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PubMed2001

Identification of numerical and structural chromosome aberrations in 15 high hyperdiploid childhood acute lymphoblastic leukemias using spectral karyotyping.

Spectral karyotyping (SKY) on metaphase spreads from 15 high hyperdiploid (>51 chromosomes) childhood acute lymphoblastic leukemias (ALL), which typically display a poor chromosome morphology, was performed in order to investigate the pattern of numerical abnormalities, reveal the chromosomal origin of marker chromosomes, and identify translocations and other interchromosomal rearrangements not detected by G-banding analysis. In all cases the numerical changes could be fully characterized, and a non-random pattern of chromosomal gain was identified, with chromosomes X, 21, 14, 17, 6, 18, 4, and 10 being most frequently gained. The numerical changes had been partly misinterpreted in 12 of the 15 ALL patients using G-banding, and the present study hence emphasizes the importance of SKY in identifying such anomalies, some of which, i.e. +4 and +10, have been suggested to be prognostically important. The chromosomal origin of all marker chromosomes and of seven structural rearrangements, one of which was the prognostically important Philadelphia chromosome, could be identified. Five rearrangements [der(1)t(1;14)(q32;q21), der(2)t(2;8)(q36;?), der(3)t(2;3)(q21;?), der(8)t(8;14)(?;?), and t(9;21)(q12;q22)] have previously not been reported in ALL, emphasizing the value of SKY in identifying novel chromosomal rearrangements.

Child↗
PubMed2006

Mitochondrial chromosome structure: an insight from analysis of complete yeast genomes.

Recent progress in the analysis of protein components of the mitochondrial nucleoid and replisome of baker's yeast, Saccharomyces cerevisiae, opens a unique opportunity for understanding the molecular principles of mitochondrial inheritance. In this work we identified homologs of proteins involved in the mitochondrial DNA packaging and replication in the complete genome sequence of the petite-negative yeast Kluyveromyces lactis. Comparative analysis of their counterparts from phylogenetically diverse yeast species revealed conserved as well as diverged features of the organellar chromosome structure and its replication strategy. Moreover, it provides a basis for subsequent functional studies of the structure and dynamics of the mitochondrial nucleoids.

Amino Acid Sequence↗
PubMed2004

Applications of genomic microarrays to explore human chromosome structure and function.

The combination of genomic microarrays with comparative genomic hybridization and with chromatin immunoprecipitation is providing an increasingly detailed view of the way in which the human genome is organized and functions and how disorganization and disfunction can lead to disease. These studies are enhanced by the flexibility of array technology, allowing resolutions from coverage of the whole genome using 200 kb cloned DNA inserts to detailed analysis using PCR products or oligonucleotides of 100 bp or less. In particular, the use of chromatin immunoprecipitation is providing new insights into chromosome structure and gene regulation and control through the analysis of protein--DNA interactions.

Chromatin Immunoprecipitation↗
PubMed2001

Drosophila rhino encodes a female-specific chromo-domain protein that affects chromosome structure and egg polarity.

Here we describe our analyses of Rhino, a novel member of the Heterochromatin Protein 1(HP1) subfamily of chromo box proteins. rhino (rhi) is expressed only in females and chiefly in the germline, thus providing a new tool to dissect the role of chromo-domain proteins in development. Mutations in rhi disrupt eggshell and embryonic patterning and arrest nurse cell nuclei during a stage-specific reorganization of their polyploid chromosomes, a mitotic-like state called the "five-blob" stage. These visible alterations in chromosome structure do not affect polarity by altering transcription of key patterning genes. Expression levels of gurken (grk), oskar (osk), bicoid (bcd), and decapentaplegic (dpp) transcripts are normal, with a slight delay in the appearance of bcd and dpp mRNAs. Mislocalization of grk and osk transcripts, however, suggests a defect in the microtubule reorganization that occurs during the middle stages of oogenesis and determines axial polarity. This defect likely results from aberrant Grk/Egfr signaling at earlier stages, since rhi mutations delay synthesis of Grk protein in germaria and early egg chambers. In addition, Grk protein accumulates in large, actin-caged vesicles near the endoplasmic reticulum of stages 6-10 egg chambers. We propose two hypotheses to explain these results. First, Rhi may play dual roles in oogenesis, independently regulating chromosome compaction in nurse cells at the end of the unique endoreplication cycle 5 and repressing transcription of genes that inhibit Grk synthesis. Thus, loss-of-function mutations arrest nurse cell chromosome reorganization at the five-blob stage and delay production or processing of Grk protein, leading to axial patterning defects. Second, Rhi may regulate chromosome compaction in both nurse cells and oocyte. Loss-of-function mutations block nurse cell nuclear transitions at the five-blob stage and activate checkpoint controls in the oocyte that arrest Grk synthesis and/or inhibit cytoskeletal functions. These functions may involve direct binding of Rhi to chromosomes or may involve indirect effects on pathways controlling these processes.

