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Special Issue "Chromosome and Karyotype Variation"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 August 2019).

Special Issue Editors

Dr. Nikolay Rubtsov
E-Mail Website
Guest Editor
Novosibirsk State University, Novosibirsk, Russian Federation
Interests: chromosome; karyotype; chromosome instability; chromosome rearrangements; speciation; germline-restricted chromosome; small supernumerary marker chromosomes; cancer; mobile elements; copy number variants
Dr. Thomas Liehr
E-Mail Website
Co-Guest Editor
Institute of Human Genetics, Jena University Hospital, Jena, Germany
Tel. +49 3641 9396850; Fax: +49 3641 9396852
Interests: small supernumerary marker chromosomes, acute leukemia, nuclear architecture
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Special Issue Information

Dear Colleagues,

Chromosomes are a microscopically visible underlying element of genomes. In times of next generation sequencing they have appeared to be in the shadow of modern techniques of molecular genetics. However, only combining the advantages of molecular cytogenetics and any kind of new high throughput approaches can provide a comprehensive view on the studied questions of genome evolution and organization. Here we welcome studies characterizing chromosome and karyotype variation in animals, plants and humans (including constitutional and acquired variations in karyotypes and individual chromosomes).

Intraspecific chromosome and karyotype variation can be involved in generating the biodiversity required for adaptation to the changing environment and introduction into new ecological niches. It promotes reproductive isolation followed by speciation. Studies on comparative genomics have revealed huge intra- and interspecific genome variation including mutations, single nucleotide polymorphisms, and copy number variations. However, we cannot understand the basic principle of genome organization and evolution without intense and ambitious research devoted to the investigation of genomic variations involving large chromosome regions or even the whole chromosomes. The biological and molecular mechanisms underlying chromosome rearrangements, the formation of new chromosomal regions and whole new chromosomes need much more attention. There are already numerous examples of chromosome and karyotype variations as the basis of speciation based on genome rediploidization after a whole genome duplication or burst of mobile element amplification and distribution. In some species, chromosome and karyotype changing appears to be involved in ontogenetic processes showing critical chromosome and karyotype reorganization up to directed chromatin and chromosome elimination. The programmed DNA elimination during ontogenesis is one of intriguing mysteries of modern biology, which could also be partially resolved through new insights through chromosome and karyotype variation studies in animals and plants.

Humans are the most studied species in terms of the characterization of constitutional and acquired chromosomal and subchromosomal changes. Here it is possible to obtain new insights into the biology of karyotype variations based on single case studies as well as systematic ones, collecting patients with similar chromosomal aberrations or heteromorphisms. However, there is still a gap between the description of chromosomal changes and understanding the underlying mechanisms leading to them. Thus, we here also invite submissions about inherited or de novo constitutional eu- or heterochromatic copy number variations or rearrangements, which lead to clinical signs and symptoms where the research community may learn something about the possible reasons leading to these karyotypic variations. This includes chromosomal rearrangements associated with cell malignization including chromothripsis.

This Special Issue “Chromosome and Karyotypic Variation” is devoted to the problems of chromosome and karyotype diversity, and its role and significance in the evolution, ontogenesis, and development of different types of pathologies in humans.

Overall, we kindly invite papers on the following fields:

  • Intra- and interspecies chromosome and karyotype variation;
  • Karyotype variation in connection with speciation;
  • B chromosomes;
  • Programed chromatin and chromosome elimination;
  • Whole genome duplication and genome rediploidization;
  • Chromosome instability;
  • Burst of mobile element amplification and distribution;
  • Chromosomal rearrangements in cancer;
  • Chromosomal diversity in humans;
  • Small supernumerary marker chromosomes in humans;
  • Pathogenic and neutral chromosomal variants;
  • New techniques and methodologies to study chromosome and karyotype variation.

