High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes

Florijn, Ralph J.; Bonden, L A; Vrolijk, Hans; Wiegant, J.; Vaandrager, Jan‐Willem; Baas, Frank; Dunnen, Johan T. den; Tanke, Hans J.; Ommen, G J van; Raap, Anton K.

doi:10.1093/hmg/4.5.831

Cited by 130 publications

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“…So, the Watson-Crick standard method has been used for several studies (PARRA and WINDLE 1993;Florijn et al 1995;HEISKANEN et al 1995;S J~B E R G et al 1997) to estimate the size of clones and the physical distances between them. The estimations from fiber-FISH mapping have been found to be in good agreement with the one from restriction mapping by PFGE analysis HEISKANEN et al 1995;SJOBERG et al 1997).…”

Section: Discussionmentioning

confidence: 99%

“…This technique is based on the hybridization of probes to unfixed linearized DNA fibers on glass slide, and has been used to establish the order, orientation and size of several probes (PARRA and WINDLE 1993;HOULEAS et al 1994;HAAF and WARD 1994;FLORIJN et al 1995;KLOCKARS et al 1996;SJOBERG et al 1997;SHIELS et al 1997), to rapidly identify aberrations and rearrangements of genes (HEISKANEN et al 1995) and also to directly visualize the DNA replication (ROSENBERG et al 1995) and exon mapping (FLORIJN et a]. 1996).…”

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Fiber-FISH Analysis of the 3'-Terminal Region of the Human L-Type Ca2+ Channel α1C Subunit gene

et al. 2004

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. and Chowdhary, B. P. 1998. Fiber-FISH analysis of the 3'-terminal region of the human L-type Ca'+ channel alC subunit gene. -Hwtditus 129: 169-175. Lund, Sweden. lSSN 0018-0661. Received May 4, 1998. Accepted November 8, 1998 Human L-type Ca'+ channel a,, subunit gene (CACNLIAI) maps to the distal region of chromosome 1 2~1 3 .and is composed of z 50 exons spanning over 150 kb of the human genome as estimated by restriction map analysis. However, the structure and the total length of the 3'-end of the gene is not clear because the size of several big introns remains unknown. Here the fiber-FISH technique was used to determine the relative order and size of eight partial genomic DNA clones from the central and 3'-terminal regions of CACNLIAI. The total physical distance of this region, including the size and gap distances between the clones were re-estimated. The results show that the physical order of the tested clones was 5'-g14-5 > g12-2 > g10-8 > g4-5 > g16-7 > g8-3 > g12-5 > g6-20 -3'. Their individual sizes vary between 6.7 and 21.9 kb. Clones g6-20 and g12-5, both containing repetitive exon 45;46-Iike element, were found to be located within 59.1 kb downstream of g8-3 containing earlier identified polyadenylation site, i t . 229.5 kb away from clone g14-5 (exons 10. 1 I ) . The possible implications of this structural complexity is discussed.Wan-SlimgLiu, Deptirtirient of' Generics, Uppsuliz Unirersiry, Bou sheng.liu@genetik.uu.se High resolution visual mapping of stretched DNA by fluorescent in situ hybridization (termed fiber-FISH) has recently been developed (WIEGANT et al. 1992; F~DLEROVA et al. 1994;SENGER et al. 1994;HEISKANEN et al. 1994HEISKANEN et al. , 1995HEISKANEN et al. , 1996. This technique is based on the hybridization of probes to unfixed linearized DNA fibers on glass slide, and has been used to establish the order, orientation and size of several probes (PARRA and WINDLE 1993;HOULEAS et al. 1994;HAAF and WARD 1994;FLORIJN et al. 1995;KLOCKARS et al. 1996;SJOBERG et al. 1997;SHIELS et al. 1997), to rapidly identify aberrations and rearrangements of genes (HEISKANEN et al. 1995) and also to directly visualize the DNA replication (ROSENBERG et al. 1995) and exon mapping (FLORIJN et a]. 1996). In combination with digital image microscopy, fiber-FISH is becoming a powerful tool for high resolution genome mapping.L-type Ca2+ channel is a member of the family of voltage-dependent ion channels. Human L-type Ca2 + channel sllC subunit gene (CACN L I Al) is composed of over 50 exons (SOLDATOV 1994) and is located in the distal region of chromosome 1 2~1 3 (SUN et al. 1992). Recently we found in clones g6-20 and g12-5 a new repetitive element of paired exon 45/46-related sequences and co-localized them to the 3'-terminal part of the a I C subunit gene by fluorescent in situ hybridization technique (SOLDATOV et al. 1998). According to PCR analysis, clone g12-5 overlaps over a 7003, SE-750 07 Uppsiilu, Swtten. E-mail: wanshort distance with g8-3. However, we failed to identify the exact position...

