Gene discovery in the embryonic chick retina

Abigail S Hackam, Rebecca L. Bradford, Rita N. Bakhru, Raza M. Shah, Ronald Farkas, Donald J. Zack, Ruben Adler

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Purpose: The chick embryo is a powerful model system for the study of retinal development. However, analysis of gene expression in the chick retina has lagged behind biological studies. The purpose of this study was to identity and characterize genes expressed in the chick embryo retina as candidate molecules involved in the development and function of photoreceptors and other retinal cell types. Methods: RNA from embryonic day (ED) 18 White Leghorn chick embryo retinae was used to generate an oligo dT-primed cDNA library. Bacterial colonies representing five thousand individual clones were arrayed onto nylon membranes using a microarray robot. Replicate membranes were hybridized with cDNA probes synthesized from ED 18 retina, brain and liver. Clones that appeared preferentially expressed in retina were identified by homology searches, and their spatial and temporal expression patterns were analyzed by in situ hybridization. Results: Two hundred and seventy-two clones were identified. Approximately forty percent of the clones represented potential novel genes, including ESTs, hypothetical proteins and clones with no assigned identities. Furthermore, many genes were identified that are the putative chick orthologues of genes cloned from other species. We determined the expression pattern of several clones for which sequence homologies suggested possible roles in transcriptional regulation, apoptosis or intercellular signaling. Their corresponding mRNAs were expressed in the embryonic retina in topographically specific, developmentally regulated patterns. Conclusions: We identified and characterized genes in the chick embryo retina using a combination of microarray analysis and in situ hybridization. Analysis of the expression patterns suggests involvement of several of these genes in key events during embryogenesis.

Original languageEnglish
Pages (from-to)262-276
Number of pages15
JournalMolecular Vision
Volume9
StatePublished - Dec 1 2003
Externally publishedYes

Fingerprint

Genetic Association Studies
Retina
Clone Cells
Chick Embryo
Genes
In Situ Hybridization
Vertebrate Photoreceptor Cells
Membranes
Nylons
Expressed Sequence Tags
Microarray Analysis
Sequence Homology
Gene Library
Embryonic Development
Complementary DNA
RNA
Apoptosis
Gene Expression
Messenger RNA
Liver

ASJC Scopus subject areas

  • Ophthalmology

Cite this

Hackam, A. S., Bradford, R. L., Bakhru, R. N., Shah, R. M., Farkas, R., Zack, D. J., & Adler, R. (2003). Gene discovery in the embryonic chick retina. Molecular Vision, 9, 262-276.

Gene discovery in the embryonic chick retina. / Hackam, Abigail S; Bradford, Rebecca L.; Bakhru, Rita N.; Shah, Raza M.; Farkas, Ronald; Zack, Donald J.; Adler, Ruben.

In: Molecular Vision, Vol. 9, 01.12.2003, p. 262-276.

Research output: Contribution to journalArticle

Hackam, AS, Bradford, RL, Bakhru, RN, Shah, RM, Farkas, R, Zack, DJ & Adler, R 2003, 'Gene discovery in the embryonic chick retina', Molecular Vision, vol. 9, pp. 262-276.
Hackam AS, Bradford RL, Bakhru RN, Shah RM, Farkas R, Zack DJ et al. Gene discovery in the embryonic chick retina. Molecular Vision. 2003 Dec 1;9:262-276.
Hackam, Abigail S ; Bradford, Rebecca L. ; Bakhru, Rita N. ; Shah, Raza M. ; Farkas, Ronald ; Zack, Donald J. ; Adler, Ruben. / Gene discovery in the embryonic chick retina. In: Molecular Vision. 2003 ; Vol. 9. pp. 262-276.
@article{73c9aacd89d24c6d92d2acdbaa5a3351,
title = "Gene discovery in the embryonic chick retina",
abstract = "Purpose: The chick embryo is a powerful model system for the study of retinal development. However, analysis of gene expression in the chick retina has lagged behind biological studies. The purpose of this study was to identity and characterize genes expressed in the chick embryo retina as candidate molecules involved in the development and function of photoreceptors and other retinal cell types. Methods: RNA from embryonic day (ED) 18 White Leghorn chick embryo retinae was used to generate an oligo dT-primed cDNA library. Bacterial colonies representing five thousand individual clones were arrayed onto nylon membranes using a microarray robot. Replicate membranes were hybridized with cDNA probes synthesized from ED 18 retina, brain and liver. Clones that appeared preferentially expressed in retina were identified by homology searches, and their spatial and temporal expression patterns were analyzed by in situ hybridization. Results: Two hundred and seventy-two clones were identified. Approximately forty percent of the clones represented potential novel genes, including ESTs, hypothetical proteins and clones with no assigned identities. Furthermore, many genes were identified that are the putative chick orthologues of genes cloned from other species. We determined the expression pattern of several clones for which sequence homologies suggested possible roles in transcriptional regulation, apoptosis or intercellular signaling. Their corresponding mRNAs were expressed in the embryonic retina in topographically specific, developmentally regulated patterns. Conclusions: We identified and characterized genes in the chick embryo retina using a combination of microarray analysis and in situ hybridization. Analysis of the expression patterns suggests involvement of several of these genes in key events during embryogenesis.",
author = "Hackam, {Abigail S} and Bradford, {Rebecca L.} and Bakhru, {Rita N.} and Shah, {Raza M.} and Ronald Farkas and Zack, {Donald J.} and Ruben Adler",
year = "2003",
month = "12",
day = "1",
language = "English",
volume = "9",
pages = "262--276",
journal = "Molecular Vision",
issn = "1090-0535",

