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PubMed2005

Frequency and distribution of chromosome abnormalities in human spermatozoa.

This study reviews the frequency and distribution of numerical and structural chromosomal abnormalities in spermatozoa from normal men obtained by the human-hamster system and by multicolor-FISH analysis on decondensed sperm nuclei. Results from large sperm karyotyping series analyzed by chromosome banding techniques and results from multicolor FISH in sperm nuclei (of at least 10(4) spermatozoa per donor and per probe) were reviewed in order to establish baseline values of the sperm chromosome abnormalities in normal men. In karyotyping studies, the mean disomy frequency in human sperm is 0.03% for each of the autosomes, and 0.11% for the sex chromosomes, lower than those reported in sperm nuclei by FISH studies using a similar methodology (0.09% and 0.26%, respectively). Both types of studies coincide in that chromosome 21 and sex chromosomes have a greater tendency to suffer segregation errors than the rest of the autosomes. The mean incidence of diploidy, only available from multicolor FISH in sperm nuclei, is 0.19%. Inter-donor differences observed for disomy and diploidy frequencies among FISH studies of decondensed sperm nuclei using a similar methodology could reflect real differences among normal men, but they could also reflect the subjective application of the scoring criteria among laboratories. The mean frequency of structural aberrations in sperm karyotypes is 6.6%, including all chromosome types of abnormalities. Chromosome 9 shows a high susceptibility to be broken and 50% of the breakpoints are located in 9q, between the centromere and the 9qh+ region. Structural chromosome aberrations for chromosomes 1 and 9 have also been analyzed in human sperm nuclei by multicolor FISH. Unfortunately, this assay does not allow to determine the specific type of structural aberrations observed in sperm nuclei. An association between advancing donor age and increased frequency of numerical and structural chromosome abnormalities has been reported in spermatozoa of normal men.

Adult↗
PubMed1993

Investigation of aneuploidy induction in mouse oocytes following exposure to vinblastine-sulfate, pyrimethamine, diethylstilbestrol diphosphate, or chloral hydrate.

The various causative and mechanistic phenomena associated with aneuploidy induction require considerable investigation to better understand the etiology of chromosome missegregation. We investigated the potential of vinblastine sulfate, pyrimethamine, diethylstilbestrol diphosphate, and chloral hydrate to induce numerical and structural chromosome changes in female mouse germ cells. Superovulated ICR mice were administered the compounds either by intraperitoneal injection or oral gavage, and oocytes were collected and processed for cytogenetic analysis 17 hr later. Vinblastine sulfate, administered i.p., induced a significant increase in the frequency of ovulated MI oocytes and of hyperploid MII oocytes compared to controls, but did not increase the frequency of structural aberrations. Pyrimethamine, diethylstilbestrol diphosphate, and chloral hydrate did not increase the frequency of numerical or structural chromosome changes in female mouse germ cells.

Aneuploidy↗
PubMedDate not supplied

Structure and chromosomal localization of chicken CD5.

CD5 is a transmembrane glycoprotein on all T cells and on a subpopulation of B cells. Based on the analysis of chicken CD5-cDNA we have previously shown that the structure of the CD5 protein is conserved between species. Here we report the isolation and chromosomal mapping of the chicken CD5 gene. The gene spans 3.4 kb and is extremely compact with a high GC-nucleotide content. There are 10 exons and the introns are spliced out similarly to those in the human CD5 gene. Each of the three extracellular scavenger receptor cysteine-rich (SRCR) domains is encoded as an exon of its own, as is the proline-rich hinge region that separates the first two membrane-distal SRCR domains. The fluorescence in situ hybridization (FISH) technique was used to map the gene to chromosome five. This is the first report describing the organization of the CD5 gene from a nonmammalian species.

Animals↗
PubMed1993

Scanning electron microscopy of polytene chromosomes (I).

