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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 mutants lose rod gene expression but up-regulate many phototransduction-unrelated cone gene transcripts. a Classification of genes within groups 1, 2, 3, and 6 as rod-enriched (dark grey), cone-enriched (light grey), or not specific to a particular cell type (N.S., white) in the normal adult retina. Rod and cone-enriched genes are defined based on the comparison of published P21 WT to Nrl−/− RNA-seq data [24]. Rod: FC ≥ 2, FDR ≤ 0.05. Cone: FC ≤ -2, FDR ≤ 0.05. Fishers exact test, *p < 0.05, ***p < 0.0005. b, c Heatmaps depict hierarchical clustering of FC relative to WT for all rod-enriched (b) and cone-enriched (c) genes. Expression data from a published RNA-seq study describing the Crx Rip/+, Rip/Rip, and Crx−/− mice are also separately presented in the order determined by the aforementioned clustering. Regions noted in (b) and (c) with asterisks are presented in larger format in Additional file 14 and represent many down-regulated genes involved in phototransduction in rods and cones. d Immunohistochemical staining for RXRγ, CNGB3, and peanut agglutinin (PNA) in P10 WT and three Crx mutant retina sections. Scale bar = 100 μm. IS inner segment, ONL outer nuclear layer
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Fig6: Crx mutants lose rod gene expression but up-regulate many phototransduction-unrelated cone gene transcripts. a Classification of genes within groups 1, 2, 3, and 6 as rod-enriched (dark grey), cone-enriched (light grey), or not specific to a particular cell type (N.S., white) in the normal adult retina. Rod and cone-enriched genes are defined based on the comparison of published P21 WT to Nrl−/− RNA-seq data [24]. Rod: FC ≥ 2, FDR ≤ 0.05. Cone: FC ≤ -2, FDR ≤ 0.05. Fishers exact test, *p < 0.05, ***p < 0.0005. b, c Heatmaps depict hierarchical clustering of FC relative to WT for all rod-enriched (b) and cone-enriched (c) genes. Expression data from a published RNA-seq study describing the Crx Rip/+, Rip/Rip, and Crx−/− mice are also separately presented in the order determined by the aforementioned clustering. Regions noted in (b) and (c) with asterisks are presented in larger format in Additional file 14 and represent many down-regulated genes involved in phototransduction in rods and cones. d Immunohistochemical staining for RXRγ, CNGB3, and peanut agglutinin (PNA) in P10 WT and three Crx mutant retina sections. Scale bar = 100 μm. IS inner segment, ONL outer nuclear layer

Mentions: Since CRX and CRL binding as well as epigenetic data implicate down-regulated genes as being active CRX targets in rods, we investigated if differentially expressed genes normally have rod or cone cell type-specific expression patterns. Using published data [24] to classify these genes as either rod- or cone-enriched (or non-specific), we found a significant overrepresentation of rod genes in groups 1 and 2, although a number of cone genes were also found in group 1 (Fig. 6a; Additional file 10). This was expected considering the mouse retina is rod-dominant and CRX acts as a transcription activator for genes critical for photoreceptor structure and function. Surprisingly, however, up-regulated groups 3 and 6 contained a significant enrichment of cone transcripts (Fig. 6a; Additional file 10).Fig. 6


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 mutants lose rod gene expression but up-regulate many phototransduction-unrelated cone gene transcripts. a Classification of genes within groups 1, 2, 3, and 6 as rod-enriched (dark grey), cone-enriched (light grey), or not specific to a particular cell type (N.S., white) in the normal adult retina. Rod and cone-enriched genes are defined based on the comparison of published P21 WT to Nrl−/− RNA-seq data [24]. Rod: FC ≥ 2, FDR ≤ 0.05. Cone: FC ≤ -2, FDR ≤ 0.05. Fishers exact test, *p < 0.05, ***p < 0.0005. b, c Heatmaps depict hierarchical clustering of FC relative to WT for all rod-enriched (b) and cone-enriched (c) genes. Expression data from a published RNA-seq study describing the Crx Rip/+, Rip/Rip, and Crx−/− mice are also separately presented in the order determined by the aforementioned clustering. Regions noted in (b) and (c) with asterisks are presented in larger format in Additional file 14 and represent many down-regulated genes involved in phototransduction in rods and cones. d Immunohistochemical staining for RXRγ, CNGB3, and peanut agglutinin (PNA) in P10 WT and three Crx mutant retina sections. Scale bar = 100 μm. IS inner segment, ONL outer nuclear layer
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Related In: Results  -  Collection

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Fig6: Crx mutants lose rod gene expression but up-regulate many phototransduction-unrelated cone gene transcripts. a Classification of genes within groups 1, 2, 3, and 6 as rod-enriched (dark grey), cone-enriched (light grey), or not specific to a particular cell type (N.S., white) in the normal adult retina. Rod and cone-enriched genes are defined based on the comparison of published P21 WT to Nrl−/− RNA-seq data [24]. Rod: FC ≥ 2, FDR ≤ 0.05. Cone: FC ≤ -2, FDR ≤ 0.05. Fishers exact test, *p < 0.05, ***p < 0.0005. b, c Heatmaps depict hierarchical clustering of FC relative to WT for all rod-enriched (b) and cone-enriched (c) genes. Expression data from a published RNA-seq study describing the Crx Rip/+, Rip/Rip, and Crx−/− mice are also separately presented in the order determined by the aforementioned clustering. Regions noted in (b) and (c) with asterisks are presented in larger format in Additional file 14 and represent many down-regulated genes involved in phototransduction in rods and cones. d Immunohistochemical staining for RXRγ, CNGB3, and peanut agglutinin (PNA) in P10 WT and three Crx mutant retina sections. Scale bar = 100 μm. IS inner segment, ONL outer nuclear layer
Mentions: Since CRX and CRL binding as well as epigenetic data implicate down-regulated genes as being active CRX targets in rods, we investigated if differentially expressed genes normally have rod or cone cell type-specific expression patterns. Using published data [24] to classify these genes as either rod- or cone-enriched (or non-specific), we found a significant overrepresentation of rod genes in groups 1 and 2, although a number of cone genes were also found in group 1 (Fig. 6a; Additional file 10). This was expected considering the mouse retina is rod-dominant and CRX acts as a transcription activator for genes critical for photoreceptor structure and function. Surprisingly, however, up-regulated groups 3 and 6 contained a significant enrichment of cone transcripts (Fig. 6a; Additional file 10).Fig. 6

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