Greenham, Jaimie Alexanda; (1998) The identificaton and integration of transcripts mapping to human chromosome 16p12.2 - p12.1. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

This thesis describes the construction of a cosmid-based transcriptional map of human chromosome 16p12.2 - p12.1. Twenty-three cosmid contigs totalling just under 2Mb of DNA were analysed for CpG islands and unique EcoRl restriction fragments. Cosmids indicating coding potential were analysed for transcribed sequences using hybridisation-based screening of cDNA libraries, cDNA selection and exon trapping. Following mapping confirmation by Southern blot analysis, transcripts were sequenced and compared to sequences deposited in GenBank. Expression of novel sequences was confirmed by hybridisation to multiple tissue northern blots. Complementary to this analysis, genes and ESTs localised to the region by independent mapping projects were also integrated into the cosmid map. This was achieved by screening associated cDNAs against a chromosome 16 cosmid library. Seventeen cDNAs and nine exons have been integrated into the chromosome 16 cosmid-based physical map. Based on location, sequence overlap and expression profile, these cDNAs and exons are predicted to represent eleven different transcriptional units, of which ten map to chromosome 16p12 and three are known genes. SCNNJB and SCNNJG are related and code for the beta and the gamma subunits of the amiloride-sensitive epithelial sodium channel. PRKCB is alternatively spliced and codes for the protein kinase C beta 1 and beta 2 isoenzymes. Further analysis on the structure of the PRKCB gene identified 18 exons, including the alternatively spliced terminal exons, which span approximately 375kb. In an attempt to increase the number of genes mapping to human chromosome 16p12.2 - p12.1, studies to determine a region of synteny in the model genome of the Japanese pufferfish Fugu rubripes proved inconclusive.

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