The structure of polytene chromosomes has been observed by conventional scanning electron microscopy and also with a high resolution 'in lens' field emission instrument. Surface imaging with secondary electron emission has characterized condensed chromatin and regions known for their RNA synthetic potential (nucleoli, Balbiani rings and puffs). In DNA-rich bands pairing of chromatids appears so perfect that individual chromomeres cannot be visualized as discrete units. In the interbands only chromatid bundles appear as elements, but not individual chromatids. High resolution scanning electron microscopy allows resolution at the nucleosome level. Improved localization of chromosomal structures is demonstrated, as in the case of the proposed separation of the prepupal 'Balbiani ring 1'. Surface images of the RNA synthetic centres of the salivary gland cell are presented. Transcripts of the Balbiani ring template can be observed in the condensed and gradually unfolded state, allowing measurement of unit ribonucleoparticles. The surfaces of puffs have been visualized and are characterized by multiple supercoiled loop structures, which are described according to size, conformation and distribution.

Animals↗
PubMed1998

Structure and chromosomal localization of mouse G protein subunit gamma 4 gene.

The G protein gamma subunits are members of a multigene family and are implicated in determining the specificity of receptor-G protein interaction. The gene structures for many of the gamma subunits remain to be determined. Here, we report the gene structure for the brain-specific gamma 4 subunit and its map position on a mouse chromosome. The gene (Gng4) comprises at least three exons spanning over 20 kb. The 225-bp coding region, which spans two exons, is interrupted by a large 18.2-kb intron whose position is conserved in other gamma subunit genes. There is a putative additional intron in the 5' untranslated region just upstream of the translation initiation codon. Introns are present in most of the other gamma subunits at this position. The mouse Gng4 gene is mapped to chromosome 13.

Amino Acid Sequence↗
PubMed1991

Mouse lipocortin I gene structure and chromosomal assignment: gene duplication and the origins of a gene family.

Using cDNA probes obtained from library screening and anchored polymerase chain reaction, we have isolated and characterized three overlapping mouse genomic clones that contain the mouse lipocortin I (Lipo I) structural gene. Restriction enzyme mapping, Southern blotting, and DNA sequencing were carried out on the cloned genomic DNA. Lipo I spans about 17 kb and is divided into 13 exons encoding a protein of 346 amino acid residues. The promoter region of the gene has a TATA box and a CCAAT box located upstream of the transcription initiation site at -31 and -76 bp, respectively. Analysis of the strain distribution pattern of Lipo 1 in BXD and AKXD collections of recombinant inbred strains establishes that Lipo I is located on chromosome 19 in close proximity to Ea-4. While no striking relationship exists between the exon/intron structure of the gene and the four repeated 70-amino-acid domains of the protein, three of the four 17-amino-acid repeats believed to be responsible for Ca2+/phospholipid binding are encoded by the last codon of one exon and the first 16 codons of the following exon. This pattern supports the gene duplication theory, and the similarity in gene structure between mouse Lipo I and Lipo II suggests they have a recent evolutionary ancestor.

Amino Acid Sequence↗
PubMed1987

Chromosomal gene structure of human myeloperoxidase and regulation of its expression by granulocyte colony-stimulating factor.

By using the full-length cDNA as a probe, the chromosomal gene for human myeloperoxidase was isolated from a human gene library. Comparison of the nucleotide sequence of the chromosomal gene with that of the cDNA has revealed that the human myeloperoxidase gene is composed of 12 exons and 11 introns. S1 mapping analysis of human myeloperoxidase mRNA identified the single transcription initiation site at 180 base pairs upstream of the ATG initiation codon. In the 5'-flanking region of the human myeloperoxidase gene, there are several blocks of sequences which are homologous to the sequences found on the 5'-promoter region of the human c-myc proto-oncogene. The myeloperoxidase gene is expressed in mouse myeloid leukemia WEHI-3B D+ and NFS-60 cells. When these cells were treated with human recombinant granulocyte colony-stimulating factor, the steady-state level of myeloperoxidase mRNA declined to zero within 36 h in WEHI-3B D+ cells, but not in NFS-60 cells.