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Section: Discussionmentioning

confidence: 99%

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Fiber-FISH Analysis of the 3'-Terminal Region of the Human L-Type Ca2+ Channel α1C Subunit gene

et al. 2004

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“…3551 ± 3571). Hybridization procedures, immunologic detection and¯uorescence microscopy were performed as described in (Florijn et al, 1995) …”

Section: Discussionmentioning

confidence: 99%

Visualization of mono-allelic chromosomal aberrations 3′ and 5′ of the cyclin D1 gene in mantle cell lymphoma using DNA fiber fluorescence in situ hybridization

et al. 1997

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In mantle cell lymphoma (MCL), in addition to the characteristic t(11;14)(q13;q32), rearrangements on the 3' side of the cyclin D1 gene have been described. In a series of 32 MCL we found three cases with 3'-rearrangements by Southern blot analysis with a probe representing the 3' untranslated region of the cyclin D1 gene. All three were characterized by the absence of the 4.5 kb transcript, and instead, two cases showed overexpression of the 1.7 kb and a third case (MCLp14) an aberrant 2.5 kb transcript. At the genomic level, ®ne mapping experiments showed in the 3' untranslated region a 2 kb deletion in MCLp14 and a breakpoint in the other two cases. Fiber FISH analysis showed that in all three cases the 3' aberration co-exists with a regular t(11;14) breakpoint 5' of cyclin D1 on a single allele. Fiber FISH analysis of 16 additional MCL revealed two other such cases with breakpoints 5' and 3' of cyclin D1. These mono-allelic aberrations aecting the cyclin D1 gene suggest that the t(11;14) as a ®rst step switches on transcription, and then sequences in the untranslated region of cyclin D1 are aected to stabilize the message.

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“…There are diferent applications which used FISH-based methods like reverse-FISH [27], ibre-FISH [28,29], M-FISH (multicolor FISH) [30], SKY (spectral karyotyping FISH) [31], low-FISH [32], Q-FISH (quantitative FISH) [33], COBRA-FISH (combined binary ratio labelling FISH) [34], cenM-FISH (centromere-speciic M-FISH) [35], podFISH (parental origin determination FISH) [36] and heterochromatin-M-FISH [37]. The most advanced FISH-based approaches included COBRA-FISH, M-FISH and SKY.…”

Section: Fish Developmentmentioning

confidence: 99%

The Use of Molecular Cytogenetic Techniques for the Identification of Chromosomal Abnormalities

Kalkan¹

2017

Chromosomal Abnormalities - A Hallmark Manifestation of Genomic Instability

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Chromosomal analysis is an increasingly important diagnostic procedure in numerous areas of clinical medicine that includes haematology, perinatology or obstetrics. Chromosomal disorders are viewed as a major category of genetic diseases, and sometimes the identiication of abnormal chromosomes is not easily applicable. Just like the identiication of the marker chromosome or the identiication of the complex karyotypes is important in clinics for the evaluation of the patient prognosis as well as the treatment response, needless to say; luorescence in situ hybridization (FISH) is the most suitable and rapid method in the above-mentioned situations. It gives chance to the rapid analysis of chromosomal aneuploidies in dividing and non-dividing cells. In this chapter, we will discuss the general principles of the chromosomal abnormalities and the molecular cytogenetic techniques that can help the identiication of presence or absence of a particular DNA sequence or the evaluation of the number of organization of a chromosome or chromosomal region.

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High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes

Cited by 130 publications

References 0 publications

Fiber-FISH Analysis of the 3'-Terminal Region of the Human L-Type Ca2+ Channel α1C Subunit gene

Fiber-FISH Analysis of the 3'-Terminal Region of the Human L-Type Ca2+ Channel α1C Subunit gene

Visualization of mono-allelic chromosomal aberrations 3′ and 5′ of the cyclin D1 gene in mantle cell lymphoma using DNA fiber fluorescence in situ hybridization

The Use of Molecular Cytogenetic Techniques for the Identification of Chromosomal Abnormalities

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