Dr. Nikolay Rubtsov

Dr. Thomas Liehr
Guest Editor

Manuscript Submission Information

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Published Papers (15 papers)

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Open AccessArticle
Evolution of the Proto Sex-Chromosome in Solea senegalensis
Int. J. Mol. Sci. 2019, 20(20), 5111; https://doi.org/10.3390/ijms20205111 - 15 Oct 2019
Abstract
Solea senegalensis is a flatfish belonging to the Soleidae family within the Pleuronectiformes order. It has a karyotype of 2n = 42 (FN = 60; 6M + 4 SM + 8 St + 24 T) and a XX/XY system. The first pair [...] Read more.
Solea senegalensis is a flatfish belonging to the Soleidae family within the Pleuronectiformes order. It has a karyotype of 2n = 42 (FN = 60; 6M + 4 SM + 8 St + 24 T) and a XX/XY system. The first pair of metacentric chromosomes has been proposed as a proto sex-chromosome originated by a Robertsonian fusion between acrocentric chromosomes. In order to elucidate a possible evolutionary origin of this chromosome 1, studies of genomic synteny were carried out with eight fish species. A total of 88 genes annotated within of 14 BACs located in the chromosome 1 of S. senegalensis were used to elaborate syntenic maps. Six BACs (BAC5K5, BAC52C17, BAC53B20, BAC84K7, BAC56H24, and BAC48P7) were distributed in, at least, 5 chromosomes in the species studied, and a group of four genes from BAC53B20 (grsf1, rufy3, slc4a4 and npffr2) and genes from BAC48K7 (dmrt2, dmrt3, dmrt1, c9orf117, kank1 and fbp1) formed a conserved cluster in all species. The analysis of repetitive sequences showed that the number of retroelements and simple repeat per BAC showed its highest value in the subcentromeric region where 53B20, 16E16 and 48K7 BACs were localized. This region contains all the dmrt genes, which are associated with sex determination in some species. In addition, the presence of a satellite “chromosome Y” (motif length: 860 bp) was detected in this region. These findings allowed to trace an evolutionary trend for the large metacentric chromosome of S. senegalensis, throughout different rearrangements, which could be at an initial phase of differentiation as sex chromosome. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Adaptive Radiation from a Chromosomal Perspective: Evidence of Chromosome Set Stability in Cichlid Fishes (Cichlidae: Teleostei) from the Barombi Mbo Lake, Cameroon
Int. J. Mol. Sci. 2019, 20(20), 4994; https://doi.org/10.3390/ijms20204994 - 09 Oct 2019
Abstract
Cichlid fishes are the subject of scientific interest because of their rapid adaptive radiation, resulting in extensive ecological and taxonomic diversity. In this study, we examined 11 morphologically distinct cichlid species endemic to Barombi Mbo, the largest crater lake in western Cameroon, namely [...] Read more.
Cichlid fishes are the subject of scientific interest because of their rapid adaptive radiation, resulting in extensive ecological and taxonomic diversity. In this study, we examined 11 morphologically distinct cichlid species endemic to Barombi Mbo, the largest crater lake in western Cameroon, namely Konia eisentrauti, Konia dikume, Myaka myaka, Pungu maclareni, Sarotherodon steinbachi, Sarotherodon lohbergeri, Sarotherodon linnellii, Sarotherodon caroli, Stomatepia mariae, Stomatepia pindu, and Stomatepia mongo. These species supposedly evolved via sympatric ecological speciation from a common ancestor, which colonized the lake no earlier than one million years ago. Here we present the first comparative cytogenetic analysis of cichlid species from Barombi Mbo Lake using both conventional (Giemsa staining, C-banding, and CMA3/DAPI staining) and molecular (fluorescence in situ hybridization with telomeric, 5S, and 28S rDNA probes) methods. We observed stability on both macro and micro-chromosomal levels. The diploid chromosome number was 2n = 44, and the karyotype was invariably composed of three pairs of meta/submetacentric and 19 pairs of subtelo/acrocentric chromosomes in all analysed species, with the same numbers of rDNA clusters and distribution of heterochromatin. The results suggest the evolutionary stability of chromosomal set; therefore, the large-scale chromosomal rearrangements seem to be unlikely associated with the sympatric speciation in Barombi Mbo. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Possible Phenotypic Consequences of Structural Differences in Idic(15) in a Small Cohort of Patients
