Atomic force microscopy for imaging human metaphase chromosomes

The present study introduces the principle of atomic force microscopy (AFM) and reviews our results of human metaphase chromosomes obtained by AFM. AFM imaging of the chromosomes revealed that the chromatid arm was not uniform in structure but had ridges and grooves along its length, which was most prominent in the late metaphase. The arrangement of these ridges and grooves was roughly symmetrical with the counterpart of the paired sister chromatids. AFM imaging of banded chromosomes also showed that the ridges and grooves were related to the G/Q-positive and G/Q-negative bands, respectively. At high magnification, the chromatid was seen to be produced by the compaction of highly twisted chromatin fiber loops, and its compaction tended to be stronger in the ridged regions of the chromosomes than in the grooved regions. Our AFM studies also showed the presence of catenation of chromatin fibers between the ridged portions of the chromatid in the late metaphase. Thus, AFM is useful for obtaining the three-dimensional surface topography not only in ambient conditions but also in physiological liquid conditions, and is expected to be an attractive tool for investigating the structure of chromosomes.     

Structural analysis of human chromosomes by atomic force and light microscopy in relation to the distribution of topoisomerase IIα

The relationship between the higher-order structure of human metaphase chromosomes and the distribution of topoisomerase IIα was analyzed by a comparison of atomic force microscope (AFM) and fluorescence microscope images of the same chromosome. AFM imaging of chromosomes in liquid revealed the presence of alternating ridges and grooves on the surfaces of the sister chromatids. In contrast, the fluorescence image of the chromosomes stained with the anti-topoisomerase IIα antibody showed that the fluorescence intensity of topoisomerase IIα was not uniform and that there were alternating strong and weak spots along the chromosome axes. A comparison of the AFM image with a fluorescence microscope image of the same chromosome further demonstrated that ridges and grooves corresponded to strong and weak fluorescence intensities of topoisomerase IIα, respectively. These findings suggest that the distribution of topoisomerase IIα has a close connection with the higher-order structure of human metaphase chromosomes.     

The structure of human metaphase chromosomes: its histological perspective and new horizons by atomic force microscopy

Studies on the structure of the human chromosome were reviewed from the histological perspective and discussed in connection with our recent findings obtained mainly by atomic force microscopy (AFM). In this paper, we introduce several hitherto known models of the high-order structure of the metaphase chromosome and discuss the actual structure of chromosomes in relation to such structures as spiral chromatids, chromosome bands, and chromosome scaffolds. In chromosomes treated with Ohnuki's hypotonic solution, the chromosome arms were elongated and showed a characteristic spiral pattern of chromatid fibers. On the other hand, alternating transverse ridges and grooves were clearly observed on the surface of chromosomes treated with 0.025% trypsin for G-banding, and these ridges and grooves corresponded to the dark and pale bands of G-banded chromosomes. Similar findings were also found in chromosomes treated with quinacrine mastards for Q-banding. Fibers bridging the gap between the sister chromatids were often observed in G/Q-banded chromosomes; these fibers tended to be restricted within the G/Q-positive portions, suggesting the presence of chromatin fibers bridging these regions. Based on these findings in conjunction with previous studies, we outlined the high-order structure of the human chromosome. Recent advances in nanotechnology have provided new AFM techniques for the imaging and handling of materials at nano-scale resolution. Application of these techniques to chromosome research is expected to provide valuable information on the chromosome structure in relation to its function.     

Replication Banding Patterns in Human Chromosomes Detected Using 5-ethynyl-2'-deoxyuridine Incorporation

A novel technique using the incorporation of 5-ethynyl-2''-deoxyuridine (EdU) into replicating DNA is described for the analysis of replicating banding patterns of human metaphase chromosomes. Human lymphocytes were synchronized with excess thymidine and treated with EdU during the late S phase of the cell cycle. The incorporated EdU was then detected in metaphase chromosomes using Alexa Fluor® 488 azides, through the 1,3-dipolar cycloaddition reaction of organic azides with the terminal acetylene group of EdU. Chromosomes with incorporated EdU showed a banding pattern similar to G-banding of normal human chromosomes. Imaging by atomic force microscopy (AFM) in liquid conditions showed that the structure of the chromosomes was well preserved even after EdU treatment. Comparison between fluorescence microscopy and AFM images of the same chromosome 1 indicated the presence of ridges and grooves in the chromatid arm, features that have been previously reported in relation to G-banding. These results suggest an intimate relationship between EdU-induced replication bands and G- or R-bands in human chromosomes. This technique is thus useful for analyzing the structure of chromosomes in relation to their banding patterns following DNA replication in the S phase.     

