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Ideograms for human chromosomes (HSA) 1 ( a ), 3 ( b ), 5 ( c ), 7 ( d ), 18 ( e ), and X ( f ) and their homologues in Papionini species (represented by M. fascicularis , MFA, due to both Papionini species share identical morphology for these chromosomes) displaying the positions of all BAC/YAC clones analysed on the right of each chromosome. Arrowheads indicate chromosome bands expressing fragile sites.
Source publication
Fragile sites are considered structural features of mammalian chromosomes and a commonly repeated hypothesis is that they are evolutionarily conserved. We tested this hypothesis by establishing the subchromosomal homology of regions harbouring fragile sites in the chromosomes of humans, Macaca fascicularis (MFA) and Mandrillus sphinx (MSP). We deli...
Contexts in source publication
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... results of the hybridizations obtained in human, M. fascicularis and M. sphinx chromo- somes reveal that all 14 human clones hybridized on the homologue Papionini chromosome band, except for BAC clone 42C19, which failed to hybridize on M. sphinx chromosomes (Table 1, Figure 1). Three of the 14 probes used spanned the induced fragile site chromosome gaps in both M. fascicularis and M. sphinx chromosomes ...
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... results con¢rm that 12 out of 14 bands con- taining fragile sites in human and macaque are indeed homologous and show the band-to-band coincidence of the fragile sites between M. fascicularis and human. Thus the data indicate the evolutionary conservation of human fragile sites FRA1B, FRA1D, FRA1H, FRA5A, FRA5C, FRA5E, FRA7D, FRA7F, FRA7H, and FRA18A in macaque (Table 1, Figure 1). Strikingly, FISH results from genomic clones (YAC) of human fragile sites FRA3B and FRAX show that these clones indeed span the homo- logous chromosome bands 3q22 and Xp22, in Papionini karyotypes (Table 1). ...
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... fascicularis and M. sphinx chromosomes 2 are homologous to human chromosome 7, and differ by multiple pericentric inversions and a fusion with the homologue to human 21 (Ruiz-Herrera et al. 2002a). The hybridization results with the BAC clone 42C19 (Figure 1), however, did allow us to precisely define the inversion points (7p22-7p21 and 7q11). The chromosome homology between human and macaque chromosome 18 has pre- viously been interpreted as a pericentric inversion (Mü ller & Wienberg 2001, Ruiz-Herrera et al. 2002b) or as a centromere shift or dislocation (Mü ller & Wienberg 2001). ...
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... band-by-band corres- pondence between human chromosome 3 and its Papionini homologues is almost impossible to determine by banding comparisons because of the highly complex evolution of this chromosome (Mˇller et al. 2000). Nevertheless the hybridiza- tion with YAC clone 850a6 is able to show that human fragile site FRA3B is, in fact, conserved as a fragile site in M. fascicularis and M. sphinx in the same chromosome band, 3q22 (Table1 , Figures 1 & 2c). Similar results were obtained for the hybridi- zation of the 29c11 clone on M. fascicularis and M. sphinx chromosomes. ...
Citations
... In addition to the above structural chromosomal damages, there are other mechanisms for this damage. So, the study of chromosomes at the cellular and molecular level showed that human chromosomes carry fragile and easy to break sites called (fragile sites), (23,24), and we also noticed such a case in the samples included in our research as in Figure (4). There are another chromosomal damages that may result from a break in the two arms of the chromosome, followed by the fusion of its ends and the loss of the final parts of it, that is, the loss of the final genetic material of the chromosome, which was maintaining the stability of the chromosome, and this condition occurs by a complex mechanism that leads to the formation of a ring chromosome (25,26) such as shown in figure (5). ...
Abstract
Background and Objectives: Analyze the chromosomes of patients with chronic lymphocytic leukemia (CLL) in Kut to identify
chromosomal abnormalities and study the chromosomal changes in patients.
Patients and Methods: Clinical notes and cytogenetic analysis were studied for all patients. Cases were collected from oncology
unit at Al Karama Hospital in Al Kut.
Results: Chromosomal analysis of all patients showed chromosomal aberrations, It was found that most of the chromosomal
changes are structural changes. The abnormalities of the patients' chromosomes were divided according to their karyotype into
3 groups: chromosomal bridge (36.8 ) , complex chromosomes (31.6 ) and normal (31.6 ) .
Conclusion: Chromosomal abnormalities, especially structural abnormalities are responsible for the occurrence and
development of chronic lymphocytic leukemia and the high complexity of karyotyping of patients
... 3 Interestingly, CFSs are not exclusive to human cells. Instead, they are well documented in a wide range of other species including nonhuman primates, 4 carnivores, 5 mice, 6,7 and avians, 8 suggesting a conserved role for CFSs. CFS expression can be induced by different replication-perturbing agents or conditions, e.g., lowdose aphidicolin (APH) that reversibly inhibits replicative DNA polymerase. ...
