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Cell Jan 2011Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. Using next-generation...
Cancer is driven by somatically acquired point mutations and chromosomal rearrangements, conventionally thought to accumulate gradually over time. Using next-generation sequencing, we characterize a phenomenon, which we term chromothripsis, whereby tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. Rearrangements involving one or a few chromosomes crisscross back and forth across involved regions, generating frequent oscillations between two copy number states. These genomic hallmarks are highly improbable if rearrangements accumulate over time and instead imply that nearly all occur during a single cellular catastrophe. The stamp of chromothripsis can be seen in at least 2%-3% of all cancers, across many subtypes, and is present in ∼25% of bone cancers. We find that one, or indeed more than one, cancer-causing lesion can emerge out of the genomic crisis. This phenomenon has important implications for the origins of genomic remodeling and temporal emergence of cancer.
Topics: Bone Neoplasms; Cell Line, Tumor; Chromosome Aberrations; Chromosome Painting; Female; Gene Rearrangement; Humans; Leukemia, Lymphocytic, Chronic, B-Cell; Middle Aged; Neoplasms
PubMed: 21215367
DOI: 10.1016/j.cell.2010.11.055 -
PLoS Genetics Jul 2021The presence of meiosis, which is a conserved component of sexual reproduction, across organisms from all eukaryotic kingdoms, strongly argues that sex is a primordial... (Review)
Review
The presence of meiosis, which is a conserved component of sexual reproduction, across organisms from all eukaryotic kingdoms, strongly argues that sex is a primordial feature of eukaryotes. However, extant meiotic structures and processes can vary considerably between organisms. The ciliated protist Tetrahymena thermophila, which diverged from animals, plants, and fungi early in evolution, provides one example of a rather unconventional meiosis. Tetrahymena has a simpler meiosis compared with most other organisms: It lacks both a synaptonemal complex (SC) and specialized meiotic machinery for chromosome cohesion and has a reduced capacity to regulate meiotic recombination. Despite this, it also features several unique mechanisms, including elongation of the nucleus to twice the cell length to promote homologous pairing and prevent recombination between sister chromatids. Comparison of the meiotic programs of Tetrahymena and higher multicellular organisms may reveal how extant meiosis evolved from proto-meiosis.
Topics: Chromosome Painting; Epigenesis, Genetic; Meiosis; Reproduction; Tetrahymena thermophila
PubMed: 34264933
DOI: 10.1371/journal.pgen.1009627 -
Molecules (Basel, Switzerland) Apr 2020Fluorescence in situ hybridization (FISH) is a standard technique used in routine diagnostics of genetic aberrations. Thanks to simple FISH procedure is possible to... (Review)
Review
Fluorescence in situ hybridization (FISH) is a standard technique used in routine diagnostics of genetic aberrations. Thanks to simple FISH procedure is possible to recognize tumor-specific abnormality. Its applications are limited to designed probe type. Gene rearrangements e.g., , reflecting numerous translocational partners, deletions of critical regions e.g., 1p and 19q, gene fusions e.g., , genomic imbalances e.g., 6p, 6q, 11q and amplifications e.g., are targets in personalized oncology. Confirmation of genetic marker is frequently a direct indication to start specific, targeted treatment. In other cases, detected aberration helps pathologists to better distinguish soft tissue sarcomas, or to state a final diagnosis. Our main goal is to show that applying FISH to formalin-fixed paraffin-embedded tissue sample (FFPE) enables assessing genomic status in the population of cells deriving from a primary tumor or metastasis. Although many more sophisticated techniques are available, like Real-Time PCR or new generation sequencing, FISH remains a commonly used method in many genetic laboratories.
Topics: Biomarkers, Tumor; Chromosome Painting; Humans; Immunohistochemistry; In Situ Hybridization, Fluorescence; Molecular Probes; Neoplasms; Precision Medicine; Reproducibility of Results
PubMed: 32316657
DOI: 10.3390/molecules25081864 -
The Plant Journal : For Cell and... Oct 2022Aegilops species represent the most important gene pool for breeding bread wheat (Triticum aestivum). Thus, understanding the genome evolution, including chromosomal...