Int. J. Mol. Sci. 2019, 20(19), 4935; https://doi.org/10.3390/ijms20194935 - 05 Oct 2019
Abstract
Among human supernumerary marker chromosomes, the occurrence of isodicentric form of 15 origin is relatively well known due to its high frequency, both in terms of gene content and associated clinical symptoms. The associated epilepsy and autism are typically more severe than in [...] Read more.
Among human supernumerary marker chromosomes, the occurrence of isodicentric form of 15 origin is relatively well known due to its high frequency, both in terms of gene content and associated clinical symptoms. The associated epilepsy and autism are typically more severe than in cases with interstitial 15q duplication, despite copy number gain of approximately the same genomic region. Other mechanisms besides segmental aneuploidy and epigenetic changes may also cause this difference. Among the factors influencing the expression of members of the GABAA gene cluster, the imprinting effect and copy number differences has been debated. Limited numbers of studies investigate factors influencing the interaction of GABAA cluster homologues. Five isodicentric (15) patients are reported with heterogeneous symptoms, and structural differences of their isodicentric chromosomes based on array comparative genomic hybridization results. Relations between the structure and the heterogeneous clinical picture are discussed, raising the possibility that the structure of the isodicentric (15), which has an asymmetric breakpoint and consequently a lower copy number segment, would be the basis of the imbalance of the GABAA homologues. Studies of trans interaction and regulation of GABAA cluster homologues are needed to resolve this issue, considering copy number differences within the isodicentric chromosome 15. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Chromosome Translocations as a Driver of Diversification in Mole Voles Ellobius (Rodentia, Mammalia)
Int. J. Mol. Sci. 2019, 20(18), 4466; https://doi.org/10.3390/ijms20184466 - 10 Sep 2019
Abstract
The involvement of chromosome changes in the initial steps of speciation is controversial. Here we examine diversification trends within the mole voles Ellobius, a group of subterranean rodents. The first description of their chromosome variability was published almost 40 years ago. Studying [...] Read more.
The involvement of chromosome changes in the initial steps of speciation is controversial. Here we examine diversification trends within the mole voles Ellobius, a group of subterranean rodents. The first description of their chromosome variability was published almost 40 years ago. Studying the G-band structure of chromosomes in numerous individuals revealed subsequent homologous, step-by-step, Robertsonian translocations, which changed diploid numbers from 54 to 30. Here we used a molecular cytogenetic strategy which demonstrates that chromosomal translocations are not always homologous; consequently, karyotypes with the same diploid number can carry different combinations of metacentrics. We further showed that at least three chromosomal forms with 2n = 34 and distinct metacentrics inhabit the Pamir-Alay mountains. Each of these forms independently hybridized with E. tancrei, 2n = 54, forming separate hybrid zones. The chromosomal variations correlate slightly with geographic barriers. Additionally, we confirmed that the emergence of partial or monobrachial homology appeared to be a strong barrier for hybridization in nature, in contradistinction to experiments which we reported earlier. We discuss the possibility of whole arm reciprocal translocations for mole voles. Our findings suggest that chromosomal translocations lead to diversification and speciation. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Deciphering the Evolutionary History of Arowana Fishes (Teleostei, Osteoglossiformes, Osteoglossidae): Insight from Comparative Cytogenomics
