Released chromatin: linearized DNA for high resolution fluorescence <i>in situ</i> hybridization

Senger, Gabriele; Ta, Jones; Fidlerová, Helena; Sanséau, Philippe; Trowsdale, John; Duff, M. J.; Sheer, Denise

doi:10.1093/hmg/3.8.1275

Cited by 51 publications

(15 citation statements)

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“…The chromosome preparations were then fixed in methanol for 30 min at -20°C. Chromatin fibers were prepared essentially as described by Senger et al (1994). Exponentially growing cells were harvested and fixed in Carnoy's fixative.…”

Section: In Situ Hybridization and G-bandingmentioning

confidence: 99%

Two extended arrays of a satellite DNA sequence at the centromere and at the short-arm telomere of Chinese hamster chromosome 5

Faravelli¹,

Moralli²,

Bertoni³

et al. 1998

Cytogenet Genome Res

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We have cloned a Chinese hamster chromosome-specific repeated sequence (SatCH5). This satellite is composed of a 33-bp unit organized in two extended tandem arrays. It is localized at the centromere and at the short-arm subtelomere of chromosome 5. Altogether, SatCH5 covers about 1–2 Mb per diploid genome and is not present in other species, including the Syrian hamster and mouse. Since it is known in the Chinese hamster and numerous other vertebrate species that telomeric (TTAGGG)_n repeats are localized at the centromeres of several chromosomes, we studied the localization of SatCH5 relative to (TTAGGG)_n sequences. Using two-color fluorescence in situ hybridization on stretched chromosomes and on DNA fibers, we have shown that at the centromere of chromosome 5 SatCH5 and the (TTAGGG)_n arrays are contiguous. SatCH5 is the first chromosome-specific repetitive sequence located at both the pericentromeric and subtelomeric regions of the same chromosome.

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Section: In Situ Hybridization and G-bandingmentioning

confidence: 99%

Two extended arrays of a satellite DNA sequence at the centromere and at the short-arm telomere of Chinese hamster chromosome 5

Faravelli¹,

Moralli²,

Bertoni³

et al. 1998

Cytogenet Genome Res

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“…The authors speculated that, with multicolor FISH, free chromatin mapping would readily resolve gene sequences separated by as little as 10 kb (Heng et al 1992). Soon thereafter, Senger et al (1994) and Fidlerova et al (1994) demonstrated the use of a sodium hydroxide/ethanol mixture or 70% formamide to prepare chromatin fibers which they called "free DNA." Hybridization signals from cosmid probes appeared as extended lines and overlaps between clones were determined using the lengths of the probe signals and their known kilobase size as an internal standard.…”

Section: Dna Fiber Mappingmentioning

confidence: 99%

DNA Fiber Mapping Techniques for the Assembly of High-resolution Physical Maps

Weier

2001

J Histochem Cytochem.

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S U M M A R Y High-resolution physical maps are indispensable for directed sequencing projects or the finishing stages of shotgun sequencing projects. These maps are also critical for the positional cloning of disease genes and genetic elements that regulate gene expression. Typically, physical maps are based on ordered sets of large insert DNA clones from cosmid, P1/PAC/BAC, or yeast artificial chromosome (YAC) libraries. Recent technical developments provide detailed information about overlaps or gaps between clones and precisely locate the position of sequence tagged sites or expressed sequences, and thus support efforts to determine the complete sequence of the human genome and model organisms. Assembly of physical maps is greatly facilitated by hybridization of non-isotopically labeled DNA probes onto DNA molecules that were released from interphase cell nuclei or recombinant DNA clones, stretched to some extent and then immobilized on a solid support. The bound DNA, collectively called "DNA fibers," may consist of single DNA molecules in some experiments or bundles of chromatin fibers in others. Once released from the interphase nuclei, the DNA fibers become more accessible to probes and detection reagents. Hybridization efficiency is therefore increased, allowing the detection of DNA targets as small as a few hundred base pairs. This review summarizes different approaches to DNA fiber mapping and discusses the detection sensitivity and mapping accuracy as well as recent achievements in mapping expressed sequence tags and DNA replication sites.

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“…Pixel data of fluorescence images were converted into physical lengths of DNA stretches as follows: first the relative lengths of signals and gaps as the unstained chromosome region between two signals were determined as described by Sjöberg et al (1997) to neutralize artificial differences due to the shape of pixels. Subsequently, the size of a gap flanked by a red and a green signal was estimated using probe size standards (PSS; Heiskanen et al, 1994;Senger et al, 1994;Florijn et al, 1995). Each probe served as PSS to measure the size of cohybridizing probes.…”

Section: In Situ Hybridization Detection and Analysis Of Signalsmentioning

confidence: 99%

Genomic organization of the bovine aromatase encoding gene and a homologous pseudogene as revealed by DNA fiber FISH

Brunner¹,

Goldammer²,

Fürbaß³

et al. 1998

Cytogenet Genome Res

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In cattle, the CYP19 locus comprises the aromatase cytochrome P450-encoding gene (CYP19) and a homologous pseudogene (CYP19P1). It has been assigned to chromosome region 10q26. Cloning of genomic DNA revealed that the CYP19 gene covers more than 56 kb. Its precise extent is still unknown because the DNA spanning the untranslated first exon 1.1 and the coding region (exons 2 to 10) have not been isolated. Furthermore, the chromosome arrangement of closely linked CYP19 and CYP19P1 was also not clear. To establish a high resolution physical map of the entire CYP19 locus, fluorescence in situ hybridization to extended bovine genomic DNA fibers (fiber FISH) was performed. The results demonstrate (1) that the clone containing exon 1.1 is located about 19 kb upstream from the CYP19 coding region. (2) Within the chromosome region 10q26 CYP19 and CYP19P1 are arranged “tail-to-head”, being separated by a distance of about 24 kb between the labeled clones. (3) The physical size of the bovine CYP19 locus amounts to a minimum of 130 kb.

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Released chromatin: linearized DNA for high resolution fluorescence in situ hybridization

Cited by 51 publications

References 0 publications

Two extended arrays of a satellite DNA sequence at the centromere and at the short-arm telomere of Chinese hamster chromosome 5

Two extended arrays of a satellite DNA sequence at the centromere and at the short-arm telomere of Chinese hamster chromosome 5

DNA Fiber Mapping Techniques for the Assembly of High-resolution Physical Maps

Genomic organization of the bovine aromatase encoding gene and a homologous pseudogene as revealed by DNA fiber FISH

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