Amino Acid Sequence↗
PubMed1994

The cryptomonad histone H4-encoding gene: structure and chromosomal localization.

Cryptomonads are unicellular flagellates whose plastids are surrounded by four membranes. A periplastidal compartment, containing eukaryote-type ribosomes, starch grains and a so-called nucleomorph, is located between the inner and outer membrane pairs. The nucleomorph has been shown to be the vestigial nucleus of a eukaryotic endosymbiont. In order to obtain more information about the chromatin structure of the nucleomorph and the host nuclear chromosomes, we studied the distribution of the histone, H4. H4 was not detectable in the nucleomorph by immunolocalization, thus supporting earlier findings by Gibbs [In: Wiesner et al. (Eds.), Experimental Phycology 1, 1990, pp. 145-157]. Likewise, no H4 DNA was demonstrable in the nucleomorph by Southern hybridization. Sequence analysis, and Southern and Northern blot data of a cryptomonad gene, H4, indicate an intermediate position for these genes between animals and plants.

Amino Acid Sequence↗
PubMed1997

cDNA cloning, genomic structure, and chromosome mapping of the human epithelial membrane protein CL-20 gene (EMP1), a member of the PMP22 family.

CL-20 is a novel gene encoding a protein that is structurally related to but distinct from the peripheral myelin protein PMP22. Like PMP22, CL-20 is likely to play important roles in the regulation of cell proliferation, differentiation, and cell death. In this study, we describe the cloning and sequencing of a cDNA encoding the human homologue of CL-20 and characterize the genomic structure of this gene. The hCL-20 gene (HGMW-approved symbol EMP1) encodes a protein of 157 amino acids that exhibits 76% identity to the rabbit CL-20 and to the rat EMP-1, which have been described recently, and 39% identity to human PMP22. CL-20 contains four hydrophobic domains, suggesting that it is an integral membrane protein. In particular the second hydrophobic domain encoded within the fourth exon is highly conserved among CL-20, EMP-1, and PMP22, suggesting a functional role for this region. CL-20 mRNA is abundant in squamous-differentiated bronchial epithelial cells; however, low levels of CL-20 mRNA can be detected in several human tissues by Northern analysis. Retinoic acid, which inhibits squamous differentiation, represses CL-20 expression in normal human bronchial epithelial cells. The genomic structure of the hCL-20 gene was analyzed using a P1 vector containing this gene. The hCL-20 gene contains five exons about 0.2, 0.12, 0.1, 0.14, and 2.2 kb and four introns about 15, 1.9, 0.1, and 0.7 kb. We have mapped the hCL-20 gene to chromosome 12p12 by fluorescence in situ hybridization.

Amino Acid Sequence↗
PubMed1977

Sister chromatid exchange and chromosome aberration analysis with the use of several carcinogens and noncarcinogens.

Several chemical carcinogens and noncarcinogens were tested for their ability to induce sister chromatid exchanges (SCE) and structural chromosome aberrations in cultured V79-4 Chinese hamster cells. All of the direct-acting carcinogens induced a large increase in SCE frequency. Two chemicals, which are mutagenic in microorganisms but whose carcinogenicity is poorly documented, also increased the frequency of SCE. Carcinogenic polycyclic hydrocarbons caused an increased incidence of SCE only when a metabolizing feeder layer was used, whereas no increase was observed with noncarcinogenic polycyclic hydrocarbons. The other noncarcinogens also did not influence the SCE frequency. Although some chemicals increased the frequency of structural chromosome aberrations, no correlation was found between the frequencies of SCE and aberrations.

2-Acetylaminofluorene↗
PubMed1994

Structure and chromosomal locus of the mouse gene encoding a cerebellar Purkinje cell-specific helix-loop-helix factor Hes-3.