Int. J. Mol. Sci. 2019, 20(17), 4296; https://doi.org/10.3390/ijms20174296 - 02 Sep 2019
Abstract
Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of [...] Read more.
Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA3/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2n = 56 and 54 in O. bicirrhosum and O. ferreirai, respectively, and 2n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Karyotypes and Sex Chromosomes in Two Australian Native Freshwater Fishes, Golden Perch (Macquaria ambigua) and Murray Cod (Maccullochella peelii) (Percichthyidae)
Int. J. Mol. Sci. 2019, 20(17), 4244; https://doi.org/10.3390/ijms20174244 - 30 Aug 2019
Abstract
Karyotypic data from Australian native freshwater fishes are scarce, having been described from relatively few species. Golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii) are two large-bodied freshwater fish species native to Australia with significant indigenous, cultural, recreational [...] Read more.
Karyotypic data from Australian native freshwater fishes are scarce, having been described from relatively few species. Golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii) are two large-bodied freshwater fish species native to Australia with significant indigenous, cultural, recreational and commercial value. The arid landscape over much of these fishes’ range, coupled with the boom and bust hydrology of their habitat, means that these species have potential to provide useful evolutionary insights, such as karyotypes and sex chromosome evolution in vertebrates. Here we applied standard and molecular cytogenetic techniques to characterise karyotypes for golden perch and Murray cod. Both species have a diploid chromosome number 2n = 48 and a male heterogametic sex chromosome system (XX/XY). While the karyotype of golden perch is composed exclusively of acrocentric chromosomes, the karyotype of Murray cod consists of two submetacentric and 46 subtelocentric/acrocentric chromosomes. We have identified variable accumulation of repetitive sequences (AAT)10 and (CGG)10 along with diverse methylation patterns, especially on the sex chromosomes in both species. Our study provides a baseline for future cytogenetic analyses of other Australian freshwater fishes, especially species from the family Percichthyidae, to better understand their genome and sex chromosome evolution. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Extensive Chromosomal Reorganization in Apistogramma Fishes (Cichlidae, Cichlinae) Fits the Complex Evolutionary Diversification of the Genus
Int. J. Mol. Sci. 2019, 20(17), 4077; https://doi.org/10.3390/ijms20174077 - 21 Aug 2019
Abstract
Neotropical cichlid fishes are one of the most diversified and evolutionarily successful species assemblages. Extremely similar forms and intraspecific polychromatism present challenges for the taxonomy of some of these groups. Several species complexes have a largely unknown origin and unresolved evolutionary processes. Dwarf [...] Read more.
Neotropical cichlid fishes are one of the most diversified and evolutionarily successful species assemblages. Extremely similar forms and intraspecific polychromatism present challenges for the taxonomy of some of these groups. Several species complexes have a largely unknown origin and unresolved evolutionary processes. Dwarf cichlids of the genus Apistogramma, comprising more than a hundred species, exhibit intricate taxonomic and biogeographic patterns, with both allopatric and sympatric distributions. However, karyotype evolution and the role of chromosomal changes in Apistogramma are still unknown. In the present study, nine South American Apistogramma species were analyzed using conventional cytogenetic methods and the mapping of repetitive DNA sequences [18S rDNA, 5S rDNA, and (TTAGGG)n] by fluorescence in situ hybridization (FISH). Our results showed that Apistogramma has unique cytogenetic characteristics in relation to closely related groups, such as a reduced 2n and a large number of bi-armed chromosomes. Interspecific patterns revealed a scenario of remarkable karyotypic changes, including a reduction of 2n, the occurrence of B-chromosomes and evolutionary dynamic of rDNA tandem repeats. In addition to the well-known pre-zygotic reproductive isolation, the karyotype reorganization in the genus suggests that chromosomal changes could act as postzygotic barriers in areas where Apistogramma congeners overlap. