A high resolution physical map of 2.5 Mbp of the Down syndrome region on chromosome 21

Abstract

The region surrounding D21S55 in band 21q22 of human chromosome 21 has been implicated in the etiology of Down syndrome (DS). In this paper, we report the construction of a high resolution map of a 2.5 Mb region around the marker D21S55. Characterization of YAC clones by accurate size determination, end isolation and marker assignment was used to build a refined YAC-based map. The YAC clones were then used to isolate 284 cosmid clones, covering 2.3 Mb, from a chromosome 21-specific cosmid library. The cosmid clones were ordered into overlapping groups and a restriction map of each group was determined. The groups of cosmids were then ordered and oriented with respect to the YAC-based map. This high resolution map provides the framework for further analysis of the region by transcribed sequence mapping and sequence determination.

Altered expression of Erg and Ets-2 transcription factors is associated with genetic changes at 21q22.2-22.3 in immortal and cervical carcinoma cell lines

“…Orientations of erg and ets-2 were derived from published data (Cre te et al, 1993;Shimizu et al, 1993). Physical linkage between erg and D21S55 was not established in this study; however, cosmid contig mapping places D21S55 proximal to erg, within 200 kb (Patil et al, 1994). The above fragment data combined with published contig data supports the proposed physical map.…”

“…To determine the nature of the observed altered fragments, a physical map ( Figure 2a) of the region containing these genes was constructed using DNA fragments from (HCX); fragment data from Table 1 were integrated with cosmid and yeast arti®cial chromosome (YAC) contig map data (Chumakov et al, 1992;Ochman and Buckholtz, 1995;Patil et al, 1994) to yield the map. 3' and 5'-ets-2 probes hybridized to adjacent 640 kb and 51000 kb NruI fragments, respectively, establishing a continuous region (within the resolution of fragment measurements) of 41.5 Mbp (Table 1, see HCX, Figure 1).…”

Localization of 102 exons to a 2.5 Mb region involved in Down syndrome

“…An attempt has been made to coordinate previously published mapping information about this region with this exon map. Therefore, the cosmids are annotated with letters to reflect those clones that have also been reported (12). Estimates of fragment sizes between various markers based on pulsed field gel electrophoresis and restriction fingerprinting of YACs (15,19,25) are given below the bottom scale along with the estimated size of the same fragment from this map in parentheses.…”

“…This cDNA detects a predominant 8 kb mRNA species that appears to be expressed at varying levels in all adult tissues assessed. The extensive amount of physical and genetic information and resources available for chromosome 21 was instrumental in allowing the construction of the next phase of higher resolution physical and transcript maps by us and others (11)(12)(13)(18)(19)(20). Our approach was to: (i) use the YAC map to identify a subset of cosmids for a 2.5 Mb region; (ii) bin the cosmids according to regions of YAC overlap; (iii) assay the cosmids for the presence of known markers; (iv) isolate exons from the cosmid bins; and (v) use the isolated exons as markers to further order cosmids within and between bins.…”

“…The last two methods are most amenable to gene isolation from megabase genomic regions. The successful application of direct cDNA selection for identifying genes from chromosome 21 has recently been reported (11)(12)(13). We have utilized exon amplification to isolate over 100 gene fragments from a 2.5 Mb region of chromosome 21 between loci CBR and ERG, which is present in three copies in common in many DS individuals with partial trisomy 21 (4,5,7,10).…”