The structure of C-banded human metaphase chromosomes as observed by atomic force microscopy

The ultrastructure of C-banded human metaphase chromosomes was studied by the combined use of light microscopy and atomic force microscopy (AFM). Light microscopy of the C-banded chromosomes showed that the centromeric regions of all chromosomes except the Y chromosome were positively stained. AFM further revealed that the C-positive region was higher than the C-negative region. The area of the C-positive region was specific depending on each chromosome; it ranged from the centromere to the proximal end of the long arm in chromosome 1, while it was restricted to the centromere in chromosomes 2 and 3. At higher magnification, chromatin fibers about 50 nm thick were clearly shown in the entire length of the chromosomes. In the C-positive region, these chromatin fibers were densely packed, while chromatin fibers were loosely packed with gentle twisting in the C-negative region. These AFM findings suggest that certain factors related to the chromatin fiber compaction remain in the C-positive region even after successive C-banging treatment.     

Scanning near field optical/atomic force microscopy of bromodeoxyuridine-incorporated human chromosomes

The present study applied scanning near field optical/atomic force microscopy (SNOM/AFM) to the observation of human chromosomes immunostained with an anti-BrdU antibody after incorporation of BrdU into DNA. Human lymphocytes were cultured in BrdU for 72 h and their chromosomes were prepared with a standard method for light microscopy. After additional fixation with 15% formalin in phosphate buffered saline, the specimens were denatured with 2N HCI with 0.1% Triton-X 100, immunostained with the anti-BrdU antibody, and observed both by fluorescence microscopy and by SNOM/AFM. The preparation technique used in the present study enabled the differential staining of sister chromatids in each chromosome, and sister chromatid exchanges (SCEs) were recognized in some chromosomes of the metaphase spread. Observations of the specimens by SNOM/AFM further provided the simultaneous collection of topographical and fluorescent images of the same portions of BrdU-incorporated chromosomes. The resolution of the fluorescence images by SNOM/AFM was greater than that obtained by fluorescence microscopy. Superimposition of topographical and fluorescent images of the chromosomes is useful for the precise analysis of the fine structure of chromosomes in relation to the SCEs. The application of SNOM/AFM to the BrdU-incorporated chromosomes is thus useful for the analysis of the fine structure of chromosomes in relation to their function.     

Atomic force microscopy of native human metaphase chromosomes in a liquid

The present study introduces a method for obtaining three-dimensional images of native (i.e., unfixed) chromosomes by atomic force microscopy (AFM) in a liquid. Human metaphase chromosomes were isolated from a human lymphoblast-like cell line, K562, by the hexylene glycol procedure according to Wray and Stubble- field (1970), adsorbed on a silane-coated glass slide, and observed in a dynamic force mode (i.e., intermittent contact mode) of AFM in a hexylene buffer solution. In adequate operating conditions, the shape of chromosomes with paired chromatids was clearly and three-dimensionally observed by AFM. At high magnification, globular or fibrous structures about 50 nm thick could be found on the surface of each chromaid, implying that chromatin fibers were strongly wound or twisted in the chromatid. Thus, AFM imaging enabled the direct visualization of native chromosomes in a liquid at high resolution--which is comparable with that of scanning electron microscopy--and can serve to analyze the mechanism of chromosome condensation and separation in relation to the structure of chromosomes.     

Three-dimensional helical coiling structures and band patterns of hydrous metaphase chromosomes observed by low vacuum scanning electron microscopy

Helical coiling structures and band patterns of hydrous metaphase chromosomes were documented three-dimensionally by low vacuum scanning electron microscopy (SEM). Fixed or unfixed isolated Chinese hamster metaphase chromosomes were stained with platinum blue (Pt blue) and observed in the backscattered electron mode for low vacuum SEM without any hypotonic treatment or drying processes. Fibrous structures were shown both in the fixed and unfixed hydrous chromosomes; helical chromatid coils and their subcoils were clarified especially in the fixed chromosomes having contrasting alternative bands of light and darkness, while the translucent perichromosomal matrix and compact fibrous structures were recognized in the unfixed chromosomes. The helical coils were more clearly represented in a loosened chromatid of metaphase chromosomes. Treatment with a tris-HCl buffer solution and Pt blue staining in a hydrous condition successfully produced banding patterns similar to G-bands on metaphase chromosomes. These banded chromosomes observed by low vacuum SEM were also analyzed stereoscopically by field emission SEM after critical point drying. These findings indicate that: 1) native or unfixed chromosomes maintain the compact arrangement of high-order helical structures covered with the peri-chromosomal matrix; 2) helical coiling appearances of chromatids frequently observed in previous papers might be caused by loosening of the final level of the high-order structure of the metaphase chromosome; and 3) banding patterns might be produced by the rearrangement or reorganization of chromatin fibers at the 30 nm fiber level after the extraction of some chromosomal components including the peri- or intra-chromosomal materials during the banding procedure.     

