GENOMICS 40, 267–276 (1997) ARTICLE NO. GE964595 Construction of a Transcription Map around the Gene for Ataxia Telangiectasia: Identification of at Least Four Novel Genes T ATJANA S TANKOVIC ,P HILIP J. BYRD,P AUL R. C OOPER ,C ARM EL M. M C C ONVILLE ,DAVID J. M UNROE ,* J OHN H. R ILEY,† GILES D. J. WATTS ,HELEN AM BROSE ,GERMAINE M C GUIRE ,ALEXANDRA D. S M ITH, A NDREW S UTCLIFFE ,T RACY M ILLS , AND A. M ALCOLM R. T AYLOR 1 CRC Institute for Cancer Studies, The Medical School, University of Birmingham, Birmingham, B15 2TA, United Kingdom; * Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; and †Zeneca, Alderley Park, Nr Macclesfield, Cheshire, SK10 4TG, United Kingdom Received August 21, 1996; accepted December 16, 1996 task (Collins, 1995). High-density transcription maps We have constructed YAC, PAC, and cosmid contigs are currently being constructed in two ways: first, in the ataxia – telangiectasia gene region and used the through systematic identification of transcribed se- assembled clones to isolate expressed sequences by quences across the whole genome and second, through exon trapping and hybridization selection. In the in- various positional cloning projects related to the identi- terval between D11S1819 and D11S2029, exons and fication of specific disease genes. While systematic cDNAs for potentially 13 different genes were identi- searches for transcribed sequences (expressed se- fied. Three of these genes, F37, K28, and 6.82, are large quence tag maps) offer the partial sequence of a large novel genes expressed in a variety of different tissues. number of genes, transcription maps derived by indi- K28 shows sequence homology to the Rab GTP binding vidual positional cloning projects are much more de- protein family and gene 6.82 homology to the rabbit tailed, as they usually provide information regarding vasopressin activated calcium mobilizing receptor, not only the number of genes in a particular region, while gene F37 has no homology to any known se- but also their orientation, order, distribution, and evo- quence in the database. Three further clones, exon 6.41 lutionary conservation as well as their pattern of ex- and cDNAs K22 and E74, from the interval between pression in different tissues. D11S1819 and D11S2029, appear to be expressed en- The gene for the recessively inherited disorder ataxia – dogenous retrovirus sequences. The fourth large novel telangiectasia (A-T) was cloned recently (Savitsky et al., gene, E14, together with two further possible novel 1995a). The identification of this gene followed several genes, E13 and E3, was identified from exons and years of genetic and physical mapping studies in different cDNAs in the more telomeric 300-kb interval between laboratories. A YAC contig of the A-T gene region (Rot- markers D11S2029 and D11S2179. These are in addi- man et al., 1994; Arai et al., 1996) and also a genomic tion to the genes for mitochondrial acetoacetyl-CoA- acetyltransferase (ACAT) and the ATM gene in the map (Ambrose et al., 1994) have been previously pub- same region. Genes E3, E13, and E14 do not show ho- lished. We have developed a refined physical map of 800 mology to any known genes. K28, 6.82, ACAT, and ATM kb–1 Mb of the A-T region and have derived a number all appear to have the same transcriptional orienta- of regional transcripts. Our map contains contigs built tion toward the telomere.  1997 Academic Press up by using three alternative cloning systems: YACs, cos- mids, and PACs. Various methods have been developed and described in detail for deriving transcripts. We used INTRODUCTION mainly exon amplification (Buckler et al., 1991; Church et al., 1994; Burfoot and Campbell, 1994), direct selection (Lovett et al., 1991), and screening of arrayed libraries The isolation and accurate mapping of genes is the (Munroe et al., 1995), but in addition we used evolution- major goal of the human genome mapping initiative. ary conservation and CpG island identification (Larsen The aim and expectation of this initiative is to develop et al., 1992; Rouleau et al., 1993). As a consequence of a transcription map of such density that positional these combined approaches, we assembled a transcrip- cloning of different disease genes will become an easy tion map of a region that includes the ATM gene and several novel widely expressed genes. Sequence data from this article have been deposited with the EMBL /GenBank Data Libraries under Accession Nos. X81882, MATERIALS AND METHODS X99961, X99962, and Y10269–Y10274. 1 To whom correspondence should be addressed. Telephone: 0121- Construction of YAC, cosmid, and PAC contigs. YACs from the region of the A-T gene were mostly obtained by screening the ICI 414-4488. Fax: 0121-414-4486. 267 0888-7543/97 $25.00 Copyright  1997 by Academic Press All rights of reproduction in any form reserved.