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. 1998 Jul 7;95(14):8141-6.
doi: 10.1073/pnas.95.14.8141.

Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site

D Mishmar  1 , A Rahat, S W Scherer, G Nyakatura, B Hinzmann, Y Kohwi, Y Mandel-Gutfroind, J R Lee, B Drescher, D E Sas, H Margalit, M Platzer, A Weiss, L C Tsui, A Rosenthal, B Kerem
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Free PMC article

Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site

D Mishmar et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

Common fragile sites are chromosomal loci prone to breakage and rearrangement, hypothesized to provide targets for foreign DNA integration. We cloned a simian virus 40 integration site and showed by fluorescent in situ hybridization analysis that the integration event had occurred within a common aphidicolin-induced fragile site on human chromosome 7, FRA7H. A region of 161 kb spanning FRA7H was defined and sequenced. Several regions with a potential unusual DNA structure, including high-flexibility, low-stability, and non-B-DNA-forming sequences were identified in this region. We performed a similar analysis on the published FRA3B sequence and the putative partial FRA7G, which also revealed an impressive cluster of regions with high flexibility and low stability. Thus, these unusual DNA characteristics are possibly intrinsic properties of common fragile sites that may affect their replication and condensation as well as organization, and may lead to fragility.

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Figures

Figure 1
Figure 1
A physical map across the 7q32 and FRA7H region. The order and extent of overlap of YAC clones was based on their DNA marker content. Distances from 7pter are shown in centirads (cR) and centimorgans (cM). Solid bar links DNA markers for which the local order could not be determined. •, genetic markers; ▪, ESTs/genes. Markers with no denotation are sequence-tagged sites (STSs) or unique DNA probes. Vertical bars within each YAC clone indicate the presence of a marker. YAC clones used for FISH analysis are colored. YAC clones that cover the same genomic region are marked by the same color. Solid box indicates the region shown in greater detail in Fig. 3. Information on this contig can be found in the Genome Database and at http://www.genet.sickkids.on.ca/chromosome7/.
Figure 2
Figure 2
Examples of hybridization signals centromeric and telomeric to FRA7H. FISH analysis was performed on metaphase chromosomes expressing FRA7H from two cell lines: GM00847 (A and C) and GM10791A (B). FISH experiments were performed with fluorescein isothiocyanate (FITC)-labeled YAC HSC7E186 (A and B) or cosmid 141e11 (C) cohybridized with a probe for chromosome 7 centromere. Propidium staining (left panel in each pair) and FISH with FITC-labeled probes (right panel in each pair) are shown. Arrows point to FRA7H.
Figure 3
Figure 3
A cosmid and PAC map covering the FRA7H region. P1-derived artificial chromosome (PAC) clones (name DJ_plate_row_column) and cosmids clones covering the region between markers D7S786 and 62D21–1.1 (see Fig. 1 for position within 7q32) are shown. Vertical bars along the horizontal baseline represent EcoRI sites. The region representing the 161-kb sequence contig is shown below. Asterisks indicate cosmids that were sequenced. Cosmids that were used for the FISH analysis are marked by colors. Clones covering the same region are marked by the same color.
Figure 4
Figure 4
Analysis of DNA flexibility. Arrows point to regions with significantly high flexibility. x axis, nucleotide position at the beginning of a 100-bp window. y axis, degrees of inclination in the twist angel. (A) FRA7H region. (B) Example of a control sequence, hsu52111. (C) FRA3B combined sequences.
Figure 5
Figure 5
Map of FRA7H showing DNA regions of high flexibility (▾), low stability (⧫), and non-B-DNA structure (formula image). The SV40 integration site and the ZNF131 pseudogene are marked. The numbers below the map represent the base location in FRA7H.
Figure 6
Figure 6
Non-B-DNA structure adopted by plasmid DNA containing site 10. Plasmid DNA with the 4.4-kb EcoRI fragment was unmodified (lanes 1 and 2) or modified with CAA (lanes 3 and 4). Lane 1, hydrazine reaction of control DNA. Lanes 2–4, formic acid reaction of control DNA (lane 2), CAA-treated DNA in the absence of Mg2+, at pH 7 (lane 3), and CAA-treated DNA in the presence of Mg2+, at pH 7 (lane 4). The nucleotide sequence is from FRA7H sequence. The asterisks mark sites that reacted prominently with CAA.
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References

    1. Sutherland G R, Richards R I. Curr Opin Genet Dev. 1995;5:323–327. - PubMed
    1. Oberle I, Rousseau F, Heitz D, Kretz C, Devys D, Hanauer A, Boue J, Bertheas M F, Mandel J L. Science. 1991;252:1097–1102. - PubMed
    1. Gecz J, Gedeon A K, Sutherland G R, Mulley J C. Nat Genet. 1996;13:105–108. - PubMed
    1. Jones C, Penny L, Mattina T, Yu S, Baker E, Voullaire L, Langdon W, Sutherland G, Richards R, Tunnacliffe A. Nature (London) 1995;376:145–149. - PubMed
    1. Kremer E J, Pritchard M, Lynch M, Yu S, Holman K, Baker E, Warren S T, Schlessinger D, Sutherland G R, Richards R I. Science. 1991;252:1711–1714. - PubMed

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