}

TY - JOUR

T1 - Gene discovery in the embryonic chick retina

AU - Hackam, Abigail S

AU - Bradford, Rebecca L.

AU - Bakhru, Rita N.

AU - Shah, Raza M.

AU - Farkas, Ronald

AU - Zack, Donald J.

AU - Adler, Ruben

PY - 2003/12/1

Y1 - 2003/12/1

N2 - Purpose: The chick embryo is a powerful model system for the study of retinal development. However, analysis of gene expression in the chick retina has lagged behind biological studies. The purpose of this study was to identity and characterize genes expressed in the chick embryo retina as candidate molecules involved in the development and function of photoreceptors and other retinal cell types. Methods: RNA from embryonic day (ED) 18 White Leghorn chick embryo retinae was used to generate an oligo dT-primed cDNA library. Bacterial colonies representing five thousand individual clones were arrayed onto nylon membranes using a microarray robot. Replicate membranes were hybridized with cDNA probes synthesized from ED 18 retina, brain and liver. Clones that appeared preferentially expressed in retina were identified by homology searches, and their spatial and temporal expression patterns were analyzed by in situ hybridization. Results: Two hundred and seventy-two clones were identified. Approximately forty percent of the clones represented potential novel genes, including ESTs, hypothetical proteins and clones with no assigned identities. Furthermore, many genes were identified that are the putative chick orthologues of genes cloned from other species. We determined the expression pattern of several clones for which sequence homologies suggested possible roles in transcriptional regulation, apoptosis or intercellular signaling. Their corresponding mRNAs were expressed in the embryonic retina in topographically specific, developmentally regulated patterns. Conclusions: We identified and characterized genes in the chick embryo retina using a combination of microarray analysis and in situ hybridization. Analysis of the expression patterns suggests involvement of several of these genes in key events during embryogenesis.

AB - Purpose: The chick embryo is a powerful model system for the study of retinal development. However, analysis of gene expression in the chick retina has lagged behind biological studies. The purpose of this study was to identity and characterize genes expressed in the chick embryo retina as candidate molecules involved in the development and function of photoreceptors and other retinal cell types. Methods: RNA from embryonic day (ED) 18 White Leghorn chick embryo retinae was used to generate an oligo dT-primed cDNA library. Bacterial colonies representing five thousand individual clones were arrayed onto nylon membranes using a microarray robot. Replicate membranes were hybridized with cDNA probes synthesized from ED 18 retina, brain and liver. Clones that appeared preferentially expressed in retina were identified by homology searches, and their spatial and temporal expression patterns were analyzed by in situ hybridization. Results: Two hundred and seventy-two clones were identified. Approximately forty percent of the clones represented potential novel genes, including ESTs, hypothetical proteins and clones with no assigned identities. Furthermore, many genes were identified that are the putative chick orthologues of genes cloned from other species. We determined the expression pattern of several clones for which sequence homologies suggested possible roles in transcriptional regulation, apoptosis or intercellular signaling. Their corresponding mRNAs were expressed in the embryonic retina in topographically specific, developmentally regulated patterns. Conclusions: We identified and characterized genes in the chick embryo retina using a combination of microarray analysis and in situ hybridization. Analysis of the expression patterns suggests involvement of several of these genes in key events during embryogenesis.

UR - http://www.scopus.com/inward/record.url?scp=0038070440&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0038070440&partnerID=8YFLogxK

M3 - Article

C2 - 12819621

AN - SCOPUS:0038070440

VL - 9

SP - 262

EP - 276

JO - Molecular Vision

JF - Molecular Vision

SN - 1090-0535

ER -