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

Abstract

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.

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

“…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). Here we report a high-resolution physical map of approximately 5.8 Mb in the proximal region of human Chr 21q22A.…”

“…Oligonucleotide sequences of each STS primer, except the markers that were newly developed for this study (Table 1), were obtained from the following sources: The YAC end-specific STSs used (from D21S 1677 to D21S 1709) were generated by Abe and associates (1995); the anonymous SfiI-linking STSs Sf-10UV, Sf-ll3UV, Sf-431UV, and Sf-624UV were reported by Tanahashi and colleagues (1994); and the geue-specific STSs CRFB4 for member 4 of cytokine receptor family II gene, IFNAR for interferon-ct receptor gene, IFNGT1 for interferon-3, transducer 1 gene, and GART for glycinamide ribonucleotide transformylase gene were developed from their sequences (Eki et al 1996). The NotI-linking clones for LB10T, LJ87, LA37, LA38 (D21S239), LB63T (D21S 1467), and LB 19S (D21S 1466) were provided by Ichikawa and Ohki (National Cancer Center Research Institute).…”

“…YAC DNA was partially digested in the presence of appropriately diluted amounts of the enzyme at 37~ for l0 h, except that SfiI was digested at 50~ After digestion, DNA was fractionated at 14~ in a 1% agarose gel (agarose NA, Pharmacia LKB) in 0.5 X TBE buffer, with a Bio-Rad (CHEF-DRII or CHEF Mapper) or Pharmacia LKB (Pulsaphor) apparatus for pulsed-field gel electrophoresis (PFGE). After the fractionated DNA was photographed with a scale, it was analyzed by Southern hybridization with each YAC end-specific probe as previously described in detail (Eki et al 1996). With the results of this analysis, the distances of the cleavage sites from each vector arm were determined, and these distances were used to map the restriction sites in the insert DNA.…”

“…Each YAC arm-specific probe used to generate YAC restriction maps was prepared by the PCR amplification, with a pair of the specific oligonucleotides and pYAC4 DNA as a template. Hybridizations were carried out as described in our previous report (Eki et al 1996).…”

Bacterial Contig Map of the 21q11 Region Associated with Alzheimer’s Disease and Abnormal Myelopoiesis in Down Syndrome

“…The map proceeded from a very early detailed genetic map (Antonarakis et al 1989;McInnis et al 1993) and a whole chromosome NotI restriction map (Ichikawa et al 1993), accompanied by YAC overlap maps (Chumakov et al 1992;Patterson et al 1993;Nizetic et al 1994;Korenberg et al 1995) and an integrated cosmidpocket map of the entire chromosome , to megabase-size bacterial contigs of selected regions Lafreniere et al 1995;Eki et al 1996;Osoegawa et al 1996;Ohira et al 1996;Stone et al 1996;Hubert et al 1997) as well as global and regional transcriptional maps (Cheng et al 1994;Peterson et al 1994;Lucente et al 1995;Tassone et al 1995, Yaspo et al 1995Chen et al 1996). Though one of the most advanced among whole human chromosome maps, the chromosome 21 map is still not sufficiently complete in its proximal half to enable detailed transcriptional mapping and large-scale sequencing.…”