Aegilops species represent the most important gene pool for breeding bread wheat (Triticum aestivum). Thus, understanding the genome evolution, including chromosomal structural rearrangements and syntenic relationships among Aegilops species or between Aegilops and wheat, is important for both basic genome research and practical breeding applications. In the present study, we attempted to develop subgenome D-specific fluorescence in situ hybridization (FISH) probes by selecting D-specific oligonucleotides based on the reference genome of Chinese Spring. The oligo-based chromosome painting probes consisted of approximately 26 000 oligos per chromosome and their specificity was confirmed in both diploid and polyploid species containing the D subgenome. Two previously reported translocations involving two D chromosomes have been confirmed in wheat varieties and their derived lines. We demonstrate that the oligo painting probes can be used not only to identify the translocations involving D subgenome chromosomes, but also to determine the precise positions of chromosomal breakpoints. Chromosome painting of 56 accessions of Ae. tauschii from different origins led us to identify two novel translocations: a reciprocal 3D-7D translocation in two accessions and a complex 4D-5D-7D translocation in one accession. Painting probes were also used to analyze chromosomes from more diverse Aegilops species. These probes produced FISH signals in four different genomes. Chromosome rearrangements were identified in Aegilops umbellulata, Aegilops markgrafii, and Aegilops uniaristata, thus providing syntenic information that will be valuable for the application of these wild species in wheat breeding.
Topics: Aegilops; Chromosome Painting; Chromosomes, Plant; In Situ Hybridization, Fluorescence; Oligonucleotides; Plant Breeding; Translocation, Genetic; Triticum
PubMed: 35998122
DOI: 10.1111/tpj.15926 -
The New Phytologist Feb 2022Karyotypes provide key cytogenetic information on the phylogenetic relationships and evolutionary origins in related eukaryotic species. Despite our knowledge of the...
Karyotypes provide key cytogenetic information on the phylogenetic relationships and evolutionary origins in related eukaryotic species. Despite our knowledge of the chromosome numbers of sugarcane and its wild relatives, the chromosome composition and evolution among the species in the Saccharum complex have been elusive owing to the complex polyploidy and the large numbers of chromosomes of these species. Oligonucleotide-based chromosome painting has become a powerful tool of cytogenetic studies especially for plant species with large numbers of chromosomes. We developed oligo-based chromosome painting probes for all 10 chromosomes in Saccharum officinarum (2n = 8x = 80). The 10 painting probes generated robust fluorescence in situ hybridization signals in all plant species within the Saccharum complex, including species in the genera Saccharum, Miscanthus, Narenga and Erianthus. We conducted comparative chromosome analysis using the same set of probes among species from four different genera within the Saccharum complex. Excitingly, we discovered several novel cytotypes and chromosome rearrangements in these species. We discovered that fusion from two different chromosomes is a common type of chromosome rearrangement associated with the species in the Saccharum complex. Such fusion events changed the basic chromosome number and resulted in distinct allopolyploids in the Saccharum complex.
Topics: Chromosome Painting; Chromosomes, Plant; In Situ Hybridization, Fluorescence; Phylogeny; Saccharum
PubMed: 34874076
DOI: 10.1111/nph.17905 -
BMC Plant Biology Jun 2018The chromosome-specific probe is a fundamental tool of chromosome painting and has been commonly applied in mammalian species. The technology, however, has not been...
BACKGROUND
The chromosome-specific probe is a fundamental tool of chromosome painting and has been commonly applied in mammalian species. The technology, however, has not been widely applied in plants due to a lack of methodologies for probe development. Identification and labeling of a large number of oligonucleotides (oligos) specific to a single chromosome offers us an opportunity to establish chromosome-specific probes in plants. However, never before has whole chromosome painting been performed in rice.
RESULTS
We developed a pooled chromosome 9-specific probe in rice, which contains 25,000 oligos based on the genome sequence of a japonica rice (Oryza sativa L., AA, 2n = 2× = 24). Chromosome 9 was easily identified in both japonica and indica rice using this chromosome 9-painting probe. The probe was also successfully used to identify and characterize chromosome 9 in additional lines of O. sativa, a translocation line, two new aneuploids associated with chromosome 9 and a wild rice (Oryza eichingeri A. Peter, CC, 2n = 2× = 24).
CONCLUSION
The study reveals that a pool of oligos specific to a chromosome is a useful tool for chromosome painting in rice.
Topics: Aneuploidy; Chromosome Aberrations; Chromosome Painting; Chromosomes, Plant; Genome, Plant; In Situ Hybridization, Fluorescence; Oligonucleotide Probes; Oryza; Translocation, Genetic
PubMed: 29879904
DOI: 10.1186/s12870-018-1325-2 -
Frontiers in Plant Science 2021The genus is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We...