Common fragile sites (CFSs) are genomic loci prone to the formation of breaks or gaps on metaphase chromosomes. They are hotspots for chromosome rearrangements and structural variations, which have been extensively implicated in carcinogenesis, aging, and other pathological processes. Although many CFSs were identified decades ago, a consensus is still lacking for why they are particularly unstable and sensitive to replication perturbations. This is in part due to the lack of high-resolution mapping data for the vast majority of the CFSs, which has hindered mechanistic interrogations. Here, we seek to map human CFSs with high resolution on a genome-wide scale by sequencing the sites of mitotic DNA synthesis (MiDASeq) that are specific for CFSs. We generated a nucleotide-resolution atlas of MiDAS sites (MDSs) that covered most of the known CFSs, and comprehensively analyzed their sequence characteristics and genomic features. Our data on MDSs tallied well with long-standing hypotheses to explain CFS fragility while highlighting the contributions of late replication timing and large transcription units. Notably, the MDSs also encompassed most of the recurrent double-strand break clusters previously identified in mouse neural stem/progenitor cells, thus bridging evolutionarily conserved break points across species. Moreover, MiDAseq provides an important resource that can stimulate future research on CFSs to further unravel the mechanisms and biological relevance underlying these labile genomic regions.
... As occurred with other species, such as human [6,7], monkey [8] and fish [9], the 45S rDNA FS in Lolium were recognized as unstable regions and hotspots for breaks that could be associated to karyotype instability [1][2][3]. Nevertheless, Rocha [10,11] confirmed that FS are resulting from DNA decondensation at 45S rDNA sites in L. perenne, L. multiflorum, Festuca arundinacea Schreb. ...
The grasses of the Lolium–Festuca complex show a prominent role in world agricultural scenario. Several studies have demonstrated that the plasticity of 45S rDNA sites has been recently associated with the possible fragility of the loci. Often, these fragile sites were observed as extended sites and gaps in metaphases. This organization can be evaluated in relation to their transcriptional activity/accessibility through epigenetic changes. Thus, this study aimed to investigate the relationship of the 5-methylcytosine and histone H3 lysine-9 dimethylation in different conformations of 45S rDNA sites in interphase nuclei and in metaphase chromosomes of L. perenne, L. multiflorum and F. arundinacea. The FISH technique using 45S rDNA probes was performed sequentially after the immunolocalization. The sites showed predominantly the following characteristics in the interphase nuclei: intra- and perinucleolar position, decondensed or partially condensed and hypomethylated and hyper/hypomethylated status. Extranucleolar sites were mainly hypermethylated for both epigenetic marks. The 45S rDNA sites with gaps identified in metaphases were always hypomethylated, which justifies it decondensed and transcriptional state. The frequency of sites with hypermethylated gaps was very low. The structural differences observed in these sites are directly related to the assessed epigenetic marks, justifying the different conformations throughout the cell cycle.
... Traditionally, CFSs have been defined and mapped cytogenetically (11,27) and are mainly characterized in humans, other primates and mice (9,22,(28)(29)(30). Here, we performed ChIP-seq of FANCD2 from cells subjected to replication stress to map fragile sites genome-wide in the avian cell line DT40. ...
Common Chromosomal Fragile Sites (CFSs) are specific genomic regions prone to form breaks on metaphase chromosomes in response to replication stress. Moreover, CFSs are mutational hotspots in cancer genomes, showing that the mutational mechanisms that operate at CFSs are highly active in cancer cells. Orthologs of human CFSs are found in a number of other mammals, but the extent of CFS conservation beyond the mammalian lineage is unclear. Characterization of CFSs from distantly related organisms can provide new insight into the biology underlying CFSs. Here, we have mapped CFSs in an avian cell line. We find that, overall the most significant CFSs coincide with extremely large conserved genes, from which very long transcripts are produced. However, no significant correlation between any sequence characteristics and CFSs is found. Moreover, we identified putative early replicating fragile sites (ERFSs), which is a distinct class of fragile sites and we developed a fluctuation analysis revealing high mutation rates at the CFS gene PARK2, with deletions as the most prevalent mutation. Finally, we show that avian homologs of the human CFS genes despite their fragility have resisted the general intron size reduction observed in birds suggesting that CFSs have a conserved biological function.
