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Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies.

Ruzycki PA, Tran NM, Kefalov VJ, Kolesnikov AV, Chen S - Genome Biol. (2015)

Bottom Line: Unlike down-regulated genes, which show a high degree of CRX binding and dynamic epigenetic profiles in normal retinas, the up-regulated cone-enriched genes do not correlate with direct activity of CRX, but instead likely reflect a change in rod cell-fate integrity.Furthermore, these analyses describe the impact of minor gene expression changes on the phenotype, as two mutants showed marginally distinguishable expression patterns but huge phenotypic differences, including distinct mechanisms of retinal degeneration.Our results implicate a threshold effect of gene expression level on photoreceptor function and survival, highlight the importance of CRX in photoreceptor subtype development and maintenance, and provide a molecular basis for phenotype variability in CRX-associated retinopathies.

View Article: PubMed Central - PubMed

Affiliation: Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, MO, USA.

ABSTRACT

Background: Mutations in the cone-rod-homeobox protein CRX are typically associated with dominant blinding retinopathies with variable age of onset and severity. Five well-characterized mouse models carrying different Crx mutations show a wide range of disease phenotypes. To determine if the phenotype variability correlates with distinct changes in CRX target gene expression, we perform RNA-seq analyses on three of these models and compare the results with published data.

Results: Despite dramatic phenotypic differences between the three models tested, graded expression changes in shared sets of genes are detected. Phenotype severity correlates with the down-regulation of genes encoding key rod and cone phototransduction proteins. Interestingly, in increasingly severe mouse models, the transcription of many rod-enriched genes decreases decrementally, whereas that of cone-enriched genes increases incrementally. Unlike down-regulated genes, which show a high degree of CRX binding and dynamic epigenetic profiles in normal retinas, the up-regulated cone-enriched genes do not correlate with direct activity of CRX, but instead likely reflect a change in rod cell-fate integrity. Furthermore, these analyses describe the impact of minor gene expression changes on the phenotype, as two mutants showed marginally distinguishable expression patterns but huge phenotypic differences, including distinct mechanisms of retinal degeneration.

Conclusions: Our results implicate a threshold effect of gene expression level on photoreceptor function and survival, highlight the importance of CRX in photoreceptor subtype development and maintenance, and provide a molecular basis for phenotype variability in CRX-associated retinopathies.

No MeSH data available.


Related in: MedlinePlus

Crx mutant retinas show graded changes in photoreceptor-specific gene expression. a, b Heatmaps present FC of gene expression in P10 Crx mutants relative to that of WT age-matched controls in subsets of genes with highest cell type specificity ratios for the six retinal neurons (a) and photoreceptor-enriched genes involved in phototransduction (b). c Changes in gene expression levels (log2 CPM) are compared for E168d2/+ (x-axis) versus E168d2neo/+ (y-axis). Highlighted genes represent 118 transcripts significantly differently expressed between the mutants (FDR ≤ 0.05, no FC cutoff; see Additional files 7 and 11 for designations). d, e Top Gene Ontology (GO) terms of down-regulated (d) and up-regulated (e) gene sets in E168d2/+ compared with E168d2neo/+
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Fig4: Crx mutant retinas show graded changes in photoreceptor-specific gene expression. a, b Heatmaps present FC of gene expression in P10 Crx mutants relative to that of WT age-matched controls in subsets of genes with highest cell type specificity ratios for the six retinal neurons (a) and photoreceptor-enriched genes involved in phototransduction (b). c Changes in gene expression levels (log2 CPM) are compared for E168d2/+ (x-axis) versus E168d2neo/+ (y-axis). Highlighted genes represent 118 transcripts significantly differently expressed between the mutants (FDR ≤ 0.05, no FC cutoff; see Additional files 7 and 11 for designations). d, e Top Gene Ontology (GO) terms of down-regulated (d) and up-regulated (e) gene sets in E168d2/+ compared with E168d2neo/+

Mentions: To ensure that decreased retinal function and impaired development of the Crx mutant mice are not a result of perturbations to other non-photoreceptor cell types, we analyzed the P10 RNA-seq data for changes in expression of genes representing different types of retinal neurons. For each cell type, we chose the ten genes with the highest specificity ratio [27] present in our data. The heatmap in Fig. 4a represents the FC from WT for each of these genes in the P10 mutants, organized by the cell type they represent. The cell types that showed the greatest gene expression changes in all mutants were rod and cone photoreceptors, whereas large-scale changes in gene expression were not observed in other retinal cell types at the age of P10.Fig. 4


Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies.