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Deciphering the Origin and Evolution of the X1X2Y System in Two Closely-Related Oplegnathus Species (Oplegnathidae and Centrarchiformes)
Int. J. Mol. Sci. 2019, 20(14), 3571; https://doi.org/10.3390/ijms20143571 - 22 Jul 2019
Cited by 1
Abstract
Oplegnathus fasciatus and O. punctatus (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an X1X2Y sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of [...] Read more.
Oplegnathus fasciatus and O. punctatus (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an X1X2Y sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of these sex chromosomes, with the aim to elucidate whether they had a single or convergent origin. To achieve this, conventional and molecular cytogenetic protocols, involving the mapping of repetitive DNA markers, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) were applied. Both species presented similar 2n, karyotype structure and hybridization patterns of repetitive DNA classes. 5S rDNA loci, besides being placed on the autosomal pair 22, resided in the terminal region of the long arms of both X1 chromosomes in females, and on the X1 and Y chromosomes in males. Furthermore, WCP experiments with a probe derived from the Y chromosome of O. fasciatus (OFAS-Y) entirely painted the X1 and X2 chromosomes in females and the X1, X2, and Y chromosomes in males of both species. CGH failed to reveal any sign of sequence differentiation on the Y chromosome in both species, thereby suggesting the shared early stage of neo-Y chromosome differentiation. Altogether, the present findings confirmed the origin of the X1X2Y sex chromosomes via Y-autosome centric fusion and strongly suggested their common origin. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Genomic Organization of Repetitive DNA Elements and Extensive Karyotype Diversity of Silurid Catfishes (Teleostei: Siluriformes): A Comparative Cytogenetic Approach
Int. J. Mol. Sci. 2019, 20(14), 3545; https://doi.org/10.3390/ijms20143545 - 19 Jul 2019
Abstract
The catfish family Siluridae contains 107 described species distributed in Asia, but with some distributed in Europe. In this study, karyotypes and other chromosomal characteristics of 15 species from eight genera were examined using conventional and molecular cytogenetic protocols. Our results showed the [...] Read more.
The catfish family Siluridae contains 107 described species distributed in Asia, but with some distributed in Europe. In this study, karyotypes and other chromosomal characteristics of 15 species from eight genera were examined using conventional and molecular cytogenetic protocols. Our results showed the diploid number (2n) to be highly divergent among species, ranging from 2n = 40 to 92, with the modal frequency comprising 56 to 64 chromosomes. Accordingly, the ratio of uni- and bi-armed chromosomes is also highly variable, thus suggesting extensive chromosomal rearrangements. Only one chromosome pair bearing major rDNA sites occurs in most species, except for Wallago micropogon, Ompok siluroides, and Kryptoterus giminus with two; and Silurichthys phaiosoma with five such pairs. In contrast, chromosomes bearing 5S rDNA sites range from one to as high as nine pairs among the species. Comparative genomic hybridization (CGH) experiments evidenced large genomic divergence, even between congeneric species. As a whole, we conclude that karyotype features and chromosomal diversity of the silurid catfishes are unusually extensive, but parallel some other catfish lineages and primary freshwater fish groups, thus making silurids an important model for investigating the evolutionary dynamics of fish chromosomes. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Chromosomal Evolution and Evolutionary Relationships of Lebiasina Species (Characiformes, Lebiasinidae)