Amino Acid Sequence↗
PubMed2003

Comprehensive expression profiling of highly homologous 39 hox genes in 26 different human adult tissues by the modified systematic multiplex RT-pCR method reveals tissue-specific expression pattern that suggests an important role of chromosomal structure in the regulation of hox gene expression in adult tissues.

Homeobox genes play a crucial role as molecular address labels in early embryogenesis by conferring cell fate and establishing regional identity in tissues. Homeobox gene expression is not restricted to the early development, but it is also observed in the differentiated cells in adult tissues. To have a better understanding of the functionality of homeobox gene expression in adult tissues in physiological and pathological phenomena, it is important to determine the expression profiles of Hox genes. We established a system to study the expression of 39 human Hox genes by the modified Systematic Multiplex RT-PCR method. Using this system, we have systematically examined their expression in 26 different adult tissues. The results showed tissue-specific differential expression. They also revealed that the posterior tissues generally express more Hox genes than the anterior tissues and that the genes located centrally in the Hox Gene Complexes are expressed in more tissues than the genes located at the 5' or 3' end of the complexes. Instead of similar expression patterns among paralogous genes, we found that several neighboring Hox genes on the same chromosomes exhibited similar tissue-specific expression pattern, which may suggest that the regulation of Hox gene expression may be more dependent on chromosomal structure in adult tissues.

Adult↗
PubMed1981

Analysis of structural chromosome changes and SCE after occupational long-term exposure to electric and magnetic fields from 380 kV-systems.

Chromosome analyses were carried out in lymphocytes of 32 workers occupationally exposed for more than 20 years to 50 Hz alternating electric magnetic fields in 380 kV switchyards. As compared with a control group of 22 workers of similar age and occupation but without field exposure neither the yields of structural chromosome changes nor the SCE-frequencies were increased. The difference of cytogenetic data after occupational exposure to ionizing radiation is discussed.

Adult↗
PubMed2025

MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.

The genome is organized into distinct chromatin compartments with at least two main classes, a transcriptionally active A and an inactive B compartment, broadly corresponding to euchromatin and heterochromatin. Chromatin regions within the same compartment preferentially interact with each other over regions in the opposite compartment. A/B compartments are traditionally identified from ensemble Hi-C contact frequency matrices using principal component analysis of their covariance matrices. However, defining compartments at the single-cell level from sparse single-cell Hi-C data is challenging, especially since homologous copies are often not resolved. To address this, we present MaxComp, an unsupervised method, for inferring single-cell A/B compartments based on 3D geometric considerations in single-cell chromosome structures-derived either from multiplexed FISH-omics imaging or 3D structure models derived from Hi-C data. By representing each 3D chromosome structure as an undirected graph with edge-weights encoding structural information, MaxComp reformulates compartment prediction as a variant of the Max-cut problem, solved using semidefinite graph programming (SPD) to optimally partition the graph into two structural compartments. Our results show that the population average of MaxComp single-cell compartment annotations closely matches those derived from ensemble Hi-C principal component analysis, demonstrating that compartmentalization can be recovered from geometric principles alone, using only the 3D coordinates and nuclear microenvironment of chromatin regions. Our approach reveals widespread cell-to-cell variability in compartment organization, with substantial heterogeneity across genomic loci. When applied to multiplexed FISH imaging data, MaxComp also uncovers relationships between compartment annotations and transcriptional activity at the single-cell level. In summary, MaxComp offers a new framework for understanding chromatin compartmentalization in single cells, connecting 3D genome architecture, and transcriptional activity with the cell-to-cell variations of chromatin compartments.

Chromatin↗
PubMed1976

Modern ideas on chromosome structure.

