BMC Genomics Research article Mapping of transcription start sites of human retina expressed genes Valeria Roni*, Ronald Carpio and Bernd Wissinger BioMed Central Open Access Address: Molecular Genetics Laboratory, University Eye Hospital, Roentgenweg 11, 72076 Tuebingen, Germany. Email: Valeria Roni* - valeria.roni@uni-tuebingen.de; Ronald Carpio - neuro100cia@yahoo.com; Bernd Wissinger - wissinger@uni- tuebingen.de * Corresponding author Published: 7 February 2007 BMC Genomics 2007, 8:42 doi:10.1186/1471-2164-8-42 This article is available from: http://www.biomedcentral.com/1471-2164/8/42 Received: 26 October 2006 Accepted: 7 February 2007 © 2007 Roni et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The proper assembly of the transcriptional initiation machinery is a key regulatory step in the execution of the correct program of mRNA synthesis. The use of alternative transcription start sites (TSSs) provides 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. While genome wide experimental and bioinformatic approaches are improving our knowledge of TSSs, they lack information concerning genes expressed in a restricted manner or at very low levels, such as tissue specific genes. Results: 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. Conclusion: 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. Background The spatial and temporal regulation of gene transcription is primarily determined by it's flanking promoter (cis-reg- ulatory DNA elements) through interaction with trans-act- ing 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 com- plete 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 pro- vide opportunities to locate TSSs. Conventional methods Page 1 of 14 (page number not for citation purposes)