Giemsa-negative chromosome bands preferentially recombine in cancer-associated translocations and gene fusions

Chromosome abnormalities, in particular translocations, and gene fusions are hallmarks of neoplasia. Although both have been recognized as important drivers of cancer for decades, our knowledge of the characterizing features of the cytobands involved in recombinations is poorly understood. The present study, based on a comparative analysis of 10 442 translocation breakpoints and 30 762 gene fusions comprising 13 864 protein-coding genes, is the most comprehensive evaluation of the interactions of cytobands participating in the formation of such rearrangements in cancer. The major conclusion is that although large G-negative, gene-rich bands are most frequently involved, the greatest impact was seen for staining properties. Thus, 60% of the recombinations leading to the formation of both translocations and fusion genes take place between two G-negative bands whereas only about 10% involve two G-positive bands. There is compelling evidence that G-negative bands contain more genes than dark staining bands and it has previously been shown that breakpoints involved in structural chromosome rearrangements and in gene fusions preferentially affect gene-rich bands. The present study not only corroborates these findings but in addition demonstrates that the recombination processes favor the joining of two G-negative cytobands and that this feature may be a stronger factor than gene content. It is reasonable to assume that the formation of translocations and fusion genes in cancer cells, irrespective of whether they have a pathogenetically significant impact or not, may be mediated by some underlying mechanisms that either favor the origin or provide a selective advantage for recombinations of G-negative cytobands.     

G-banding and chromosome condensation in the ant,Tapinoma nigerrimum

Well-defined G-bands were obtained on metaphase chromosomes fromTapinoma nigerrimum using trypsin and warm 2×SSC in sequence. The G-banded pattern allowed the identification of all chromosomes. Evidence for asynchronous condensation of the chromosomes of this species is provided. Different banding patterns were obtained when metaphase chromosomes were stained with DA/DAPI alone and with DA/DAPI after a standard G-banding procedure. The G-banding phenomenon is discussed using the result obtained.accepted for publication by H. C. Macgregor     

人胎手指真皮乳头嵴形成的光镜和扫描电镜观察

用光镜和扫描电技术了２－１０月龄人胎手指端真皮乳头嵴的形成过程。结果证实：３个月龄时真皮表现出现了原始真皮嵴，５个月龄时每条原始真皮嵴开始分化形成两条同源的真嵴，６个月龄时每条真皮嵴又开始分化形成许多真皮乳头，并由真皮乳头组成真皮乳头嵴，以后随胎龄的增加真皮乳头嵴逐渐增大。汗腺导管于４月龄时出现于原始真皮嵴间沟内，阴着同源真皮嵴和真皮乳头嵴的形成，使汗腺导管位于两条非同源真皮乳头嵴间沟内，每条表面     

A differential staining technique for chromosome identification and its comparison with fluorescence technique

A cytochemical differential staining technique for localizing repetitive DNA in metaphase preparations and quinacrine fluorescent staining of metaphase preparations were used simultaneously, and the methodology is described. An idiogram for the differential staining technique was developed and a comparison of the idiograms of both techniques revealed that the differential staining technique involves primarily the localization of repetitive DNA at or near the centromere, whereas with the quinacrine fluorescence technique nearly the entire length of the chromosome fluoresces to produce characteristic banding patterns. The combined use of these methods can be a valuable tool in the study of human chromosomes and provides a practical aid in the identification of individual chromosomes and the further definition of their structure.     

The topology of early- and late-replicating chromatin in differentially decondensed chromosomes

In this study we used a novel technique to reveal both longitudinal and transverse differentiation within mammalian mitotic chromosomes. Structural changes in chromosomes that we term ‘differential decondensation’ were produced in cells that were first incubated in hypotonic medium (15% Hanks’ solution), then adapted to normotonic conditions and thereafter exposed to a second short hypotonic shock. Such a double hypotonic treatment (DHT) is not critical for cell viability, but considerably elongates the G2 phase of the cell cycle. Giemsa staining of differentially decondensed chromosomes corresponds to standard G-banding, but does not need the standard post-fixation treatment. Using ‘dynamic’ BrdU banding, we show that such ‘differential’ staining is a result of differential resistance of the R- and G-bands to DHT. Thus, early-replicating foci, markers of R-bands, are localized in the peripheral chromatin halo, whereas late-replicating foci, corresponding to G-bands, remain associated with the axial regions of chromatids. Remarkably, despite these major changes in the structure of the chromosomal bands, the replication foci still preserve their discrete structure.     