Int. J. Mol. Sci. 2019, 20(12), 2944; https://doi.org/10.3390/ijms20122944 - 16 Jun 2019
Abstract
We present the first cytogenetic data for Lebiasina bimaculata and L. melanoguttata with the aim of (1) investigating evolutionary events within Lebiasina and their relationships with other Lebiasinidae genera and (2) checking the evolutionary relationships between Lebiasinidae and Ctenoluciidae. Both species have a [...] Read more.
We present the first cytogenetic data for Lebiasina bimaculata and L. melanoguttata with the aim of (1) investigating evolutionary events within Lebiasina and their relationships with other Lebiasinidae genera and (2) checking the evolutionary relationships between Lebiasinidae and Ctenoluciidae. Both species have a diploid number 2n = 36 with similar karyotypes and microsatellite distribution patterns but present contrasting C-positive heterochromatin and CMA3+ banding patterns. The remarkable interstitial series of C-positive heterochromatin occurring in L. melanoguttata is absent in L. bimaculata. Accordingly, L. bimaculata shows the ribosomal DNA sites as the only GC-rich (CMA3+) regions, while L. melanoguttata shows evidence of a clear intercalated CMA3+ banding pattern. In addition, the multiple 5S and 18S rDNA sites in L. melanogutatta contrast with single sites present in L. bimaculata. Comparative genomic hybridization (CGH) experiments also revealed a high level of genomic differentiation between both species. A polymorphic state of a conspicuous C-positive, CMA3+, and (CGG)n band was found only to occur in L. bimaculata females, and its possible relationship with a nascent sex chromosome system is discussed. Whole chromosome painting (WCP) and CGH experiments indicate that the Lebiasina species examined and Boulengerella maculata share similar chromosomal sequences, thus supporting the relatedness between them and the evolutionary relationships between the Lebiasinidae and Ctenoluciidae families. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessArticle
Detection and Correlation of Single and Concomitant TP53, PTEN, and CDKN2A Alterations in Gliomas
Int. J. Mol. Sci. 2019, 20(11), 2658; https://doi.org/10.3390/ijms20112658 - 30 May 2019
Abstract
Gliomas are the most frequent primary tumors of central nervous system and represent a heterogeneous group of tumors that originates from the glial cells. TP53, PTEN, and CDKN2A are important tumor suppressor genes that encode proteins involved in sustaining cellular homeostasis [...] Read more.
Gliomas are the most frequent primary tumors of central nervous system and represent a heterogeneous group of tumors that originates from the glial cells. TP53, PTEN, and CDKN2A are important tumor suppressor genes that encode proteins involved in sustaining cellular homeostasis by different signaling pathways. Though genetic alterations in these genes play a significant role in tumorigenesis, few studies are available regarding the incidence and relation of concomitant TP53, PTEN, and CDKN2A alterations in gliomas. The purpose of this study was to evaluate the occurrence of mutation and deletion in these genes, through single-strand conformational polymorphism, array-comparative genomic hybridization, and fluorescence in situ hybridization techniques, in 69 gliomas samples. Molecular results demonstrated a significant higher prevalence of TP53, PTEN, and CDKN2A alterations in astrocytoma than other tumor subtypes, and heterozygous deletion was the most frequent event. In addition, a significant association was observed between TP53 and CDKN2A alterations (p = 0.0424), which tend to coexist in low grade astrocytomas (5/46 cases (10.9%)), suggesting that they are early events in development of these tumors, and PTEN and CDKN2A deletions (p = 0.0022), which occurred concomitantly in 9/50 (18%) patients, with CDKN2A changes preceding PTEN deletions, present preferably in high-grade gliomas. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Review

