GENOMICS 45, 59–67 (1997) ARTICLE NO. GE974861 Cosmid Contig and Transcriptional Map of Three Regionsof Human Chromosome 21q22: Identification of 37 Novel Transcripts by Direct Selection Jordi Guimera,* ,1 Carles Pucharco ´ s,* ,1 Anna Dome `nech,* Cat y Casas,* Asun Solans,* Teresa Gallardo,† Jennifer Ashley,† Michael Lovett,† Xavier Estivill,* ,2 and Melanie Pritchard * ,2 * Molecular Genetics Department, Cancer Research Institute, Hospital Duran i Reynals, Avia. de Castelldefels Km 2,7, L’Hospitalet de Llobregat, 08907 Barcelona, Spain; and †Department of Otorhinolaryngology, Department of Molecular Biology, and Department of Oncology and the McDermott Center, University of Texas Southwestern Medical Center,5323 Harry Hines Boulevard, Dallas, Texas 75235-8591 Received January 10, 1997; accepted June 17, 1997 amyotrophic lateral sclerosis, holoprosencephaly, auto- Human chromosome 21 is associated with many dis- immune disorders, epilepsy, deafness, and susceptibil- orders, including Down syndrome (DS). In an effort to ity to bipolar affective disorder (St George-Hyslop et identify genes involved in brain development or func- al., 1987; Siddique et al., 1991; Muenke et al., 1995; tion and therefore implicated in the mental retarda- Aaltonen et al., 1994; Lehesjoki et al., 1991; Veske et tion associated with DS, we chose YACs from three al., 1996; Straub et al., 1994). Chromosome 21 is also regions of chromosome 21: a region within the so- associated with syndromic chromosomal aneuploidy, called ‘‘Down syndrome critical region,’’ a region prox- both monosomy and trisomy. Trisomy 21 or Down syn- imal to it, and one distal to it. We made cosmid libraries drome (DS) is one of the most frequent congenital de- from these YACs and generated high-resolution physi- fects, affecting 1 in 700 newborns, and is associated cal maps by constructing cosmid contigs. These are with mental retardation, heart disease, anomalies of the first cosmid contigs on chromosome 21 outside the the gastrointestinal tract, increased risk of childhood critical region. The cosmids were used for direct selec- leukemia, and defects of the immune and endocrine tion of cDNAs to isolate chromosome 21 expressed se- systems, as well as dysmorphic physical features (Ep- quences. We have isolated 45 nonredundant partial stein, 1986; Hassold and Jacobs, 1984). With the aim of cDNAs and mapped these back to the cosmid contigs. identifying candidate genes for some of these disorders, We isolated 3 nonoverlapping portions of DSCR1 and a intensive efforts have focused on the generation of tran- part of GIRK2 and identified 3 nonoverlapping partial scriptional maps (Cheng et al., 1994; Kao et al., 1994; cDNAs with similarity to the rat Dyrk gene, which turned out to be the human homologue (MNB) of the Peterson et al., 1994; Lucente et al., 1995; Tassone et Drosophila minibrain gene. Twelve sequences had al., 1995; Yaspo et al., 1995; Chen et al., 1996). High- matches with either STS or EST entries in the data- resolution physical maps have not kept pace with the bases, including a chromosome 21 EST, a chromosome transcriptional maps but it is imperative to develop 21 STS, and 6 unmapped expressed sequence entries. these to enable expressed sequences to be matched Only 1 sequence resulted in a match with a protein more precisely with disease candidate regions and also entry. The remaining 25 sequences revealed no simi- to enable the coverage of the transcriptional maps to larity to any database entry. All of these partial cDNAs be assessed. Regions of cosmids or individual cosmids are expressed as determined by Northern blotting or with no corresponding cDNAs can be systematically by RT-PCR.  1997 Academic Press searched for expressed sequences. Cosmids provide readily manipulable material for the isolation of genes and are also the resource of choice for large-scale se- INTRODUCTION quencing projects. High-resolution cosmid contig maps Numerous genetic diseases have been linked to hu- along with the positional information they provide also man chromosome 21, including Alzheimer disease, help in grouping cDNAs into transcriptional units. For instance, if nonoverlapping partial cDNAs map to the Sequence data from this article have been deposited with the Gen- Bank Data Library under Accession Nos. U81187 – U81231. 1 Both authors contributed equally to the work. Reynals, Avia. de Castelldefels Km 2,7, L’Hospitalet de Llobregat, 08907 Barcelona, Spain. Telephone: (34-3) 263 0039. Fax: (34-3) 263 2 To whom correspondence should be addressed at the Molecular Genetics Department, Cancer Research Institute, Hospital Duran i 2251. E-mail: mpritchard@iro.es or estivill@iro.es. 59 0888-7543/97 $25.00 Copyright  1997 by Academic Press All rights of reproduction in any form reserved.