Towards a Transcriptional Map of the q21-q22 Region of Chromosome 7

Procedures that directly select cDNAs from genomic DNA facilitate the rapid isolation of candidate genes from genomic DNA for the identification of genetic defects of known chromosome location. In such procedures, cDNA fragments are retrieved following the hybridization of cDNA pools to immobilized cosmid or YAC clones. This methodology is also applicable for the systematic identification of transcribed sequences over large regions of the genome. We propose to use such methodology to build a transcription map of the q21-q22 region of chromosome 7. This model region spans approximately 30 Megabases, corresponds to a light band with Giemsa staining and is therefore predicted to be relatively rich in genes. Extensive overlapping contigs of YAC clones from the q21-q22 region have been aligned and are being used as a starting resource. In total, over 120 YAC clones are being immobilized onto nylon filters and subjected to two rounds of hybridization with pooled cDNAs of combinations of fetal and adult tissues. Primary sources of cDNA are being generated with ends of known sequence such that each cDNA retains identification of tissue source and also instructs subsequent expansion as well as amplification and cloning steps. While the hybridization steps and washing conditions are critical, the nature of the sequences present in the starting genomic clones also influence the percentage of retrieved clones that map appropriately to the original YAC clones. We observe that rRNA or repetitive sequences are present in 4–30% of the retrieved clones, with 60–100% of those remaining originating from the correct YAC. Contributing to the population of clones that do not map appropriately are low copy repeat elements that are transcribed, pseudogenes or genes that are members of gene families. Through a combination of characterizations including physical mapping and RNA hybridization, the selected cDNAs will be arranged into tentative transcription units to provide the preliminary framework for a detailed transcription map of the region. This map will provide insight into the organization and function of this chromosome region. Further, the genes that are identified will provide candidates for the diseases and conditions that map to 7q21-q22.