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Open AccessReview
DNA Copy Number Variations as Markers of Mutagenic Impact
Int. J. Mol. Sci. 2019, 20(19), 4723; https://doi.org/10.3390/ijms20194723 - 24 Sep 2019
Abstract
DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution [...] Read more.
DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution of environmental factors, such as mutagens, in the origin of CNVs, is poorly understood. In this review, we summarize current knowledge about mutagen-induced CNVs in human, animal and plant cells. Differences in CNV frequencies induced by radiation and chemical mutagens, distribution of CNVs in the genome, as well as adaptive effects in plants, are discussed. Currently available information concerning impact of mutagens in induction of CNVs in germ cells is presented. Moreover, the potential of CNVs as a new endpoint in mutagenicity test-systems is discussed. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
Open AccessReview
Cytogenetics and Cytogenomics Evaluation in Cancer
Int. J. Mol. Sci. 2019, 20(19), 4711; https://doi.org/10.3390/ijms20194711 - 23 Sep 2019
Abstract
The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer [...] Read more.
The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer candidate biomarkers associated with diagnosis, prognosis, and therapeutics. The advent of array comparative genomic hybridization and next-generation sequencing technologies has significantly improved the knowledge about cancer biology, underlining driver genes to guide targeted therapy development, drug-resistance prediction, and pharmacogenetics. However, few of these candidate biomarkers have made the transition to the clinic with a clear benefit for the patients. Technological progress helped to demonstrate that cellular heterogeneity plays a significant role in tumor progression and resistance/sensitivity to cancer therapies, representing the major challenge of precision cancer therapy. A paradigm shift has been introduced in cancer genomics with the recent advent of single-cell sequencing, since it presents a lot of applications with a clear benefit to oncological patients, namely, detection of intra-tumoral heterogeneity, mapping clonal evolution, monitoring the development of therapy resistance, and detection of rare tumor cell populations. It seems now evident that no single biomarker could provide the whole information necessary to early detect and predict the behavior and prognosis of tumors. The promise of precision medicine is based on the molecular profiling of tumors being vital the continuous progress of high-throughput technologies and the multidisciplinary efforts to catalogue chromosomal rearrangements and genomic alterations of human cancers and to do a good interpretation of the relation genotype—phenotype. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessReview
The Pleiotropic Role of Retinoic Acid/Retinoic Acid Receptors Signaling: From Vitamin A Metabolism to Gene Rearrangements in Acute Promyelocytic Leukemia
Int. J. Mol. Sci. 2019, 20(12), 2921; https://doi.org/10.3390/ijms20122921 - 14 Jun 2019
Cited by 1
Abstract
The family of retinoic acid receptors (RARs: RARα, -β, and -γ) has remarkable pleiotropy characteristics, since the retinoic acid/RARs pathway is involved in numerous biological processes not only during embryonic development, but also in the postnatal phase and during adulthood. In this review, [...] Read more.
The family of retinoic acid receptors (RARs: RARα, -β, and -γ) has remarkable pleiotropy characteristics, since the retinoic acid/RARs pathway is involved in numerous biological processes not only during embryonic development, but also in the postnatal phase and during adulthood. In this review, we trace the roles of RA/RARs signaling in the immune system (where this pathway has both an immunosuppressive role or is involved in the inflammatory response), in hematopoiesis (enhancing hematopoietic stem cell self-renewal, progenitor cells differentiation or maintaining the bone marrow microenvironment homeostasis), and in bone remodeling (where this pathway seems to have controversial effects on bone formation or osteoclast activation). Moreover, in this review is shown the involvement of RAR genes in multiple chromosomal rearrangements generating different fusion genes in hematological neoplasms, with a particular focus on acute promyelocytic leukemia and its variant subtypes. The effect of different RARs fusion proteins on leukemic transformation, on patients’ outcome, and on therapy response is also discussed. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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Open AccessReview
From Human Cytogenetics to Human Chromosomics
Int. J. Mol. Sci. 2019, 20(4), 826; https://doi.org/10.3390/ijms20040826 - 14 Feb 2019
Abstract
Background: The concept of “chromosomics” was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a “chromosomic view” of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is [...] Read more.
Background: The concept of “chromosomics” was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a “chromosomic view” of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is dedicated to the memory of Prof. Uwe Claussen (30 April 1945–20 July 2008). Recent findings: Chromosomics is the study of chromosomes, their three-dimensional positioning in the interphase nucleus, the consequences from plasticity of chromosomal subregions and gene interactions, the influence of chromatin-modification-mediated events on cells, and even individuals, evolution, and disease. Progress achieved in recent years is summarized, including the detection of chromosome-chromosome-interactions which, if damaged, lead to malfunction and disease. However, chromosomics in the Human Genetics field is not progressing presently, as research interest has shifted from single cell to high throughput, genomic approaches. Conclusion: Chromosomics and its impact were predicted correctly in 2005 by Prof. Claussen. Although some progress was achieved, present reconsiderations of the role of the chromosome and the single cell in Human Genetic research are urgently necessary. Full article
(This article belongs to the Special Issue Chromosome and Karyotype Variation)
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