Scanning Near-field Optical/Atomic Force Microscopy detection of fluorescence in situ hybridization signals beyond the optical limit

Fukushi, Daisuke; Shichiri, Motoharu; Sugiyama, Shigeru; Yoshino, Tomoyuki; Hagiwara, Shoji; Ohtani, Toshio

doi:10.1016/s0014-4827(03)00259-3

Cited by 20 publications

(9 citation statements)

References 34 publications

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“…Moreover, AFM and other new technologies such as scanning near‐field optical microscopy (SNOM) (Fukushi et al ., 2003), may allow in the future more exhaustive examinations of metaphase chromosomes and associations between chromosomal aberrations and diseases. SNOM/AFM, in fact, can simultaneously obtain topographic and fluorescent images with nanometer‐scale resolution.…”

Section: Discussionmentioning

confidence: 99%

Cytogenetic stability of chicken T‐cell line transformed with Marek's disease virus: atomic force microscope, a new tool for investigation

Bucchianico¹,

Giardi²,

Marco³

et al. 2010

J of Molecular Recognition

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The Marek's disease virus (MDV) integration may induce a novel organization of chromatin architecture with a modified genetic expression. In our opinion it is worthwhile trying to relate cytogenetic stability to functional modifications. Recently, atomic force microscopy technique was applied to study the structure of chromosomes at a nanoscale level. This high resolution allows to investigate the different structure of chromatin in order to study cytogenetic stability and chromosome aberrations due to MDV insertion. In this paper data are presented indicating a duplication [78,WZ,dup(1p)(p22-p23)] and a deletion [78,WZ cht del(3)(q2.10)] of Chromosomes 1 and 3 relatively. Relationships between GTG (G-bands by Trypsin using Giemsa) bands and the topography of chromosomes are also discussed, naming them Topographic Banding. The architecture of chromosomes observed by AFM can be related to the data obtained with classic banding techniques thus overcoming the optical resolution limits. The presence of chromatin bridges between sister chromatids at most of the heterochromatic regions is also evidenced. Besides, we present different studies of the longitudinal and transversal symmetry of the hetero and euchromatic regions to clearly demonstrate a different underlying architecture of these regions. It is indeed evident that the heterochromatic bands are more symmetrical than euchromatic bands.

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Section: Discussionmentioning

confidence: 99%

Cytogenetic stability of chicken T‐cell line transformed with Marek's disease virus: atomic force microscope, a new tool for investigation

Bucchianico¹,

Giardi²,

Marco³

et al. 2010

J of Molecular Recognition

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“…Chromosomal analysis was performed using GTG-banded chromosomes at a resolution of 400-550 bands. Fluorescence in situ hybridization (FISH) was performed as described (with modification; Fukushi et al, 2003), with metaphase chromosome spreads obtained from both patients. Bacterial artificial chromosome (BAC) clones, RP11-533L19 (Xq27.1) and RP11-102A7 (Xp22; Thermo Fisher Scientific), fosmid clones, WI2-2895K2 (Xq27.1), WI2-3804K18 (Xq27.1), WI2-3562H11 (Xq28) and WI2-3825B5 (Xq28; BACPAC Resources Center), and IDS genomic DNA (exons 2-7; 13,998 bp) were used as probes.…”

Section: Cytogenetic Analysismentioning

confidence: 99%

Clinical and molecular genetic characterization of two female patients harboring the Xq27.3q28 deletion with different ratios of X chromosome inactivation

et al. 2020

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A heterozygous deletion at Xq27.3q28 including FMR1, AFF2, and IDS causing intellectual disability and characteristic facial features is very rare in females, with only 10 patients having been reported. Here, we examined two female patients with different clinical features harboring the Xq27.3q28 deletion and determined the chromosomal breakpoints. Moreover, we assessed the X chromosome inactivation (XCI) in peripheral blood from both patients. Both patients had an almost overlapping deletion at Xq27.3q28, however, the more severe patient (Patient 1) showed skewed XCI of the normal X chromosome (79:21) whereas the milder patient (Patient 2) showed random XCI. Therefore, deletion at Xq27.3q28 critically affected brain development, and the ratio of XCI of the normal X chromosome greatly affected the clinical characteristics of patients with deletion at Xq27.3q28. As the chromosomal breakpoints were determined, we analyzed a change in chromatin domains termed topologically associated domains (TADs) using published Hi‐C data on the Xq27.3q28 region, and found that only patient 1 had a possibility of a drastic change in TADs. The altered chromatin topologies on the Xq27.3q28 region might affect the clinical features of patient 1 by changing the expression of genes just outside the deletion and/or the XCI establishment during embryogenesis resulting in skewed XCI.

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“…For example, acetic acid treatment, drying, and heating affect alignment of chromatin fibers on the surface of barley somatic chromosomes, flattening the chromosomes and increasing arm width Fukushi et al 2003;Sugiyama et al 2004), all of which can cause inconsistency in cytological mapping depending on the technique used. The correspondence of pachytene chromosome 9 features (length, arm ratio, and relative FISH probe positions) on our preparations with squashed and 3D preparations presented by Wang et al (2006) indicate that during our FISH procedure, chromosomes keep their structure sufficiently well for reliable measurements both on pachytene and somatic preparations.…”

Section: Fish Probesmentioning

confidence: 99%

Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development

Danilova

Birchler

2008

Chromosoma

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To study the correlation of the sequence positions on the physical DNA finger print contig (FPC) map and cytogenetic maps of pachytene and somatic maize chromosomes, sequences located along the chromosome 9 FPC map approximately every 10 Mb were selected to place on maize chromosomes using fluorescent in situ hybridization (FISH). The probes were produced as pooled polymerase chain reaction products based on sequences of genetic markers or repeat-free portions of mapped bacterial artificial chromosome (BAC) clones. Fifteen probes were visualized on chromosome 9. The cytological positions of most sequences correspond on the pachytene, somatic, and FPC maps except some probes at the pericentromeric regions. Because of unequal condensation of mitotic metaphase chromosomes, being lower at pericentromeric regions and higher in the arms, probe positions are displaced to the distal ends of both arms. The axial resolution of FISH on somatic chromosome 9 varied from 3.3 to 8.2 Mb, which is 12-30 times lower than on pachytene chromosomes. The probe collection can be used as chromosomal landmarks or as a "banding paint" for the physical mapping of sequences including transgenes and BAC clones and for studying chromosomal rearrangements.

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Scanning Near-field Optical/Atomic Force Microscopy detection of fluorescence in situ hybridization signals beyond the optical limit

Cited by 20 publications

References 34 publications

Cytogenetic stability of chicken T‐cell line transformed with Marek's disease virus: atomic force microscope, a new tool for investigation

Cytogenetic stability of chicken T‐cell line transformed with Marek's disease virus: atomic force microscope, a new tool for investigation

Clinical and molecular genetic characterization of two female patients harboring the Xq27.3q28 deletion with different ratios of X chromosome inactivation

Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development

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