HES-3 is a cerebellar Purkinje cell-specific helix-loop-helix factor structurally related to the products of the Drosophila hairy and Enhancer of split genes. Here, we report the nucleotide sequence and chromosomal locus of the mouse Hes-3 gene. This gene consists of four exons and the exon-intron boundaries are well conserved when compared with those of the mouse Hes-1 and Drosophila hairy genes. Southern blot and interspecies backcross analyses show that the mouse Hes-3 gene is a single-copy gene and is located around position 80 on chromosome 4. Further analysis indicates that this locus is close to the Hes-5 locus, which is different from the Hes-1 locus (position 26 on chromosome 16). These results suggest that the Hes-3 and Hes-5 genes may be clustered on chromosome 4 while the Hes-1 gene is not.

Amino Acid Sequence↗
PubMed2002

The 3D structure of human chromosomes in cell nuclei.

The spatial arrangement of some genetic elements relative to chromosome territories and in parallel with the cell nucleus was investigated in human lymphocytes. The structure of the chromosome territories was studied in chromosomes containing regions (clusters) of highly expressed genes (HSA 9, 17) and those without such clusters (HSA 8, 13). In chromosomes containing highly expressed regions, the elements pertaining to these regions were found close to the centre of the nucleus on the inner sides of chromosome territories; those pertaining to regions with low expression were localized close to the nuclear membrane on the opposite sides of the territories. In chromosomes with generally low expression (HSA 8, 13), the elements investigated were found symmetrically distributed over the territories. Based on the investigations of the chromosome structure, the following conclusions are suggested: (1) Chromosome territories have a non-random internal 3D structure with defined average mutual positions between elements. For example, RARalpha, TP53 and Iso-q of HSA 17 are nearer to each other than they are to the HSA 17 centromere. (2) The structure of a chromosome territory reflects the number and chromosome location of clusters of highly expressed genes. (3) Chromosome territories behave to some extent as solid bodies: if the territory is found closer to the nuclear centre, the individual genetic elements of this chromosome are also found, on average, closer the centre of the nucleus. (4) The positions of centromeres are, on average, nearer to the fluorescence weight centre of the territory (FWCT) than to genes. (5) Active genes are not found near the centromeres of their own territory. A simple model of the structure of chromosome territory is proposed.

Cell Compartmentation↗
PubMed2025

Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction.

MOTIVATION: Single-cell Hi-C (scHi-C) data provide critical insights into chromatin interactions at individual cell levels, uncovering unique genomic 3D structures. However, scHi-C datasets are characterized by sparsity and noise, complicating efforts to accurately reconstruct high-resolution chromosomal structures. In this study, we present ScUnicorn, a novel blind super-resolution framework for scHi-C data enhancement. ScUnicorn uses an iterative degradation kernel optimization process, unlike traditional super-resolution approaches, which rely on downsampling, predefined degradation ratios, or constant assumptions about the input data to reconstruct high-resolution interaction matrices. Hence, our approach more reliably preserves critical biological patterns and minimizes noise. Additionally, we propose 3DUnicorn, a maximum likelihood algorithm that leverages the enhanced scHi-C data to infer precise 3D chromosomal structures. RESULTS: Our evaluation demonstrates that ScUnicorn achieves superior performance over the state-of-the-art methods in terms of Peak Signal-to-Noise Ratio, Structural Similarity Index Measure, and GenomeDisco scores. Moreover, 3DUnicorn's reconstructed structures align closely with experimental 3D-FISH data, underscoring its biological relevance. Together, ScUnicorn and 3DUnicorn provide a robust framework for advancing genomic research by enhancing scHi-C data fidelity and enabling accurate 3D genome structure reconstruction. AVAILABILITY AND IMPLEMENTATION: Unicorn implementation is publicly accessible at https://github.com/OluwadareLab/Unicorn.

Single-Cell Analysis↗
PubMedDate not supplied

[Visualization of elementary structures in polytene chromosomes of Drosophila melanogaster].

