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

Sperm nuclear architecture is locally modified in presence of a Robertsonian translocation t(13;17)

In mammals, the non-random organization of the sperm nucleus supports an early function during embryonic development. Altering this organization may interfere with the zygote development and reduce fertility or prolificity. Thus, rare studies on sperm cells from infertile patients described an altered nuclear organization that may be a cause or a consequence of their respective pathologies. Thereby, chromosomal rearrangements and aneuploidy can be studied not only for their adverse effects on production of normal/balanced gametes at meiosis but also for their possible impact on sperm nuclear architecture and the epigenetic consequences of altered chromosome positioning. We decided to compare the global architecture of sperm nuclei from boars, either with a normal chromosome composition or with a Robertsonian translocation involving chromosomes 13 and 17. We hypothesized that the fusion between these chromosomes may change their spatial organization and we examined to what extend it could also modify the global sperm nuclear architecture. Analysis of telomeres, centromeres and gonosomes repartition does not support a global nuclear disorganization. But specific analysis of chromosomes 13 and 17 territories highlights an influence of chromosome 17 for the positioning of the fused chromosomes within the nucleus. We also observed a specific clustering of centromeres depending of the chromosome subtypes. Altogether our results showed that chromosome fusion does not significantly alter sperm nucleus architecture but suggest that centromere remodelling after chromosome fusion locally impacts chromosome positioning.

Comparative karyotype using bidirectional chromosome painting: how and why?

Rat is widely used in biomedical and pharmaceutical research but its genome has been significantly less studied than that of the mouse. This represents a major limitation for studying cytogenetic and molecular mechanisms in the rat model. As Muridae species underwent an intense chromosome evolution it is not possible to directly transpose knowledge of the mouse genome to that of the rat. For establishing a comparative karyotype between rat and mouse, painting probes of both species were prepared by PARM-PCR (Priming Authorizing Random Mismatches PCR) from a low copy number of sorted chromosomes, the mouse and rat specific painting probes being then hybridized on rat and mouse metaphases, respectively. The availability of rodent species chromosome painting probes as well as the information obtained by the comparative karyotype and comparative gene mapping data are of great interest to improve knowledge on species evolution but also to better understand carcinogenesis process, as illustrated by our data concerning the cytogenetic characterization of radon-induced rat lung tumors. Detailed methods for obtaining painting probes by PARM-PCR from sorted mouse and rat chromosomes and for their hybridization in homologous or heterologous conditions are described. Usefulness of chromosome painting is illustrated by the characterization of chromosomal abnormalities in a radon-induced rat lung tumor. Advantages and limitations of this technique as compared to classical cytogenetics, FISH and CGH are discussed.

Quantitative fluorescence in situ hybridization in lung cancer as a diagnostic marker

The diagnosis of lung cancer is quite often hampered by the existence of various cell types within samples such as biopsies or pleural effusions. We have established a new marker for image cytometry of interphase tumor cells of the lung by using the most recurrent and early cytogenetic event in lung cancer, the loss of the short arm of chromosome 3. The method is based on the detection of the imbalance between the long and the short arms of chromosome 3 by performing two-color fluorescence in situ hybridization on both arms. Fourteen tumors were analyzed after short-term culture and compared with the corresponding cytogenetic data obtained from metaphase analysis. Results on interphase nuclei and control experiments on metaphases were the same, with imbalance ratios ranging from 1.0 to 2.0 (mean value 1.6, median 1.5). To assess the clinical significance of this approach, three pleural effusions were analyzed. Data showed that normal cells within the sample could have been distinguished from the tumor cells based on different imbalance values between the long and the short arms. Thus, our method allows refined detection of lung tumor cells within samples containing heterogeneous cell populations.

Chromosome painting in farm, pet and wild animal species

Among the advanced karyotype analysis approaches embraced by animal cytogenetics during the past decade, chromosome painting has had the greatest impact. Generation of chromosome specific paints is considered pivotal to his development. Additionally, ability to use these paints across species (referred to as Zoo-FISH or comparative painting) is undisputedly the most important breakthrough that has contributed to our ability to compare karyotypes of a wide range of evolutionarily highly diverged chromosome painting, and makes them aware of the tools/resources available to carry out this research in a variety of animal species. An overview of the current status of comparative chromosome painting results across closely as well as distantly related species is presented. Findings from different studies show how some segmental syntenies are more conserved as compared to others. The comparisons provide insight into the likely constitution of a vertebrate/mammalian ancestral karyotype and help understand some of the intricacies about karyotype evolution. Importance of comparative painting in setting the stage for rapid development of gene maps in a number of economically important species is elaborated.

