NEIBank: Est Analysis and Bioinformatics for Ocular Geno

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). A project called NEIBank was begun to improve the EST coverage and to develop a molecular encyclopedia for the eye (http://neibank.nei.nih.gov). Many human eye (and also ear)tissues and those of important animal models have now been analyzed. Recent additions are human and mouse lacrimal gland, keratoconus cornea, mouse retina and RPE and several libraries from dog, rabbit and zebrafish tissues. The human DNA resource generated by this work has been used to create cDNA microarrays with 13,000 non-redundant human eye expressed sequences and 6500 sequences from mouse eye. This database is also an important source of gene discovery. Several genes are under further investigation, including lengsin, a marker for terminal differentiation in the lens; PDGF-D, a important mitogen for lens development that is secreted into the aqueous humor and is also expressed in the outer plexiform layer of the retina; retbindin a candidate carotenoid binding protein of the retina; and a novel cornea-specific gene that may be associated with stem cell populations. Mouse models for the function of these genes are being developed using """"""""recombineering"""""""" technology. A recent addition to the informatics tools for eye research is EyeBrowse, a dedicated genome browser for eye-expressed genes, produced in collaboration with CIT. http://eyebrowse.cit.nih.gov/genome/

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Eye Institute (NEI)
• Type: Intramural Research (Z01)
• Project #: 1Z01EY000320-06
• Application #: 6968517
• Study Section: (MSF)
• Support Year: 6
• Fiscal Year: 2004

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

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

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

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