Electron microscopic study of total polytene chromosome preparations makes it possible to reveal elementary structures of polytene chromosomes. Elementary chromosomes are detected which contain chromomeric and interchromomeric regions. Transcription is seen in puffs and in many bands. Chromatin spreading shows that both chromomeric and interchromomeric regions of elementary chromosomes consist of nucleosomes. A ribbon-like model of polytene chromosome structure is suggested and discussed. In the ribbon-like chromosome each elementary chromosome gels conjugated only with the two adjacent sister chromosomes. Conjugation occurs only in the chromomeric regions, interchromomeric regions do not conjugate. Both chromomeric and interchromomeric regions are duplicated during polytenization which ensure proportional replication of all the bands and interbands in the course of polytenization.

Animals↗
PubMed2002

Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications.

In the nucleus of animal and plant cells individual chromosomes maintain a compartmentalized structure. Chromosome territories (CTs), as these structures were named by Theodor Boveri, are essential components of the higher-order chromatin architecture. Recent studies in mammals and non-mammalian vertebrates indicate that the radial position of a given CT (or segments thereof) is correlated with its size, its gene-density and its replication timing. As a representative case, chicken cell nuclei show highly consistent radial chromatin arrangements: gene-rich, early replicating microchromosomes are clustered within the nuclear interior, while gene-poor, later replicating macrochromosomes are preferentially located at the nuclear periphery. In humans, chromosomes 18 and 19 (HSA18 and 19) territories that are of similar size show a distinctly different position in the cell nuclei of lymphocytes and lymphoblastoid cells: the gene-rich and early replicating HSA19 CTs are typically found close to the nuclear center, while the gene-poor and later replicating HSA18 CTs are preferentially located at the nuclear periphery. Recent comparative maps between human and chicken chromosomes revealed that the chicken macrochromosomes 2 and Z contain the genes homologous to HSA18, while the genes on HSA19 are located onto the chicken microchromosomes. These data lend tentative support to the hypothesis that differences in the radial nuclear positions of gene-rich, early replicating and gene-poor, later replicating chromatin have been evolutionarily conserved during a period of more than 300 million years irrespective of the evolution of highly divergent karyotypes between humans and chicken.

Animals↗
PubMed1994

The murine interleukin-5 receptor alpha-subunit gene: characterization of the gene structure and chromosome mapping.

To understand better the regulation of interleukin-5 receptor alpha-subunit (IL-5R alpha) expression, we have isolated the genomic clones of mouse IL-5R alpha (mIL-5R alpha) and analyzed the structure of the gene. The gene spans more than 35 kb and is composed of 11 exons. We found that two mRNAs encoding secreted forms of mIL-5R alpha result from differential splicing events. We identified the transcriptional start site by primer extension analysis of mIL-5R alpha mRNA. Nucleotide sequence of the 5'-flanking region contains potential binding sites for transcription factor Ap1, AP-1, GATA-1, and PU.1. About 260 bp sequence of the 5'-flanking region exhibited promoter activity when it was linked to a promoterless bacterial chloramphenicol acetyltransferase (CAT) gene. The promoter activity was seen not only in the IL-5-dependent pre-B-cell line Y16, but also in fibroblast cell line NIH-3T3. Comparison of the exon-intron boundaries of mIL-5R alpha genes with those of other members of the cytokine receptor family reveals a conserved evolutionary structure. By fluorescence in situ hybridization analysis, the mIL-5R alpha gene has been assigned to chromosome 6.

Animals↗
PubMed2006

Analysis of non-B DNA structure at chromosomal sites in the mammalian genome.

Changes at sites of genetic instability ultimately involve DNA repair pathways. Some sites of genetic instability in the mammalian genome appear to be unstable because they adopt a non-B DNA conformation. We describe two structural approaches for determination of whether a genomic region is configured in a non-B DNA conformation. Our studies indicate that at least some chromosomal fragile sites can be explained by such altered DNA conformations. One of the methods that we describe is called the bisulfite modification assay. This is a powerful assay because it provides information on individual DNA molecules. The second approach uses preexisting DNA structural reagents, but describes our specific application of them to analysis of DNA in vivo.

Animals↗