorphic microsatellites in the development of a low density map of the canine genome. The assignment of linkage groups of markers to chromosomes by physical mapping requires reliable cytogenetic techniques for routine production of metaphase cells. The dog has 78 chromosomes, many of which are smaller and more contracted than those of other mammals. Although the molecular study of inherited disease in dogs has important implications for both improved welfare in dogs and the provision of animal models for human diseases, the small size and large number of chromosomes in the canine genome has discouraged the inclusion of cytogenetic analysis in the planning of relevant research protocols. In this report, Fluorescence In Situ Hybridization (FISH) techniques have been optimized for the physical mapping of probes in C. familiaris. A method to obtain a good yield of early and midmetaphases from short-term peripheral blood cultures and the optimal conditions for hybridization and detection of probes is described. Thirteen microsatellite-containing cosmid probes from a canine genomic library in pWE15, a highly repetitive probe (human ribosomal DNA pHr14E3), and a human X Chromosome (Chr) paint have been mapped. Six microsatellites, two ribosomal sites, and the human paint have been assigned to specific chromosomes.

Fluorescence in situ hybridization: a brief review

Fluorescence in situ hybridization (FISH) is used for many purposes, including analysis of chromosomal damage, gene mapping, clinical diagnostics, molecular toxicology and cross-species chromosome homology. FISH allows an investigator to identify the presence and location of a region of cellular DNA or RNA within morphologically preserved chromosome preparations, fixed cells or tissue sections. This report describes in situ hybridization, and discusses the past, present and future applications of this method for genetic analysis and molecular toxicology.

ZOO-FISH analysis: cat and human karyotypes closely resemble the putative ancestral mammalian karyotype

DNA in situ hybridization with human chromosome specific DNA libraries was applied to compare the karyotypes of humans (Homo sapiens, 2n = 46) and cats (Felis catus, 2n = 38). For the autosomes alone, 30 segments of conserved synteny were revealed. The arrangement of these segments in the feline karyotype differs by only seven single chromosome breaks and one intrachromosomal inversion from their arrangement in humans. Comparison of these data with those recently obtained for pig and those available from conventional gene mapping studies in mice and cattle has allowed us to develop a model of karyotype evolution in mammals. The cat and human karyotypes, with 36 and 44 autosomes respectively, were found to be very similar to a putative ancient mammalian founder karyotype. It would appear that during evolution to the human karyotype the status quo has been conserved for at least some 100-120 million years. There has been no need to alter the well-balanced gene arrangement of the mammalian founder karyotype.

Morphology of a human-derived YAC in yeast meiosis

In meiosis of human males DNA is packaged along pachytene chromosomes about 20 times more compactly than in meiosis of yeast. Nevertheless, a human-derived yeast artificial chromosome (YAC) shows the same degree of compaction of DNA as endogenous chromosomes in meiotic prophase nuclei of yeast. This suggests that in yeast meiosis, human and yeast DNA adopt a similar organization of chromatin along the pachytene chromosome cores. Therefore meiotic chromatin organization does not seem to be an inherent chromosomal property but is governed by the host-specific cellular environment. We suggest that there is a correlation between the less dense DNA packaging and the increased rate of recombination that has been reported for human-derived YACs as compared with human DNA in its natural environment.

A comparative study of karyotypes of muntjacs by chromosome painting

We have used a combination of chromosome sorting, degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), chromosome painting and digital image capturing and processing techniques for comparative chromosome analysis of members of the genus Muntiacus. Chromosome-specific "paints" from a female Indian muntjac were hybridised to the metaphase chromosomes of the Gongshan, Black, and Chinese muntjac by both single and three colour chromosome painting. Karyotypes and idiograms for the Indian, Gongshan, Black and Chinese muntjac were constructed, based on enhanced 4', 6-diamidino-2-phenylindole (DAPI) banding patterns. The hybridisation signal for each paint was assigned to specific bands or chromosomes for all of the above muntjac species. The interspecific chromosomal homology was demonstrated by the use of both enhanced DAPI banding and comparative chromosome painting. These results provide direct molecular cytogenetic evidence for the tandem fusion theory of the chromosome evolution of muntjac species.

