Mapping of transcription start sites of human retina expressed genes

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Mapping of transcription start sites of human retina expressed genes

BioMed Central
Publication Date
Feb 07, 2007
  • Biology
  • Computer Science

Abstract ral ss BioMed CentBMC Genomics Open AcceResearch article Mapping of transcription start sites of human retina expressed genes Valeria Roni*, Ronald Carpio and Bernd Wissinger Address: Molecular Genetics Laboratory, University Eye Hospital, Roentgenweg 11, 72076 Tuebingen, Germany. Email: Valeria Roni* - [email protected]; Ronald Carpio - [email protected]; Bernd Wissinger - [email protected] * Corresponding author 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 TSS

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