Generation of 28 sequence-tagged sites (STSs) from yeast artificial chromosome (YAC) clones anchored at human chromosome 21q22.1 region

Abe, Makoto; Furuya, Kaori; Fujishima, Naoe; Shiratori, Akiko; Arai, Takahiro; Sakakura, Teruyo; Yokoyama, Kazushige; Paslier, Denis Le; Cohen, Daniel; Murakami, Yasufumi; Eki, Toshihiko

doi:10.3109/10425179509030973

Cited by 2 publications

(3 citation statements)

References 16 publications

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“…Three different conditions (A-C) of PCR were used to determine the size of amplified DNA. PCR was carried out for 35 cycles (A and B) or for 30 cycles (C) at 94~ (20 s) for denaturation, 65~ (A and C) or 55~ (B) for annealing (30 s), and at 72~ (1 min) for elongation in the reaction mixture reported previously (Abe et al 1995) in a GeneAmp PCR System 9600 thermal cycler (Perkin-Elmer, Foster City, Calif.).…”

Section: Methodsmentioning

confidence: 99%

“…To rescue the right arm, the primer sets YR(YAC Right arm)-#1 (#B5617 and #/35951) for HinclI, YR-#4 (#135617 and #B5673) for AtuI, and YR-#5 (#B5617 and #B6888) for PstI and EcoRV were used. The vector-insert junctions were isolated as described in our previous paper (Abe et al 1995). A pair of STS oligonucleotides was designed on the basis of the unique nucleotide sequences of the obtained fragment and its chromosomal location tested by the PCR with the panel DNAs from monochromosomal human-rodent hybrids (NIGMS Human/Rodent Somatic Cell Hybrid Mapping Panel #2, Coriell Cell Repositories, Camden, NJ).…”

Section: Preparation Of Yac End-specific Stssmentioning

confidence: 99%

“…We previously generated STSs specific to Chr 21 and isolated YACs anchored at these loci around the 21q22.1 region (Tang et al 1992;Eki et al 1991;Abe et al 1995). More recently, we reported a high-resolution physical map of the 1.8-Mb region at the distal portion of the 21q22.1 region, which encompasses the interferon-c~ receptor gene (IFNAR) and AML1 loci (Eki et al 1996).…”

Section: Introductionmentioning

confidence: 97%

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A long-range physical map of human Chromosome 21q22.1 band from the YAC continuum

et al. 1996

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The human Chromosome (Chr) 21q22.1 region contains several genes for cytokines and neurotransmitters and the gene for superoxide dismutase (mutant forms of which can cause familial amyotrophic lateral sclerosis). A region of approximately 5.8 Mb encompassing D21S82 and the glycinamide ribonucleotide transformylase (GART) loci was covered by overlapping YAC clones, which were contiguously ordered by clone walking with sequence-tagged site (STSs). A total of 76 markers, including 29 YAC end-specific STSs, were unambiguously ordered in this 5.8-Mb region, and the average interval between markers was 76 kb. Restriction maps of the YAC clones with rare-cutting enzymes were simultaneously prepared, and the restriction sites were aligned to obtain a consensus restriction map of the proximal region of the 21q22.1 band. The restriction map made from 44 overlapping YACs contains 54 physically assigned STSs. By integrating the consensus map of the adjacent 1.8-Mb region, we obtained a fine physical map spanning 6.5 Mb of human Chr 21q22.1. This map contains 24 precisely positioned end-specific STSs and 12 NotI-linking markers. More than 39 potential CpG islands were identified in this region and were found to be unevenly distributed. This physical map and the YACs should be useful as a reference map and as a resource for further structural analysis of the Giemsa-negative band (R-band) of Chr 21q22.1.

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Section: Methodsmentioning

confidence: 99%

Section: Preparation Of Yac End-specific Stssmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

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A long-range physical map of human Chromosome 21q22.1 band from the YAC continuum

et al. 1996

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1.8–megabases fine physical map encompassing IFNAR and AML1 loci on human chromosome 21q22.1

Eki¹,

Abe²,

Furuya³

et al. 1996

DNA Sequence

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A long-range restriction map of the 1.8-megabases (mb) region encompassing the area between the interferon-alpha receptor and the acute myelogenous leukemia loci on human chromosome 21q22.1 was constructed after analysis of both the contiguous yeast artificial chromosome (YAC) clones and genomic DNA. Analysis of pulsed-field gel electrophoresis of lymphoblastoid DNA digested with three rare-cutting enzymes, Not I, Mlu I, and Nru I, revealed the positions of 17 markers on each restriction map. The 1.8-mb YAC contig that covers this region was obtained through YAC walking mediated by sequence-tagged sites (STSs), with 29 STSs including 12 newly generated YAC end-specific STSs. The consensus restriction map from 15 overlapping YACs and the positioning of the STS markers on each clone allowed 24 markers including 4 Not I-linking STSs to be ordered and mapped physically. Comparison of the maps revealed that the proximal region contains more unmethylated CpG islands than the distal region, which suggests that many expressed genes are in the proximal region. This fine consensus physical map will be informative and useful for construction of contigs of cosmid, P1, or BAC clones for further large-scale sequencing in this gene-rich region.

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Generation of 28 sequence-tagged sites (STSs) from yeast artificial chromosome (YAC) clones anchored at human chromosome 21q22.1 region

Cited by 2 publications

References 16 publications

A long-range physical map of human Chromosome 21q22.1 band from the YAC continuum

A long-range physical map of human Chromosome 21q22.1 band from the YAC continuum

1.8–megabases fine physical map encompassing IFNAR and AML1 loci on human chromosome 21q22.1

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