Comparative karyotype of rat and mouse using bidirectional chromosome painting

A comparative karyotype of rat (Rattus norvegicus) and mouse (Mus musculus) based on chromosome G-banding morphology, heterologous chromosome painting results and available gene mapping data is proposed. Whole chromosome painting probes from both species were generated by PARM-PCR amplification of flow sorted chromosomes. Bidirectional chromosome painting identifies 36 segments of syntenic homology and allows us to propose a nearly complete comparative karyotype of mouse and rat (except for RNO 13 p and RNO 19 p12-13). Seven segments completely covered the RNO chromosomes 3, 5, 8, 11, 12, 15 and 18. Eight segments completely covered the MMU chromosomes 3, 4, 6, 7, 9, 12, 18 and 19. The RNO chromosomes 5, 8, 18 show complete homology with the MMU chromosomes 4, 9 and 18, respectively. Bidirectional hybridization results clearly assign 16 segments to subchromosomal regions in both species. Interpretation of the results allows subchromosomal assignment of all the remaining segments apart from seven distributed on chromosomes MMU 15, MMU 10 B2-D3 and MMU 17 E3-E5. The proposed comparative karyotype shows overall agreement with available comparative mapping data. The proposed repartition of syntenic homologous segments between the two species provides useful data for gene-mapping studies. In addition, these results will enable the reconstruction of the karyotype of the Cricetidae and Muridae common ancestor and the definition of the precise rearrangements which have occurred in both mouse and rat lineages during evolution.

Comparative karyotype of pig and cattle using whole chromosome painting probes

The extent and distribution of conserved chromosomal segments between pig and cattle chromosomes were established using hybridization of porcine chromosome painting probes on bovine metaphases. A total of 44 segments of conserved synteny were identified, resulting in a nearly complete coverage of the bovine karyotype. This study provides new data on chromosome evolution of mammals.

Characterization of reciprocal translocations in pigs using dual-colour chromosome painting and primed in situ DNA labelling

We report the use of dual-colour chromosome painting to determine the exact nature of certain chromosome rearrangements observed in the pig (Sus scrofa domestica). The chromosomal abnormalities were detected by GTG- and RBG-banding techniques. The initially proposed interpretations were: (1) rcp(6;13)(p1.5;q4.1); (2) rcp(11;16)(p1.4;q1.4); (3) rcp(6;16)(p1.1;q1.1); (4) rcp(13;17)(q4.1;q1.1); (5) rcp(6;14)(q2.7;q2.1); (6) rcp(3;5)(p1.3;q2.3); (7) rcp(2; 14)(q1.3;q2.7); (8) rcp(15;17)(q1.3;q2.1). Hybridizations were carried out with biotin- and digoxigenin-labelled probes obtained by priming authorizing random mismatches polymerase chain reaction (PARM-PCR) amplification of porcine flow-sorted chromosomes. In some cases, i.e. (1), (4), (5), (6), (7) and (8), the fluorescence in situ hybridization (FISH) results allowed confirmation of the interpretations proposed with classical cytogenetic methods. Chromosome painting proved the reciprocity of the translocation in cases (1), (6) and (8), whereas modifications of the formula were proposed for case (2). Primed in situ DNA labelling (PRINS) experiments have also been carried out in case (3) using a primer specific for the centromeres of acrocentric chromosomes (first experiment) or a primer specific for the centromeres of a subset of meta- and submetacentric chromosomes including chromosome 6 (second experiment). It allowed us to demonstrate that the breakpoints occurred in the centromeric region of chromosome 16 and in the p. arm of chromosome 6, just above the centromere.

Emerging patterns of comparative genome organization in some mammalian species as revealed by Zoo-FISH

Although gene maps for a variety of evolutionarily diverged mammalian species have expanded rapidly during the past few years, until recently it has been difficult to precisely define chromosomal segments that are homologous between species. A solution to this problem has come from the development of Zoo-FISH, also known as cross-species chromosome painting. The use of Zoo-FISH to identify regions of chromosomal homology has allowed the transfer of information from map-rich species such as human and mouse to a wide variety of other species. From a Zoo-FISH analysis spanning four mammalian orders (Primates, Artiodactyla, Carnivora, and Perissodactyla), and involving eight species (human, pig, cattle, Indian muntjac, cat, American mink, harbor seal, and horse), three distinct classes of synteny conservation have been designated: (1) conservation of whole chromosome synteny, (2) conservation of large chromosomal blocks, and (3) conservation of neighboring segment combinations. This analysis has also made it possible to identify a set of chromosome segments (based on human chromosome equivalents) that probably made up the karyotype of the common ancestor of the four orders. This approach provides a basis for developing a picture of the ancestral mammalian karyotype, but a full understanding will depend on studies encompassing more diverse combinations of mammalian orders.