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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

RNA-seq analyses detect graded changes in gene expression in P10 heterozygous Crx mutant retinas. a-c Gene expression (log2 CPM) in the indicated heterozygotes (y-axes) are compared with the WT control (C57BL/6 J, x-axes). Prototypical photoreceptor transcripts are labeled in white. White diagonal lines represent ±2 FC. d, e Venn diagrams illustrate the numbers of significantly affected genes that are shared or are uniquely changed in the indicated mutants (FC ≥ 2 or ≤ -2, FDR ≤ 0.05). f, g Analysis of the union of genes affected in heterozygous mutants (FC ≥ 2 or ≤ -2, FDR ≤ 0.05) presented as FC relative to WT control. Significance calculated by Wilcoxon rank-sum test with Bonferroni correction. Notched box whisker plot describes median and quartiles of data
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Fig3: RNA-seq analyses detect graded changes in gene expression in P10 heterozygous Crx mutant retinas. a-c Gene expression (log2 CPM) in the indicated heterozygotes (y-axes) are compared with the WT control (C57BL/6 J, x-axes). Prototypical photoreceptor transcripts are labeled in white. White diagonal lines represent ±2 FC. d, e Venn diagrams illustrate the numbers of significantly affected genes that are shared or are uniquely changed in the indicated mutants (FC ≥ 2 or ≤ -2, FDR ≤ 0.05). f, g Analysis of the union of genes affected in heterozygous mutants (FC ≥ 2 or ≤ -2, FDR ≤ 0.05) presented as FC relative to WT control. Significance calculated by Wilcoxon rank-sum test with Bonferroni correction. Notched box whisker plot describes median and quartiles of data

Mentions: To determine if heterozygous mutants also share gene expression changes between genotypes, we compared RNA-seq data from heterozygous mutants E168d2/+, R90W/+, as well as E168d2neo/+. At P10, the heterozygous mutants showed fewer gene changes than the respective homozygous counterparts (Table 2). Similar to the homozygous mutants, the number of significantly affected genes in heterozygotes correlated with phenotype severity in the order E168d2/+ > E168d2neo/+ > R90W/+. Figure 3a–c and Figure S2a in Additional file 4 show that, qualitatively, the white highlighted photoreceptor transcripts were most severely affected in the E168d2/+ mutant, less affected in E168d2neo/+ and showed no change greater than twofold in the R90W/+ line. Furthermore, affected transcripts in heterozygotes also showed a high degree of overlap between the genotypes (Fig. 3d, e).Fig. 3


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)

RNA-seq analyses detect graded changes in gene expression in P10 heterozygous Crx mutant retinas. a-c Gene expression (log2 CPM) in the indicated heterozygotes (y-axes) are compared with the WT control (C57BL/6 J, x-axes). Prototypical photoreceptor transcripts are labeled in white. White diagonal lines represent ±2 FC. d, e Venn diagrams illustrate the numbers of significantly affected genes that are shared or are uniquely changed in the indicated mutants (FC ≥ 2 or ≤ -2, FDR ≤ 0.05). f, g Analysis of the union of genes affected in heterozygous mutants (FC ≥ 2 or ≤ -2, FDR ≤ 0.05) presented as FC relative to WT control. Significance calculated by Wilcoxon rank-sum test with Bonferroni correction. Notched box whisker plot describes median and quartiles of data
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Related In: Results  -  Collection

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Fig3: RNA-seq analyses detect graded changes in gene expression in P10 heterozygous Crx mutant retinas. a-c Gene expression (log2 CPM) in the indicated heterozygotes (y-axes) are compared with the WT control (C57BL/6 J, x-axes). Prototypical photoreceptor transcripts are labeled in white. White diagonal lines represent ±2 FC. d, e Venn diagrams illustrate the numbers of significantly affected genes that are shared or are uniquely changed in the indicated mutants (FC ≥ 2 or ≤ -2, FDR ≤ 0.05). f, g Analysis of the union of genes affected in heterozygous mutants (FC ≥ 2 or ≤ -2, FDR ≤ 0.05) presented as FC relative to WT control. Significance calculated by Wilcoxon rank-sum test with Bonferroni correction. Notched box whisker plot describes median and quartiles of data
Mentions: To determine if heterozygous mutants also share gene expression changes between genotypes, we compared RNA-seq data from heterozygous mutants E168d2/+, R90W/+, as well as E168d2neo/+. At P10, the heterozygous mutants showed fewer gene changes than the respective homozygous counterparts (Table 2). Similar to the homozygous mutants, the number of significantly affected genes in heterozygotes correlated with phenotype severity in the order E168d2/+ > E168d2neo/+ > R90W/+. Figure 3a–c and Figure S2a in Additional file 4 show that, qualitatively, the white highlighted photoreceptor transcripts were most severely affected in the E168d2/+ mutant, less affected in E168d2neo/+ and showed no change greater than twofold in the R90W/+ line. Furthermore, affected transcripts in heterozygotes also showed a high degree of overlap between the genotypes (Fig. 3d, e).Fig. 3

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