Mapping of transcription start sites of human retina expressed genes

In this study we describe the mapping of TSSs of genes expressed in human retina. Genes have been selected on the basis of their physiological or developmental role in this tissue. Our work combines in silico analysis of ESTs and known algorithm predictions together with their experimental validation via Cap-finder RACE. We report here the TSSs mapping of 54 retina expressed genes: we retrieved new sequences for 41 genes, some of which contain un-annotated exons. Results can be grouped into five categories, compared to the RefSeq; (i) TSS located in new first exons, (ii) splicing variation of the second exon, (iii) extension of the annotated first exon, (iv) shortening of the annotated first exon, (v) confirmation of previously annotated TSS.In silico and experimental analysis of the transcripts proved to be essential for the ultimate mapping of TSSs. Our results highlight the necessity of a tissue specific approach to complete the existing gene annotation. The new TSSs and transcribed sequences are essential for further exploration of the promoter and other cis-regulatory sequences at the 5'end of genes.The spatial and temporal regulation of gene transcription is primarily determined by it's flanking promoter (cis-regulatory DNA elements) through interaction with trans-acting regulatory proteins (transcription factors) [1,2]. The start of transcription is accomplished by the formation of a pre-initiation complex on the DNA, yet our knowledge of transcriptional initiation sequences in the human genome is still limited despite the availability of the complete genome sequence [3,4]. Therefore one of the main remaining challenges is to locate these gene sequences, defined as the transcription start site (TSS), in order to explore core promoter and cis-regulatory elements that direct the start of every transcript. Genomic structure and full length cDNA sequences aligned on the genome provide opportunities to locate TSSs. Conventional methods for determining exact TSSs,