High resolution physical map of the region surrounding the spinal muscular atrophy gene

Abstract

Spinal muscular atrophy (SMA) is the second most common lethal, autosomal recessive disease in Caucasians, second only to cystic fibrosis. In an effort to identify the causative gene in SMA, we have used radiation hybrid (RH) mapping to prepare a high resolution physical map of the proximal region of chromosome 5 (5q11-13) which contains the SMA gene. The map of the SMA region, which spans approximately 4 Mb, contains 19 loci including 9 polymorphic DNA markers, 8 monomorphic sequence tagged sites (STS) and two genes. Based upon the RH map the two polymorphic loci which most closely flank the SMA locus were estimated to be separated by approximately 750 kb. Using two different directional cloning schemes, several new clones between the genetic markers which most closely flank SMA were isolated. These new clones within the SMA candidate region, together with cosmid clones prepared from one RH hybrid which retains an approximately 1 Mb segment spanning the SMA region as its only human DNA, will greatly facilitate efforts to identify the gene for SMA. In addition, analysis of cloned DNA segments from within the SMA candidate region has identified the presence of a novel, chromosome 5-specific, low copy repeated sequence which is distributed throughout the region containing the SMA gene as well as in at least four other regions of chromosome 5. Whether or not these novel repeated sequences throughout the SMA region are involved in the disease remains to be determined.

A Radiation Hybrid Map of Human Chromosome 5 with Integration of Cytogenetic, Genetic, and Transcript Maps

“…Calibration of the chromosome 5 RH map using the total chromosome size of 194 Mb and the total length of the framework map of 7092 cR yielded 29 kb/cR. This is consistent with the 17-50 kb/cR range obtained with a previous radiation hybrid panel generated using the same dosage of radiation as in this study (Altherr et al 1992;Thompson et al 1993;Warrington and Bengtsson 1994;Warrington and Wasmuth 1996).…”

“…Some of these discrepancies may be attributable to the presence of the previously described chromosome 5-specific block repeats in the PCR products. The regions to which these apparent fragments hybridized were similar to the localization of the block repeats (Thompson et al 1993). It is also possible that the fragments observed in some of the sfRHs were collinear fragments derived during chromosomal repair immediately following the irradiation of the parental cell line.…”

“…Several regional RH maps focusing on specific disease loci or gene-dense segments of this chromosome have been reported previously (Warrington et al 1991(Warrington et al , 1992Ryan et al 1992; Thompson et al 1993;Warrington and Wasmuth 1996). Recently, whole-genome RH maps have become available [Hudson et al (1995) with supplementary data from the Whitehead Institute/MIT Center for Genome Research, data release 11 (October 1996); Schuler et al 1996; The Stanford Human Genome Center (SHGC, http://shgc.stanford.edu)], which naturally include markers on chromosome 5.…”

Expressed cadherin pseudogenes are localized to the critical region of the spinal muscular atrophy gene.

“…These events can cause mutations leading to genetic disease (1)(2)(3). Human chromosome 5 contains such an area at 5q13-14, where the abundance of low-copy repeats has been well documented (4)(5)(6)(7)(8)(9). Interestingly, the gene for spinal muscular atrophy (SMA) has been mapped in tight linkage to this region (10,11).…”

Application of comparative genomics in chicken gene mapping

“…Rh is based on strict experiments and methods of bioinformatics and the results should be accurate and reliable if performed exactly according to the protocols. Rh in the present study is a quick, precise and powerful tool in gene mapping and it contributes to the positional candidate gene cloning approach for hematopoietic regulatory factors and disease gene identification (Abel et al 1993;Thompson et al 1993;oshima et al 1994). as this approach is finding more and more applications, and the refinement of Rh map is improving, genomic research will benefit immensely.…”