Ruzycki PA, Tran NM, Kefalov VJ, Kolesnikov AV, Chen S - Genome Biol. (2015)

Crx mutant retinas show graded changes in photoreceptor-specific gene expression. a, b Heatmaps present FC of gene expression in P10 Crx mutants relative to that of WT age-matched controls in subsets of genes with highest cell type specificity ratios for the six retinal neurons (a) and photoreceptor-enriched genes involved in phototransduction (b). c Changes in gene expression levels (log2 CPM) are compared for E168d2/+ (x-axis) versus E168d2neo/+ (y-axis). Highlighted genes represent 118 transcripts significantly differently expressed between the mutants (FDR ≤ 0.05, no FC cutoff; see Additional files 7 and 11 for designations). d, e Top Gene Ontology (GO) terms of down-regulated (d) and up-regulated (e) gene sets in E168d2/+ compared with E168d2neo/+
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig4: Crx mutant retinas show graded changes in photoreceptor-specific gene expression. a, b Heatmaps present FC of gene expression in P10 Crx mutants relative to that of WT age-matched controls in subsets of genes with highest cell type specificity ratios for the six retinal neurons (a) and photoreceptor-enriched genes involved in phototransduction (b). c Changes in gene expression levels (log2 CPM) are compared for E168d2/+ (x-axis) versus E168d2neo/+ (y-axis). Highlighted genes represent 118 transcripts significantly differently expressed between the mutants (FDR ≤ 0.05, no FC cutoff; see Additional files 7 and 11 for designations). d, e Top Gene Ontology (GO) terms of down-regulated (d) and up-regulated (e) gene sets in E168d2/+ compared with E168d2neo/+
Mentions: To ensure that decreased retinal function and impaired development of the Crx mutant mice are not a result of perturbations to other non-photoreceptor cell types, we analyzed the P10 RNA-seq data for changes in expression of genes representing different types of retinal neurons. For each cell type, we chose the ten genes with the highest specificity ratio [27] present in our data. The heatmap in Fig. 4a represents the FC from WT for each of these genes in the P10 mutants, organized by the cell type they represent. The cell types that showed the greatest gene expression changes in all mutants were rod and cone photoreceptors, whereas large-scale changes in gene expression were not observed in other retinal cell types at the age of P10.Fig. 4

Bottom Line: Unlike down-regulated genes, which show a high degree of CRX binding and dynamic epigenetic profiles in normal retinas, the up-regulated cone-enriched genes do not correlate with direct activity of CRX, but instead likely reflect a change in rod cell-fate integrity.Furthermore, these analyses describe the impact of minor gene expression changes on the phenotype, as two mutants showed marginally distinguishable expression patterns but huge phenotypic differences, including distinct mechanisms of retinal degeneration.Our results implicate a threshold effect of gene expression level on photoreceptor function and survival, highlight the importance of CRX in photoreceptor subtype development and maintenance, and provide a molecular basis for phenotype variability in CRX-associated retinopathies.

View Article: PubMed Central - PubMed

Affiliation: Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, MO, USA.

ABSTRACT

Background: Mutations in the cone-rod-homeobox protein CRX are typically associated with dominant blinding retinopathies with variable age of onset and severity. Five well-characterized mouse models carrying different Crx mutations show a wide range of disease phenotypes. To determine if the phenotype variability correlates with distinct changes in CRX target gene expression, we perform RNA-seq analyses on three of these models and compare the results with published data.

Results: Despite dramatic phenotypic differences between the three models tested, graded expression changes in shared sets of genes are detected. Phenotype severity correlates with the down-regulation of genes encoding key rod and cone phototransduction proteins. Interestingly, in increasingly severe mouse models, the transcription of many rod-enriched genes decreases decrementally, whereas that of cone-enriched genes increases incrementally. Unlike down-regulated genes, which show a high degree of CRX binding and dynamic epigenetic profiles in normal retinas, the up-regulated cone-enriched genes do not correlate with direct activity of CRX, but instead likely reflect a change in rod cell-fate integrity. Furthermore, these analyses describe the impact of minor gene expression changes on the phenotype, as two mutants showed marginally distinguishable expression patterns but huge phenotypic differences, including distinct mechanisms of retinal degeneration.

Conclusions: Our results implicate a threshold effect of gene expression level on photoreceptor function and survival, highlight the importance of CRX in photoreceptor subtype development and maintenance, and provide a molecular basis for phenotype variability in CRX-associated retinopathies.

No MeSH data available.


Related in: MedlinePlus