The structural element of an eukaryotic chromosome is the so-called chromatin fibre. It is a DNA-protein complex of about 100-200 A thickness and most probably running through from one end of a chromatid to the other. The fine structure of this DNA-protein fibre suggests a core of globular histone subunits around which the DNA-molecule is wound. The single strandedness of chromatids is suggested by the structure of premature condensed chromosomes. The course G-banding seen in metaphase chromosomes is presumably caused by groups of much finer bands seen in decondensed chromosomes. The number of such fine bands in the human genome is estimated to be 10 000-100 000, figures which are in the range of the number of genes in man.

Animals↗
PubMed1990

Dose-response relationship for the induction of structural chromosome aberrations in human spermatozoa after in vitro exposure to tritium beta-rays.

The effects of tritium (HTO) beta-rays on human sperm chromosomes were studied using our interspecific in vitro fertilization system between human spermatozoa and zona-free hamster oocytes. Semen samples were treated with media containing 1.53-24.3 mCi/ml HTO for about 80 min. 1290 spermatozoa from the controls and 1842 spermatozoa from the irradiated groups were karyotyped. The incidence of spermatozoa with structural chromosome aberrations increased linearly with increasing dosage. Breakage-type aberrations occurred far more frequently than exchange-type. Chromosome-type aberrations appeared far more frequently than chromatid-type. All of these types of aberrations showed linear dose-dependent increases. The RBE values of HTO beta-rays relative to X-rays were calculated for the above-mentioned 5 indices, respectively. Their RBE values ranged from 1.89 to 3.00 when the absorbed dose was estimated to be the minimum, whereas the values ranged between 1.04 and 1.65 when the absorbed dose was estimated to be the maximum.

Beta Particles↗
PubMed1998

Structure, chromosomal localisation and expression of the murine dominant negative helix-loop-helix Id4 gene.

Id proteins antagonise the functional properties of DNA-binding, basic helix-loop-helix transcription factors. Id proteins inhibited cell differentiation in various model systems, both in vitro and in vivo. They are transcriptionally and post-transcriptionally regulated during cell cycle progression and promote cell proliferation. In order to establish the molecular and functional properties of Id4, we analysed structure, chromosomal localisation and expression of the murine Id4 gene. Sequence analysis indicated that the Id4 gene consists of three exons. Multiple transcription start sites map about 300 bp upstream of the ATG translational start codon within a 30-bp region of the Id4 promoter, which lacks a classic TATA box. Expression of the Id4 gene results in four major transcripts, most likely generated by differential use of polyadenylation sites. Abundance of the four transcripts varies across tissues, suggesting tissue-specific regulation of polyadenylation and/or post-transcriptional regulation of Id4 expression. However, the Id4 gene seems to be expressed as a single protein. Id4 expression is switched on during embryogenesis between day 7.5 and 9.5 of gestation and is most abundant in adult brain, kidney and testis. Id4 maps to chromosome 13 of the mouse.

Animals↗
PubMed1983

Induction of structural chromosome aberrations and sister chromatid exchanges in human lymphocytes in vitro by aristolochic acid.

The medicinal use of Aristolochia clematitis has been known for some time. The main active agent of this medicinal plant is aristolochic acid, a nitrophenanthrenecarbonic acid. Very recently, however, the Federal Health Office withdrew the licence for all drugs containing aristolochic acid, because of the well-founded suspicion that aristolochic acid may be a very potent carcinogen. We investigated the induction of structural chromosome aberrations and sister chromatid exchanges (SCEs) by aristolochic acid in human lymphocytes in vitro. Cells were treated with the agent tested throughout culture time and during the G0 phase of the cell cycle. We tested concentrations over a range of 1 to 20 micrograms/ml. Both treatment conditions resulted in an increased aberration frequency. The induction of gaps and breaks as well as the induction of SCEs showed a dose-dependent increase. The number of SCEs per metaphase was enhanced by a factor of 2 to 3. If conventional cytogenetic methods had been applied in time, one would have recognized the mutagenic risk of aristolochic acid earlier.

Aristolochic Acids↗
PubMed1989

Structural chromosome aberrations in lymphocytes from children previously treated for Wilms' tumor or Hodgkin's disease.

