A biphasic pattern of gene expression during mouse retina development

Samuel Shao Min Zhang, Xuming Xu, Mugen Liu, Hongyu Zhao, Marcelo Bento Soares, Colin J. Barnstable, Xin Yuan Fu

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Background: Between embryonic day 12 and postnatal day 21, six major neuronal and one glia cell type are generated from multipotential progenitors in a characteristic sequence during mouse retina development. We investigated expression patterns of retina transcripts during the major embryonic and postnatal developmental stages to provide a systematic view of normal mouse retina development, Results: A tissue-specific cDNA microarray was generated using a set of sequence non-redundant EST clones collected from mouse retina. Eleven stages of mouse retina, from embryonic day 12.5 (El2.5) to postnatal day 21 (PN21), were collected for RNA isolation. Non-amplified RNAs were labeled for microarray experiments and three sets of data were analyzed for significance, hierarchical relationships, and functional clustering. Six individual gene expression clusters were identified based on expression patterns of transcripts through retina development. Two developmental phases were clearly divided with postnatal day 5 (PN5) as a separate cluster. Among 4,180 transcripts that changed significantly during development, approximately 2/3 of the genes were expressed at high levels up until PN5 and then declined whereas the other 1/3 of the genes increased expression from PN5 and remained at the higher levels until at least PN21. Less than 1% of the genes observed showed a peak of expression between the two phases. Among the later increased population, only about 40% genes are correlated with rod photoreceptors, indicating that multiple cell types contributed to gene expression in this phase. Within the same functional classes, however, different gene populations were expressed in distinct developmental phases. A correlation coefficient analysis of gene expression during retina development between previous SAGE studies and this study was also carried out. Conclusion: This study provides a complementary genome-wide view of common gene dynamics and a broad molecular classification of mouse retina development. Different genes in the same functional clusters are expressed in the different developmental stages, suggesting that cells might change gene expression profiles from differentiation to maturation stages. We propose that large-scale changes in gene regulation during development are necessary for the final maturation and function of the retina.

Original languageEnglish (US)
Article number48
JournalBMC Developmental Biology
Volume6
DOIs
StatePublished - Oct 17 2006
Externally publishedYes

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Retina
Gene Expression
Genes
RNA
Retinal Rod Photoreceptor Cells
Expressed Sequence Tags
Multigene Family
Oligonucleotide Array Sequence Analysis
Transcriptome
Neuroglia
Population
Cluster Analysis
Clone Cells
Genome

ASJC Scopus subject areas

  • Developmental Biology

Cite this

Zhang, S. S. M., Xu, X., Liu, M., Zhao, H., Soares, M. B., Barnstable, C. J., & Fu, X. Y. (2006). A biphasic pattern of gene expression during mouse retina development. BMC Developmental Biology, 6, [48]. https://doi.org/10.1186/1471-213X-6-48

A biphasic pattern of gene expression during mouse retina development. / Zhang, Samuel Shao Min; Xu, Xuming; Liu, Mugen; Zhao, Hongyu; Soares, Marcelo Bento; Barnstable, Colin J.; Fu, Xin Yuan.

In: BMC Developmental Biology, Vol. 6, 48, 17.10.2006.

Research output: Contribution to journalArticle

Zhang, Samuel Shao Min ; Xu, Xuming ; Liu, Mugen ; Zhao, Hongyu ; Soares, Marcelo Bento ; Barnstable, Colin J. ; Fu, Xin Yuan. / A biphasic pattern of gene expression during mouse retina development. In: BMC Developmental Biology. 2006 ; Vol. 6.
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abstract = "Background: Between embryonic day 12 and postnatal day 21, six major neuronal and one glia cell type are generated from multipotential progenitors in a characteristic sequence during mouse retina development. We investigated expression patterns of retina transcripts during the major embryonic and postnatal developmental stages to provide a systematic view of normal mouse retina development, Results: A tissue-specific cDNA microarray was generated using a set of sequence non-redundant EST clones collected from mouse retina. Eleven stages of mouse retina, from embryonic day 12.5 (El2.5) to postnatal day 21 (PN21), were collected for RNA isolation. Non-amplified RNAs were labeled for microarray experiments and three sets of data were analyzed for significance, hierarchical relationships, and functional clustering. Six individual gene expression clusters were identified based on expression patterns of transcripts through retina development. Two developmental phases were clearly divided with postnatal day 5 (PN5) as a separate cluster. Among 4,180 transcripts that changed significantly during development, approximately 2/3 of the genes were expressed at high levels up until PN5 and then declined whereas the other 1/3 of the genes increased expression from PN5 and remained at the higher levels until at least PN21. Less than 1{\%} of the genes observed showed a peak of expression between the two phases. Among the later increased population, only about 40{\%} genes are correlated with rod photoreceptors, indicating that multiple cell types contributed to gene expression in this phase. Within the same functional classes, however, different gene populations were expressed in distinct developmental phases. A correlation coefficient analysis of gene expression during retina development between previous SAGE studies and this study was also carried out. Conclusion: This study provides a complementary genome-wide view of common gene dynamics and a broad molecular classification of mouse retina development. Different genes in the same functional clusters are expressed in the different developmental stages, suggesting that cells might change gene expression profiles from differentiation to maturation stages. We propose that large-scale changes in gene regulation during development are necessary for the final maturation and function of the retina.",
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