Genomic Analysis of Mouse Retinal Development

By S. Blackshaw, S. Harpavat, J. Trimarchi, Li Cai, Haiyan Huang, W. Kuo, Griffin M. Weber, Kyungjoon Lee, R. Fraioli, Seo-Hee Cho and 5 more. PLoS Biology, 2004

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The vertebrate retina is comprised of seven major cell types that are generated in overlapping but well-defined intervals. To identify genes that might regulate retinal development, gene expression in the developing retina was profiled at multiple time points using serial analysis of gene expression (SAGE). The expression patterns of 1,051 genes that showed developmentally dynamic expression by SAGE were investigated using in situ hybridization. A molecular atlas of gene expression in the developing and mature retina was thereby constructed, along with a taxonomic classification of developmental gene expression patterns. Genes were identified that label both temporal and spatial subsets of mitotic progenitor cells. For each developing and mature major retinal cell type, genes selectively expressed in that cell type were identified. The gene expression profiles of retinal Müller glia and mitotic progenitor cells were found to be highly similar, suggesting that Müller glia might serve to produce multiple retinal cell types under the right conditions. In addition, multiple transcripts that were evolutionarily conserved that did not appear to encode open reading frames of more than 100 amino acids in length (“noncoding RNAs”) were found to be dynamically and specifically expressed in developing and mature retinal cell types. Finally, many photoreceptor-enriched genes that mapped to chromosomal intervals containing retinal disease genes were identified. These data serve as a starting point for functional investigations of the roles of these genes in retinal development and physiology.

Subfields: Cell Biology, Cellular and Molecular Neuroscience, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ea1d24518950433b9dbfa563b888f3585b044751

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Citations in the corpus

Validation of oligoarrays for quantitative exploration of the transcriptome (2008, positive): “The most abundant transcripts are known to be involved in visual perception (Pdc, Rbp3, Guca1a, Unc119, Guca1b, Pde6b) or play another role in retinal function (Calm1, Syp) [30].”
New functions of Müller cells (2013, background): “Müller cells of the mature rodent retina display a gene expression profile resembling that of progenitor cells (Blackshaw et al., 2004); a subset of Müller cells express progenitor genes such as Car2, Dkk3, Chx10, and Pax6 (Rowan and Cepko, 2004; Roesch et al., 2008).”
Comprehensive analysis of retinal development at single cell resolution identifies NFI factors as essential for mitotic exit and specification of late-born cells (2018, background): “Notably, we identify previously established markers of both early (Fgf15 and Sfrp2) and late (Crym and Car2) RPCs (Blackshaw et al., 2004) and a host of previously unidentified markers of early versus late RPCs, including the NFI family transcription factors (Nfia, Nfib, and Nfix; Figure 3E).”
Long noncoding RNAs: functional surprises from the RNA world. (2009, background): “…the biological relevance of these transcripts, multiple studies have shown that significant numbers of long ncRNAs are regulated during development (Blackshaw et al. 2004; Rinn et al. 2007; Dinger et al. 2008), exhibit cell typespecific expression (Ravasi et al. 2006; Mercer et al. 2008), localize…”
lincRNAs: Genomics, Evolution, and Mechanisms (2013, neutral): “Miat (also called Gomafu or Rncr2) was originally discovered as a lincRNA highly enriched in specific neurons in mouse retina (Blackshaw et al., 2004; Sone et al., 2007) and later found to be more widely expressed in the nervous system and cultured neurons, where it specifies cell identify (Sone et…”
Non-coding RNA. (2006, background): “Second, it is clear that many of these transcripts are celltype specific, with specific subcellular locations, and are developmentally regulated (77,98,99).”