Imaging of chromosomes at nano-meter scale resolution using scanning near-field optical/atomic force microscopy

Topographic and fluorescent images of whole barley chromosomes stained with YOYO-1 were observed simultaneously by scanning near-field optical/ atomic force microscopy (SNOM/AFM). The chromosome was relatively smooth and flat in the topographic images and no significant difference in height was present between regions of high fluorescent and low fluorescent intensity in the chromosomes. The telomeric region, labeled by fluorescence in situ hybridization (FISH) method, was also observed by SNOM/AFM at high resolution, and fluorescent signals of the telomeric region were clearly defined on the topographic image of chromatin fibers on the chromosome at the nano-meter scale level. Although the telomeric signals were usually visualized as a single fluorescent region at the end of sister chromatids by conventional light microscopy, they were observed separately as two fluorescent regions, less than 100-200 nm distance, using the SNOM/AFM. The SNOM/AFM offers great potential in identifying particular single gene location on chromosomes in the near future.     

Changes in chromosomal surface structure by different isolation conditions

The human cell cycle was synchronized and the chromosomes were isolated by a centrifugation method using two representative solutions for chromosome isolation (a polyamine buffer, PAB and citric acid solution, CAS) and fixatives. The centrifugation method yielded sufficient amounts of human metaphase chromosomes. Observation of the isolated chromosomes by scanning electron microscopy (SEM) revealed two types of surface structure which have been repeatedly reported to date: the human chromosomes in the PAB were relatively smooth but covered irregularly with scaly structures, while the surface of the chromosomes in the CAS exhibited a dense fibrous structure with a uniform diameter of 50-70 nm. Comparison of proteins extracted from chromosomes isolated with the PAB and CAS clearly indicated the removal of linker histones, H1, from chromosomes isolated with the CAS. These findings imply that the two different images of human chromosomes frequently observed by SEM are due to the removal of peripheral chromosomal materials including linker histones and/or the depletion of linker histones which prevent the surface chromatin fibers from scattering.     

Atomic force microscopy of human metaphase chromosomes after differential staining of sister chromatids

Human metaphase chromosomes, in which 5-bromo-deoxyuridine (BrdU) had been incorporated into the DNA, were treated with the fluorescent plus Giemsa (FPG) method. Use of this method distinctly stained one of the paired sister chromatids with the Giemsa solution due to the difference in content of BrdU in the two chromatids. These chromosomes with their differential staining of sister chromatids were observed by atomic force microscopy (AFM). In the air-dried specimens, one of the paired chromatids that was stained strongly with Giemsa solution was about two times higher than the counterpart that was stained faintly with Giemsa solution. In the critical point dried chromosomes, the height of the Giemsa positive chromatid roughly matched that of the Giemsa negative counterpart. These findings imply that the arrangement of the Giemsa negative chromatid after FPG staining is fragile and easily collapses due to the surface tension of water during air-drying. At higher magnifications, the surface structure differed between Giemsa positive and negative chromatids; the Giemsa positive chromatid (i.e., unifilarly BrdU-incorporated chromatid) was composed of fibrous structures while the Giemsa negative chromatid (i.e., bifilarly BrdU-incorporated chromatid) exhibited a fine granular appearance. These structural changes in the sister chromatids are thought to arise from the ultraviolet irradiation and heating of the chromosomes during FPG staining.     

Effects of titanium-coated micromachined grooved substrata on orienting layers of osteoblast-like cells and collagen fibers in culture

Osteogenic cells from newborn rat calvariae were cultured on titanium surfaces on which cell orientation could be manipulated. Substrata included smooth surfaces and substrata with smooth regions (gaps) flanked by grooves of 47-microm pitch and 3-, 10-, or 30-microm depth. Orientation angles of the cells were measured over time using propidium-iodide staining and confocal laser scanning microscopy. In addition, collagen fibers were identified using picro-sirius staining and reflected light polarization microscopy. Grooves proved effective in orienting cells, but their orienting ability decreased above the ridge level. Cells on the smooth surface showed no preferred orientation. Cells in the gaps became oriented as a result of cell-cell interactions with the cells on the flanking grooves. Cells in grooves produced oriented collagen fibers, but in the gaps, fibers could be parallel, perpendicular, or diagonal to the grooves. Collagen fibers on the smooth surfaces formed arrays of parallel fibers in a crisscross pattern. In long-term cultures, bone-like nodules were formed, but mostly above the ridge level. These data demonstrate that grooved surfaces can influence cell orientation both in cell populations above the cells in contact with the grooves and in cell populations adjacent to the grooves.     

