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R. E. Carpio, V. Roni, W. Raffelsberger, B. Wissinger; Mapping of Transcription Start Sites of Human Retina Expressed Genes, a First Insight in the Control of its Gene Regulation. Invest. Ophthalmol. Vis. Sci. 2007;48(13):3787.
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© ARVO (1962-2015); The Authors (2016-present)
Proper assembly of the machinery carrying out transcription initiation is a key regulatory step in the execution of the correct program of mRNA synthesis and use of alternative transcription start sites (TSSs) is a mechanism for cell and tissue specific gene regulation. Our knowledge of transcriptional initiation sequences in the human genome is limited despite the availability of the complete genome sequence. Genome wide experimental and bioinformatics approaches are improving on the knowledge of TSSs, but they lack in information concerning genes expressed in a restricted manner or at very low levels, as tissue specific 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 and Luciferase Reporter gene Assay.
We report here the TSSs mapping of 54 retina expressed genes: we retrieved new sequences for 41 genes, some of which contain not yet annotated exons. Results can be grouped in five categories as 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. The new TSSs and transcribed sequences are essential for further exploration of the promoter and other cis-regulatory sequences at the 5'end of the genes.
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