Construction of cosmid contigs and high-resolution restriction mapping of the Huntington disease region of human chromosome 4

Zuo, Jian; Robbins, Carolyn; Baharloo, Siamak; Dr, Cox; Myers, R

doi:10.1093/hmg/2.7.889

Cited by 19 publications

(13 citation statements)

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“…Genomic mappers and gene hunters would do well to pay attention to the staining intensi ties of their chromosome region of interest. A lightly-staining G-band usually contains many CpG islands and Notl sites, many coding sequences and a high density of Alu repeats, as exemplified by the HD region in 4p 16.3 (Zuo et al, 1993). A dark G-band is poor in coding sequences but rich in LI type interspersed repeats.…”

Section: Discussionmentioning

confidence: 99%

Digitized and differentially shaded human chromosome ideograms for genomic applications

Francke¹

1994

Cytogenet Genome Res

185

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Human chromosome ideograms that depict 850 bands, numbered in agreement with ISCN (1981) nomenclature but based on actual measurements of band sizes and differentiated by five shades of staining intensity, have been digitized using commercially available graphics software. They provide for more accurate estimates of distances within chromosome arms, DNA content of chromosome bands and correlation between cytogenetic, molecular and genetic linkage maps than the standard ISCN ideograms.

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Section: Discussionmentioning

confidence: 99%

Digitized and differentially shaded human chromosome ideograms for genomic applications

Francke¹

1994

Cytogenet Genome Res

185

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“…Our laboratories (Zuo et al 1993;Patil et al 1994) and others (e.g., see Baxendale et al 1993;Xie et al 1993;Murrell et al 1995) have generated cosmid contigs of several hundred kilobase stretches in a few regions of the human genome by using yeast artificial chromosome (YAC) clones to isolate cosmid clones. However, because we were unable to identify YAC clones in most of the segment of chromosome 21 containing the EPM1 gene, we used an alternative strategy to build a bacterial clone contig of the region.…”

Section: Strategymentioning

confidence: 99%

“…Hybridizations were performed in 1 M NaC1, 1% SDS, and 10% dextran sulfate for -16 hr at 65°C, and repetitive sequences were blocked with excess human placental DNA as described previously (Zuo et al 1993). Filters were washed three times in 0.1 X SSC, 0.1% SDS, at 65°C for 20 min.…”

Section: Hybridizationsmentioning

confidence: 99%

Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the progressive myoclonus epilepsy gene.

Stone¹,

Fan²,

Willour³

et al. 1996

Genome Res.

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The gene responsible for progressive myoclonus epilepsy of the Unverricht-Lundborg type (EPMI) is located on human chromosome 21q22.3 in a region defined by recombination breakpoints and linkage disequilibrium. As part of an effort to clone the EPM1 gene on the basis of its chromosomal location, we have constructed a 753-kb bacterial clone contig that encompasses the region containing the gene. Because DNA markers from the region did not identify intact yeast artificial chromosome (YAC) clones after screening several libraries, we built the contig from cosmid clones and used bacterial artificial chromosome (BAC) and bacteriophage PI clones to fill gaps. In addition to constructing the clone contig, we determined the locations of the E¢oRI, Sadl, EaBI, and Nod restriction sites in the clones, resulting in a high-resolution restriction map of the region. Most of the contig is represented by a level of redundancy that allows the orders of most restriction sites to be determined, provides multiple data points supporting the clone orders and orientations, and allows a set of clones with a minimum degree of overlap to be chosen for efficient additional analysis. The clone and restriction maps are in excellent agreement with maps generated of the region by other methods. These ordered bacterial clones and the mapping information obtained from them provide valuable reagents for isolating candidate genes for EPMI, as well as for determining the nucleotide sequence of a 750 kb region of the human genome.Progressive myoclonus epilepsy of the Unverricht-Lundborg type (EPM1) is inherited as an autosomal recessive disorder and is characterized by severe stimulus-sensitive myoclonus, tonicclonic seizures, and progressive neural degeneration. The age of onset is typically between 6 and 15 years. This condition is one of a group of five different subtypes of progressive myoclonus epilepsy, all of which show progressive neurodegeneration and variable degrees of severity. Unlike the other progressive myoclonus epilepsies, EPM1 is not characterized by biochemical markSCorresponding author. E-MAIL myers@shgc.stanford.edu; FAX (415) 725-9689.

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“…These subcloned probes, in addition to YAC end probes, gene markers, and MIT markers, can be further categorized into groups or "bins" (Zuo et al 1993). Each bin consists of markers that hybridize to the same set of YACs (Table 1).…”

Section: Subcloning Yacs To Obtain High Density Markers From the Lc Rmentioning

confidence: 99%

Generation of a high-resolution genetic map and a YAC contig of the Lurcher locus on mouse chromosome 6.

Zuo

Jager²,

Norman³

1995

Genome Res.

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Lurcher (L0 is a semidominant mouse mutant that displays progressive neurodegeneration during perinatal development. This genetic lesion results in apoptotic neuronal death in a dosage dependent and cell autonomous manner in specific neurons during their terminal differentiation. To understand the molecular basis of the Lc mutation, we have adopted a positional cloning approach based on its location on mouse chromosome 6. To define the Lc locus, we have extended our previous analysis of an intersubspecific backcross between Plus m. castaneus and B6CBACa-AW-~IA-Lc consisting of 504 animals [Norman et al. 1991). in addition, 580 animals of a generic backcross between Mus spretus and CS7BL/6 (The European Collaborative Interspecific Backcross) were utilized for the fine genetic mapping of the Lc locus. Using three RFLP markers and nine microsatellite markers in the vicinity of the Lc locus, we determined the order and relative genetic distances of these markers at a resolution of 0.1 cM. The Lc mutation was mapped between two flanking markers, D6Mitl21 and D61it175, separated by a genetic distance of 0.5 cM. We then initiated the cloning of the genomic region surrounding these two markers by screening a YAC library and characterizing YAC end sequences for further screening. This effort has resulted in the construction of a YAC contig consisting of 14 YACs and spanning a 3-Mb region. Markers isolated from these YACs were used to further define the Lc locus, resulting in a physical map that places the Lc gene within an estimated 300-kb interval. This set of YACs and markers will serve as DNA sources for the identification of the Lc gene.

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Construction of cosmid contigs and high-resolution restriction mapping of the Huntington disease region of human chromosome 4

Cited by 19 publications

References 0 publications

Digitized and differentially shaded human chromosome ideograms for genomic applications

Digitized and differentially shaded human chromosome ideograms for genomic applications

Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the progressive myoclonus epilepsy gene.

Generation of a high-resolution genetic map and a YAC contig of the Lurcher locus on mouse chromosome 6.

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