Integration of the cytogenetic map with the draft human genome sequence

Chemically staining metaphase chromosomes resulting in an alternating dark and light banding pattern provide a tool by which abnormalities in chromosomes from diseased cells can be identified. The localization of these aberrations to a chromosomal region provides clues as to which gene or genes may contribute to a particular disease. With the sequencing of the human genome, it became critical to determine the positions of these cytogenetic bands within the sequence in order to take advantage of vast amount of information now anchored to the sequence, especially the locations of genes. The molecular basis of cytogenetic bands is not well understood, therefore their positions cannot be determined solely based on sequence information. We developed a dynamic programming algorithm that employs results from approximately 9500 fluorescence in situ hybridization experiments to approximate the locations of the 850 high-resolution bands in the June 2002 version of the draft human genome sequence. These band predictions support previously identified correlations between band stain intensity and certain structural characteristics of chromosomes, namely GC content, repeat structure content, CpG island density, gene density and degree of condensation.     

Variation in basement membrane topography in human thick skin

Samples of human plantar and palmar skin were excised and incubated in 20 mM EDTA after which the epidermis was gently separated from the dermis with the plane of separation occurring in the lamina lucida. Scanning electron microscopic examination of the dermal component revealed the classically described series of regularly spaced grooves and papillae that characterize the epidermal-dermal junction in thick skin. Primary dermal grooves exhibited evenly spaced tunnels that were originally occupied by sweat gland ducts. The basement membrane (basal lamina) in the primary grooves was relatively smooth but did exhibit a flattened, reticulated pattern at high magnifications. The basement membrane of secondary dermal grooves and papillae was in the form of numerous, elevated microridges off of which septae arose at roughly right angles. The surface appearance of the basement membrane in these areas was that of a honeycomb owing to the numerous compartments and recesses formed by the ridges and septae. Degradation of the basement membrane by trypsin demonstrated that the foundation for the highly folded and compartmentalized basement membrane was composed of dermal collagen fibrils, 60-70 nm in diameter, that were arranged in a series of variably sized, interconnected collagen bundles or walls. Epidermal basal cells extended cytoplasmic (foot) processes into two or more compartments, formed by the ridges and septae, which considerably amplified the basement membrane surface available for epidermal attachment. Scanning electron microscopic studies of the epidermal-dermal junction confirm the variable surface character of this interface previously reported by others using sectioned material.(ABSTRACT TRUNCATED AT 250 WORDS)     

Dose-response relationship for the induction of chromosomal abnormalities in gamma-irradiated human spermatozoa

The cytogenetic effects of in vitro irradiation on human spermatozoa have been studied by the interspecific in vitro fertilization system between human sperm and hamster oocytes. Semen samples from three healthy men were irradiated at doses of 0.00, 0.10, 0.25, 0.50, 1.00, 2.00, and 4.00 Gy. A total of 340 chromosome complements derived from non-irradiated human spermatozoa and 987 complements from irradiated spermatozoa were analyzed after sequential uniform stain G banding. Both the frequency of spermatozoa with structural chromosome abnormalities, and the incidence of such abnormalities per cell, showed strong dose-effect relationships that were best expressed by linear-quadratic equations: Y = 0.06413(±0.00475) + 0.1982(±0.00833)D − 0.00763(±0.00204)D² and Y = 0.07385(±0.00838) + 0.23329(±0.03124)D + 0.02317(±0.00955)D², respectively. When analyzing separately unrejoined and rejoined structural abnormalities, we found that the incidence of unrejoined lesions was four times higher than the incidence of rejoined anomalies. The induction of unrejoined abnormalities showed a linear, dose-dependent increase, whereas the incidence of rejoined abnormalities showed a quadratic, dose-dependent increase. The distribution of radiation-induced breakpoints was also analyzed. Breakpoints were found to be randomly distributed among chromosomes, but a clustering of breakpoints in G-negative bands was found: 71.5% of breakpoints were located in G-negative bands, and 28.5% in G-positive bands. Environ. Mol. Mutagen. 29:357–366, 1997 © 1997 Wiley-Liss, Inc.