Identification of highly conserved loci by genome painting

Fluorescence in situ hybridization was used to identify patterns of DNA similarity among the genomes of several rodent taxa. Total genomic or Cot-1 DNAs were used as hybridization probes against metaphase preparations across different taxonomic levels, including three species of Microtus (suborder Sciurognathi), three species of Microtus (suborder Sciurognathi), Mus musculus (suborder Sciurognathi) and Ctenomys steinbachi (suborder Hystricognathi). The hybridization patterns of Mus or Peromyscus (sciurognath) DNA to Mus metaphases, which were consistent with what is known of the satellite sequences in these species, demonstrated the efficacy of this approach for molecular cytogenetics and evolutionary biology. Additional hybridizations to chromosomes of Ctenomys or Microtus identified loci consisting of highly conserved DNA sequences. This approach has proved useful in investigating genome homologies across divergent rodent lineages. Chromosome microdissection can be used to characterize these regions further.

Chromosome specific paints from a high resolution flow karyotype of the mouse

Chromosomes from antigen stimulated B-cells from spleens of inbred mice have been separated using flow cytometry into 18 distinguishable peaks. Using locus-specific oligonucleotides and fluorescence in situ hybridization to banded metaphase spreads, 15 individual chromosomes were identified: 1, 2, 3, 6, 7, 8, 9, 11, 12, 16, 17, 18, 19, X and Y. The remaining six chromosomes, occurring as pairs in three peaks, 4 with 5, 10 with 13, and 14 with 15, were resolved by flow sorting chromosomes from mice carrying an appropriate homozygous translocation and 4, 5 and 14 have been isolated in this way. This is the first demonstration of how a complete set of mouse chromosome paints can be produced.

Visualization of the conservation of synteny between humans and pigs by heterologous chromosomal painting

By comparative gene mapping, extended conservation of synteny between different mammalian species has become apparent. Mapping in these species could be accelerated by exact visualization of the chromosomal segments that exhibit conserved synteny. We have hybridized human chromosome-specific DNA libraries onto porcine metaphase spreads to examine the extent of conservation of synteny between the two species. The hybridization signals on pig chromosomes are of variable quality, but the analysis allowed us to assign for all human autosomes homologous chromosomal segments in the pig karyotype. Extended conservation of synteny was observed, often comprising whole chromosomes. In our analysis 47 segments of conserved synteny common to the human and pig karyotype were identified. Intrachromosomal rearrangements by inversion within and between these segments are described. These rearrangements are common events during evolution. Our analysis shows that conservation of synteny between human and pig is three times more than between humans and mice and, consequently, is characterized by fewer, but larger conserved segments.

Comparative mapping reveals extensive linkage conservation--but with gene order rearrangements--between the pig and the human genomes

A porcine comparative map based on 83 coding loci was constructed. Comparisons to the human and mouse genetic maps revealed linkage conservation between humans and pigs more extensive than that between any of these and the mouse. The average lengths of conserved chromosome segments between pig and human and between pig and mouse were estimated at 37 and 21 cM, respectively. Rearrangements of gene orders within homologous chromosome segments were found to be common among these distantly related mammals. The development of a comparative map is an advance in pig genome analysis and contributes to the dissection of mammalian genome evolution.

Chromosome painting in plants: in situ hybridization with a DNA probe from a specific microdissected chromosome arm of common wheat

We report here on the successful painting of a specific plant chromosome within its own genome. Isochromosomes for the long arm of chromosome 5 of the wheat B genome (5BL) were microdissected from first meiotic metaphase spreads of a monoisosomic 5BL line of the common wheat Triticum aestivum cv. Chinese Spring. The dissected isochromosomes were amplified by degenerate oligonucleotide-primed PCR in a single tube reaction. The amplified DNA was used as a complex probe mixture for fluorescent in situ hybridization on first meiotic metaphase spreads of lines carrying 5BL as a distinctive marker. Hybridization signals were observed, specifically, along the entire 5BL. In some of the cells, labeling was also detected in two bivalents, presumably those of the 5B "homoeologues" (partial homologues) found in common wheat (5A and 5D). The probe also revealed discrete domains in tapetal nuclei at interphase, further supporting the probe's high specificity. These data suggest that chromosome and homoeologous group-specific sequences are more abundant in 5BL than genome-specific sequences. Chromosome-painting probes, such as the one described here for 5BL, can facilitate the study of chromosome evolution in polyploid wheat.