Nineteen children treated for Wilms' tumor (thirteen cases) or Hodgkin's disease (six cases) with cytostatic agents and/or radiotherapy were studied cytogenetically on lymphocytes cultivated from blood samples drawn after at least 1 year of complete remission after end of therapy. A reference group of children was matched for age, sex, and residence. The frequencies of sister chromatid exchange (5.4 versus 5.6 SCE/cell), and chromosome damage type gaps (6.6 versus 7.1%) and breaks (1.9 versus 1.9%) were not different in the two groups, but exchange type aberrations were more frequent in the patients (0.9 versus 0.06%). Fifty karyotypes were analyzed in all but two cases of Hodgkin's disease. The overall frequency of stable (3.1 versus 3.8%) and unstable (1.7 versus 1.4%) structural chromosome changes such as translocations, deletions, chromatid exchanges, and dicentrics were not different in the patient and the control groups. If the chromosome data reflect a general cancer risk, this risk cannot be considerably higher among the cancer-treated children.

Adolescent↗
PubMed1990

Types of structural chromosome aberrations and their incidences in human spermatozoa X-irradiated in vitro.

We studied the effects of in vitro X-irradiation on human sperm chromosomes, using our interspecific in vitro fertilization system between human spermatozoa and zona-free hamster oocytes. 28 semen samples from 5 healthy men were exposed to 0.23, 0.45, 0.91 and 1.82 Gy of X-rays. Totals of 2098 and 2862 spermatozoa were karyotyped in the control and the irradiated groups, respectively. The incidence of spermatozoa with X-ray-induced structural chromosome aberrations (Y) increased linearly with increasing dosage (D), being best expressed by the equation, Y = 0.08 + 34.52 D. The incidence of breakage-type aberrations was more than 9 times higher than that of exchange-type aberrations. Both of them showed linear dose-dependent increases, which were expressed by the regression lines, Y = -0.014 + 0.478 D and Y = -0.010 + 0.057 D, respectively. The incidence of chromosome-type aberrations was about 6 times higher than that of chromatid-type aberrations. Their dose-dependent increases were expressed by the regression lines, Y = -0.015 + 0.462 D and Y = -0.006 + 0.079 D, respectively. These results are discussed in relation to the previous data obtained with gamma-rays. The repair mechanism of X-ray-induced sperm DNA lesions is also discussed.

Animals↗
PubMed1992

Detection of structural chromosome aberrations in immunophenotyped mitoses.

The recently developed MAC (morphology-antibody-chromosome) method allows simultaneous immunophenotype and karyotype analysis in the same cell. To date, application of this new method has been hampered by the poor quality of chromosome banding. In this paper, we describe a modified simultaneous immunofluorescence and Q-banding technique, as well as a new combination of immunohistochemical and fluorescent R-banding methods. By further modifying the MAC method, we were able not only to achieve unequivocal results with weakly expressed antigens but also to improve the quality of the banding techniques, so that even structural chromosome abnormalities were well defined.

Chromosome Aberrations↗
PubMed1994

Leptomycin B targets a regulatory cascade of crm1, a fission yeast nuclear protein, involved in control of higher order chromosome structure and gene expression.

The molecular action of leptomycin B (LMB), an agent inducing arrest of the eukaryotic cell cycle at G1 and G2 phases, was investigated by analyzing an LMB resistance gene of Schizosaccharomyces pombe. A genomic library of an LMB-resistant mutant was screened for LMB resistance, and a DNA fragment containing an open reading frame (ORF) of 1078 amino acids was cloned on a multicopy vector. The plasmid was found to confer drug resistance specifically to LMB. Nucleotide sequencing revealed that the ORF was a mutant gene for the essential nuclear protein crm1, which had been reported to complement a cold-sensitive mutation causing deformed nuclear morphology. The gene product named crm1-N1 had two amino acid replacements (Gly-503 to Asp and Met-546 to Ile). Two allelic mutants of crm1 (crm1-809 and crm1-119) were found to be hypersensitive and resistant, respectively, to LMB. Nuclear morphology of the cold-sensitive crm1-809 mutant at the restrictive temperature was almost the same as that of the wild-type cells treated with LMB. Furthermore, a low concentration of LMB induced the intracellular accumulation of a 25-kDa protein in the wild-type cells, which was immunologically identical to the protein accumulating in the crm1-809 mutant cells. These results strongly suggest that LMB primarily inhibits the function of the crm1 gene which is required for maintaining higher order chromosome structures, correct gene expression, and cell growth in the fission yeast.

Alkaloids↗
PubMedDate not supplied

A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function.