The genus is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We developed a chromosome 2 painting (CP2) probe by designing oligonucleotides covering chromosome 2 of (2n = 8x = 64). Fluorescence hybridization (FISH) using this CP2 probe revealed six types of ploidies from twenty clones, including 6x, 8x, 10x, 11x, 12x, and 13x clones. The finding of clones with uneven of ploid suggested that certain clones come from hybridization. It renews our knowledge that is derived from autopolyploidization. Combined with a -specific probe, chromosome 2-derived chromosome or fragments from either or can be identified in sugarcane modern cultivars. We revealed unexpected high level of interspecific recombination from introgressive chromosomes (>50.0%) in cultivars ROC22 and ZZ1, indicating frequent chromosome exchange in cultivars. Intriguingly, we observed interspecific recombination recurring among either homoeologous or non-homoeologous chromosomes in sugarcane cultivars. These results demonstrated that chromosome painting FISH is a powerful tool in the genome dissection of sugarcane and provide new insights into the genome structure and evolution of the complex genus .
PubMed: 34512706
DOI: 10.3389/fpls.2021.731664 -
Methods in Molecular Biology (Clifton,... 2019Current methods for chromosome painting via fluorescence in situ hybridization (FISH) are costly, time-consuming, and limited in complexity. In contrast to conventional...
Current methods for chromosome painting via fluorescence in situ hybridization (FISH) are costly, time-consuming, and limited in complexity. In contrast to conventional sources of probe, Oligopaints are computationally designed, synthesized on microarrays, and amplified by PCR. This approach allows for precise control over the sequences they target, which can range from a few kilobases to entire chromosomes with the same basic protocol. We have utilized the flexibility and scalability of Oligopaints to generate low-cost and renewable chromosome paints for Drosophila, mouse, and human chromosomes. These Oligopaint libraries can be customized to label any genomic feature(s) in a chromosome-wide manner. Additionally, this method is compatible with sequential FISH to label entire genomes with a single denaturation step. Here, we outline a protocol and considerations to scale the Oligopaint technology for fluorescent labeling of whole chromosomes.
Topics: 3T3 Cells; Animals; Chromosome Painting; Chromosomes, Human; Chromosomes, Insect; Chromosomes, Mammalian; Drosophila melanogaster; Fluorescent Dyes; HCT116 Cells; Humans; Mice; Microscopy, Fluorescence; Oligonucleotides
PubMed: 31407284
DOI: 10.1007/978-1-4939-9674-2_11 -
Cytogenetic and Genome Research 2012The order of Carnivora has been very well characterized with over 50 species analyzed by chromosome painting and with painting probe sets made for 9 Carnivora species.... (Comparative Study)
Comparative Study Review
The order of Carnivora has been very well characterized with over 50 species analyzed by chromosome painting and with painting probe sets made for 9 Carnivora species. Representatives of almost all families have been studied with few exceptions (Otariidae, Odobenidae, Nandiniidae, Prionodontidae). The patterns of chromosome evolution in Carnivora are discussed here. Overall, many Carnivora species retained karyotypes that only slightly differ from the ancestral carnivore karyotype. However, there are at least 3 families in which the ancestral carnivore karyotype has been severely rearranged - Canidae, Ursidae and Mephitidae. Here we report chromosome painting of yet another Carnivora species with a highly rearranged karyotype, Genetta pardina. Recurrent rearrangements make it difficult to define the ancestral chromosomal arrangement in several instances. Only 2 species of pangolins (Pholidota), a sister order of Carnivora, have been studied by chromosome painting. Future use of whole-genome sequencing data is discussed in the context of solving the questions that are beyond resolution of conventional banding techniques and chromosome painting.
Topics: Animals; Canidae; Carnivora; Cats; Chromosome Painting; Chromosomes, Mammalian; Dogs; Evolution, Molecular; Felidae; Female; Humans; Karyotype; Male; Mephitidae; Mustelidae; Phylogeny; Procyonidae; Species Specificity; Ursidae; Viverridae
PubMed: 22889959
DOI: 10.1159/000341389 -
Comparative Cytogenetics 2023A brief overview of the current stage of the chromosome study of the insect order Hymenoptera is given. It is demonstrated that, in addition to routine staining and... (Review)
Review
A brief overview of the current stage of the chromosome study of the insect order Hymenoptera is given. It is demonstrated that, in addition to routine staining and other traditional techniques of chromosome research, karyotypes of an increasing number of hymenopterans are being studied using molecular methods, e.g., staining with base-specific fluorochromes and fluorescence hybridization (FISH), including microdissection and chromosome painting. Due to the advent of whole genome sequencing and other molecular techniques, together with the "big data" approach to the chromosomal data, the current stage of the chromosome research on Hymenoptera represents a transition from Hymenoptera cytogenetics to cytogenomics.
PubMed: 37953851
DOI: 10.3897/compcytogen.17.112332