... Fluorescence in situ hybridization (FISH) with specific BAC clones was performed on metaphase chromosomes as previously described [64] with modifications. Briefly, 1 μg of the BAC DNA was labelled with digoxigenin-11-dUTP or biotin-11-dUTP by Nick Translation technique (Abbot kit) and ethanol precipitated with competitor DNA (melon genomic DNA), salmon sperm DNA (Invitrogen, 10 mg/ml) and 1/10 volume of 3 M sodium acetate overnight at −20°C. ...
Background
The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insufficient marker coverage and a lack of recombination left several large, gene rich scaffolds unanchored, and some anchored scaffolds unoriented. To improve the anchoring and orientation of the melon genome assembly, we used resequencing data between the parental lines of DHL92 to develop a new set of SNP markers from unanchored scaffolds.ResultsA high-resolution genetic map composed of 580 SNPs was used to anchor 354.8 Mb of sequence, contained in 141 scaffolds (average size 2.5 Mb) and corresponding to 98.2% of the scaffold assembly, to the 12 melon chromosomes. Over 325.4 Mb (90%) of the assembly was oriented. The genetic map revealed regions of segregation distortion favoring SC alleles as well as recombination suppression regions coinciding with putative centromere, 45S, and 5S rDNA sites. New chromosome-scale pseudomolecules were created by incorporating to the previous v3.5 version an additional 38.3 Mb of anchored sequence representing 1,837 predicted genes contained in 55 scaffolds. Using fluorescent in situ hybridization (FISH) with BACs that produced chromosome-specific signals, melon chromosomes that correspond to the twelve linkage groups were identified, and a standardized karyotype of melon inbred line T111 was developed.Conclusions
By utilizing resequencing data and targeted SNP selection combined with a large F2 mapping population, we significantly improved the quantity of anchored and oriented melon scaffold genome assembly. Using genome information combined with FISH mapping provided the first cytogenetic map of an inodorus melon type. With these results it was possible to make inferences on melon chromosome structure by relating zones of recombination suppression to centromeres and 45S and 5S heterochromatic regions. This study represents the first steps towards the integration of the high-resolution genetic and cytogenetic maps with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft sequence.
... It has been described that CFRs are conserved in primates and other mammalian species (Arlt et al. 2003). Orthologous sequences have been found in rodents, pig, cow, horse, cat, dog or distinct primate species for some CFRs in human sequences (Elder and Robinson 1989;Fundia et al. 2000;Glover et al. 1998;Helmrich et al. 2006;Krummel et al. 2002;Rodriguez et al. 2002;Ronne 1992Ronne , 1995aRuiz-Herrera et al. 2004, 2002Shiraishi et al. 2001;Yang and Long 1993). The conservation of fragile sites across a wide range of species might imply that these regions play a functional role (Schwartz et al. 2006). ...
Chromosomal evolution involves multiple changes at structural and numerical levels. These changes, which are related to the variation of the gene number and their location, can be tracked by the identification of syntenic blocks (SB). First reports proposed that ~180-280 SB might be shared by mouse and human species. More recently, further studies including additional genomes have identified up to ~1,400 SB during the evolution of eutherian species. A considerable number of studies regarding the X chromosome's structure and evolution have been undertaken because of its extraordinary biological impact on reproductive fitness and speciation. Some have identified evolutionary breakpoint regions and fragile sites at specific locations in the human X chromosome. However, mapping these regions to date has involved using low-to-moderate resolution techniques. Such scenario might be related to underestimating their total number and giving an inaccurate location. The present study included using a combination of bioinformatics methods for identifying, at base-pair level, chromosomal rearrangements occurring during X chromosome evolution in 13 mammalian species. A comparative technique using four different algorithms was used for optimizing the detection of hotspot regions in the human X chromosome. We identified a significant interspecific variation in SB size which was related to genetic information gain regarding the human X chromosome. We found that human hotspot regions were enriched by LINE-1 and Alu transposable elements, which may have led to intraspecific chromosome rearrangement events. New fragile regions located in the human X chromosome have also been postulated. We estimate that the high resolution map of X chromosome fragile sites presented here constitutes useful data concerning future studies on mammalian evolution and human disease.
... Species from the Tribe Papioniniincluding Macaca, Papio, Mandrillus and Cercocebusare characterized by sharing the same karyotype and large-scale chromosomal reorganizations since their divergence from a common primate ancestor [34,35]. When comparing these species with the human karyotype, previous cytogenetic studies described the presence of 20 intra-and inter-chromosomal reorganizations [34,35,37,40]. These rearrangements include 12 pericentric inversions affecting eleven chromosomes, four paracentric inversions involving four chromosomes and four fusions/fissions [34,35,37,40]. ...
