neibank: Est Analysis And Bioinformatics For Ocular Geno

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The eye is a complex system of highly differentiated tissues of various developmental origins. Many genes essential for eye function are tissue-specific and many of those known are associated with genetic eye diseases. The majority of human expressed genes are known only through expressed sequence tags (ESTs). However many eye tissues have been poorly represented in the cDNA libraries that have so far contributed to dbEST. To address this situation a project, NEIBank, has been initiated to improve the EST coverage of the human eye and to develop a molecular encyclopedia for the eye. cDNA libraries for several human eye tissues, including lens,iris,RPE/choroid, retina and trabecular meshwork have been constructed and examined by in-depth sequencing. Between 2,000 and 10,000 clones from each un-normalized library have been sequenced, analyzed and clustered using custom software, GRIST. Lens and iris libraries have been normalized for deeper sequence. Libraries for rat whole eye, iris/ciliary body/TM and retina and mouse whole eye, retina and RPE/choroid have also been created. Other libraries, including human lacrimal galnd have been contributed to the analysis. Many novel genes have been identified, including opticin/oculoglycan (an eye-specific leucine-rich repeat protein whose gene maps close to ARMD), lengsin (LGS)(an abundant lens specific transcript related to glutamine synthetase and a marker for terminal differentiation in the lens, oculospanin in iris and RPE, IEGF (iris-expressed growth factor), which is a VEGF/PDGF relative, and retbindin, a novel secreted protein of the retina that is related to flavionoid binding proteins. In addition we have identifed numerous alternative splice forms of important eye transcripts that could give rise to modified proteins. These include a larger version of the lens membrane protein MP19/Lim2 and modifed versions of Nrl, a retina transcriptoin factor, and Bestrophin, a protein of the retinal pigment epithelium. In total, approximately 20,000 ocular cDNA clones, representing over 12,000 individual GRIST clusters (potential genes), have been sequenced and organized in a web-based database (neibank.nei.nih.gov)that contains keyword and chromosomal location data. The DNA resource generated by this work is now being used to create micro-arrays for ocular studies. The GRIST procedure is also being used to analyse similar data for projects in NIDCD.