Aegilops tauschii (Coss.) Schmal. (2n = 2x = 14, DD) (syn. A. squarrosa L.; Triticum tauschii) is well known as the D-genome donor of bread wheat (T. aestivum, 2n = 6x = 42, AABBDD). Because of conserved synteny, a high-density map of the A. tauschii genome will be useful for breeding and genetics within the tribe Triticeae which besides bread wheat also includes barley and rye. We have placed 249 new loci onto a high-density integrated cytological and genetic map of A. tauschii for a total of 732 loci making it one of the most extensive maps produced to date for the Triticeae species. Of the mapped loci, 160 are defense-related genes. The retrotransposon marker system recently developed for cultivated barley (Hordeum vulgare L.) was successfully applied to A. tauschii with the placement of 80 retrotransposon loci onto the map. A total of 50 microsatellite and ISSR loci were also added. Most of the retrotransposon loci, resistance (R), and defense-response (DR) genes are organized into clusters: retrotransposon clusters in the pericentromeric regions, R and DR gene clusters in distal/telomeric regions. Markers are non-randomly distributed with low density in the pericentromeric regions and marker clusters in the distal regions. A significant correlation between the physical density of markers (number of markers mapped to the chromosome segment/physical length of the same segment in microm) and recombination rate (genetic length of a chromosome segment/physical length of the same segment in microm) was demonstrated. Discrete regions of negative or positive interference (an excess or deficiency of crossovers in adjacent intervals relative to the expected rates on the assumption of no interference) was observed in most of the chromosomes. Surprisingly, pericentromeric regions showed negative interference. Islands with negative, positive and/or no interference were present in interstitial and distal regions. Most of the positive interference was restricted to the long arms. The model of chromosome structure and function in cereals with large genomes that emerges from these studies is discussed.

Chromosome Mapping↗
PubMed1996

Short-range order in two eukaryotic genomes: relation to chromosome structure.

Fourier transform techniques have been used to analyze the distributions of all ten independent DNA dinucleotide steps in two eukaryotic genomes and one prokaryotic genome, for periodicities of approximately 2 to 500 bp. The results reveal systematic deviations from random expectation for certain dinucleotide steps over this entire range of periodicities, together with striking peaks at certain spatial periodicities for particular dinucleotide steps. Several dinucleotides yield peaks at a periodicity of approximately 10.2 bp that are unique to the eukaryotic genomes. Certain members of this set of dinucleotide signals were previously identified as involved in nucleosome positioning, while others were previously unrecognized. In real-space, these dinucleotides are uncorrelated or even anticorrelated (relative to random expectation) at distances of 10 and 11 bp, despite having greater than random spectral power at the corresponding periodicity. Real-space correlations of these dinucleotides at distances of 10 and 11 bp are suppressed by another spectral component, a 3 bp periodicity attributed to codons, which has a local minimum probability at approximately 10.5 bp. When the two eukaryotic genomes are encoded for the signal "AA or TT", the peak at approximately 10.2 bp periodicity is strengthened, whereas for the prokaryotic genome such a peak remains absent. For the Caenorhabditis elegans genome, this peak becomes the dominant feature in the transform, surpassing a peak owing to the existence of codons in both height and integrated intensity. These results suggest that the requirements of chromosome structure place significant constraints on eukaryotic genome organization; they reveal additional signals that may be related to nucleosome positioning; and they reveal a wealth of additional new non-random aspects of genome sequence organization.

Animals↗
PubMed2003

Development of binary classification of structural chromosome aberrations for a diverse set of organic compounds from molecular structure.

Classification models are generated to predict in vitro cytogenetic results for a diverse set of 383 organic compounds. Both k-nearest neighbor and support vector machine models are developed. They are based on calculated molecular structure descriptors. Endpoints used are the labels clastogenic or nonclastogenic according to an in vitro chromosomal aberration assay with Chinese hamster lung cells. Compounds that were tested with both a 24 and 48 h exposure are included. Each compound is represented by calculated molecular structure descriptors encoding the topological, electronic, geometrical, or polar surface area aspects of the structure. Subsets of informative descriptors are identified with genetic algorithm feature selection coupled to the appropriate classification algorithm. The overall classification success rate for a k-nearest neighbor classifier built with just six topological descriptors is 81.2% for the training set and 86.5% for an external prediction set. The overall classification success rate for a three-descriptor support vector machine model is 99.7% for the training set, 92.1% for the cross-validation set, and 83.8% for an external prediction set.

Algorithms↗