... When comparing these species with the human karyotype, previous cytogenetic studies described the presence of 20 intra-and inter-chromosomal reorganizations [34,35,37,40]. These rearrangements include 12 pericentric inversions affecting eleven chromosomes, four paracentric inversions involving four chromosomes and four fusions/fissions [34,35,37,40]. Overall, our in silico approach confirmed the presence of the above-mentioned macro-reorganizations and, thus, refined the breakpoints involved in both genomes (Additional file 1: Table S1). ...
... DNA from BACs was extracted according to standard protocols using a commercial kit (QIAGEN Plasmid). Fluorescence in situ hybridization (FISH) with specific BAC clones was performed on both metaphase chromosomes and spermatocyte spreads as previously described [40,64]. Briefly, 1 μg of the DNA plasmid was labeled with dUTP-digoxygenine by Nick Translation (Abbot kit) and ethanol precipitated with competitor DNA (Cot-1 human DNA, Invitrogen, 1 mg/ml), salmon sperm DNA (Invitrogen, 10 mg/ml) and 1/10 volume of 3 mol/L sodium acetate overnight at -20°C. ...
BACKGROUND:By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution.
RESULTS:We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages.
CONCLUSIONS:Our data suggest that adaptive alleles - in this case, genes involved in the immune response - might have been favored by genome rearrangements in the macaque lineage.
... MFA was studied before by banding cytogenetics (FERNANDEZ-DONOSO et al., 1970, KANAGAWA et al., 1971; to the best of our knowledge FISH was only applied for single loci (KASAI et al., 2000;KOSTOVA et al., 2002;RUIZ-HERRERA et al., 2004;LIU et al., 2007) and not for the whole genome yet, also a new alphoid DNA sequence was isolated from MFA and used in FISH (CROVELLA et al., 1999). Here we provide the first genome wide MCB-based FISH-banding study in MFA. ...
Comparative chromosome banding analysis and/or fluorescence in situ
hybridization (FISH) studies are established approaches to compare human and
ape chromosomes. FISH-banding is a relatively new and not routinely applied
method suited very well to provide to a better understanding of the
evolutionary history of primate and human phylogeny. Here multicolor banding
(MCB) applying probes derived from Homo sapiens was used to analyze the
chromosomes of Thai crab-eating macaque (Macaca fascicularis). The results
agree with those of previous studies in other macaques, e.g. Macaca sylvanus
or Macaca nemestrina. This result pinpoints, that morphological differences
within the Ceropithecoidae must be founded rather in subchromosomal changes
or even in epigenetics than in gross structural alterations.
... MFA was previously studied by banding cytogenetics (Fernandez-Donoso et al., 1970, Kanagawa et al., 1971Brown et al., 1986); to the best of our knowledge, FISH was only applied for single loci (Archidiacono et al., 1998;Kasai et al., 2000;Kostova et al., 2002;Ruiz-Herrera et al., 2004;Liu et al., 2007) and not for the whole genome. In addition, a new alphoid DNA sequence was isolated from MFA and used in FISH (Crovella et al., 1999). ...
Comparative chromosome banding analysis and/or fluorescence in situ
hybridization (FISH) studies are established approaches to compare human and
ape chromosomes. FISH banding is a relatively new and not routinely applied
method very well suited to provide to a better understanding of the
evolutionary history of primate and human phylogeny. Here multicolor banding
(MCB)-applying probes derived from Homo sapiens were used to analyze the
chromosomes of Thai crab-eating macaque (Macaca fascicularis). The results
agree with those of previous studies in other macaques, e.g. Macaca sylvanus
or Macaca nemestrina. This result highlights that morphological differences
within the Cercopithecoidea must be found rather in subchromosomal changes or
even in epigenetics than in gross structural alterations.
... By contrast, common fragile sites (CFSs) form breaks or gaps (often termed CFS 'expression') in most individuals, and over 200 of these seemingly problematic loci have been identified in the human genome [1,3]. CFSs, including the well-studied FRA16D and FRA3B loci, can span several hundred kb and are evolutionarily conserved regions of the genome [4]. Their instability is evident in several chromosome instability (CIN) disorders, neurodevelopmental diseases, and many cancers [5]. ...
Fragile sites are conserved loci predisposed to form breaks in metaphase chromosomes. The inherent instability of these loci is associated with chromosomal rearrangements in cancers and is a feature of cells from patients with chromosomal instability syndromes. One class of fragile sites, the common fragile sites (CFSs), have previously been shown to recruit several DNA repair proteins after the completion of bulk DNA synthesis in the cell, probably indicative of their inability to complete timely DNA replication. CFS loci are also prone to trigger mitotic non-disjunction of sister chromatids, leading to the formation of ultra-fine anaphase bridges (UFBs) and micronuclei. We discuss recent developments in the CFS field; in particular, the role of DNA structure-specific endonucleases in promoting cleavage at CFSs.
