""""""""NEIBANK: EST Analysis and Bioinformatics for Ocular Genomics""""""""

Wistow, Graeme J.

Abstract

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. cDNA libraries for human lens, ciliary body/iris,RPE/choroid, retina and cornea have been constructed and examined by in-depth sequencing. Typically 2000 clones from each un-normalized library have been sequenced, analyzed and clustered. Libraries for rat iris/ciliary body/TM and retina have also been created. Several novel genes have been identified, including Oculoglycan (an eye-specific LRR protein whose gene maps close to ARMD), lengsin (LGS)(an abundant lens specific transcript related to glutamine synthestase), Oculospanin (a novel tetraspan that maps to chr17, close to the disease locus RP17), Iris-derived growth factor (a VEGF relative) and many others. Lens and iris libraries have been normalized for deeper sequence. The RPE library has produced over 8000 sequences. So far approximately 20,000 ocular cDNA clones, representing about 10,000 individual clusters (potential genes), have been sequenced and organized in a web-based database that contains keyword and chromosomal location data. This resource is now being used to create micro-arrays for ocular studies.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Eye Institute (NEI)
• Type: Intramural Research (Z01)
• Project #: 1Z01EY000320-02
• Application #: 6432479
• Study Section: (MSF)
• Support Year: 2
• Fiscal Year: 2000

Institution

• Name: U.S. National Eye Institute
• Country: United States

Publications

Wistow, Graeme; Peterson, Katherine; Gao, James et al. (2008) NEIBank: genomics and bioinformatics resources for vision research. Mol Vis 14:1327-37

Harding, Rachel L; Howley, Sinead; Baker, Lee J et al. (2008) Lengsin expression and function during zebrafish lens formation. Exp Eye Res 86:807-18

Purkiss, Andrew G; Bateman, Orval A; Wyatt, Keith et al. (2007) Biophysical properties of gammaC-crystallin in human and mouse eye lens: the role of molecular dipoles. J Mol Biol 372:205-22

Popp, Michael P; Liu, Li; Timmers, Adrian et al. (2007) Development of a microarray chip for gene expression in rabbit ocular research. Mol Vis 13:164-73

Wistow, Graeme (2006) The NEIBank project for ocular genomics: data-mining gene expression in human and rodent eye tissues. Prog Retin Eye Res 25:43-77

Wyatt, Keith; White, Helen E; Wang, Luchun et al. (2006) Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. Structure 14:1823-34

Bowes Rickman, Catherine; Ebright, Jessica N; Zavodni, Zachary J et al. (2006) Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE. Invest Ophthalmol Vis Sci 47:2305-16

Vihtelic, Thomas S; Fadool, James M; Gao, James et al. (2005) Expressed sequence tag analysis of zebrafish eye tissues for NEIBank. Mol Vis 11:1083-100

Rabinowitz, Yaron S; Dong, Lijin; Wistow, Graeme (2005) Gene expression profile studies of human keratoconus cornea for NEIBank: a novel cornea-expressed gene and the absence of transcripts for aquaporin 5. Invest Ophthalmol Vis Sci 46:1239-46

Ozyildirim, Aylin M; Wistow, Graeme J; Gao, James et al. (2005) The lacrimal gland transcriptome is an unusually rich source of rare and poorly characterized gene transcripts. Invest Ophthalmol Vis Sci 46:1572-80