Ruzycki Philip A, Tran Nicholas M, Kefalov Vladimir J, Kolesnikov Alexander V, Chen Shiming
Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, MO, USA.
Molecular Genetics and Genomics Graduate Program, Division of Biology & Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO, USA.
Genome Biol. 2015 Sep 1;16(1):171. doi: 10.1186/s13059-015-0732-z.
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.
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.
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.
视锥-视杆同源盒蛋白CRX的突变通常与具有不同发病年龄和严重程度的显性致盲性视网膜病变相关。五个携带不同Crx突变的特征明确的小鼠模型表现出广泛的疾病表型。为了确定表型变异性是否与CRX靶基因表达的明显变化相关，我们对其中三个模型进行了RNA测序分析，并将结果与已发表的数据进行比较。
尽管所测试的三个模型之间存在显著的表型差异，但在共享的基因集中检测到了分级表达变化。表型严重程度与编码关键视杆和视锥光转导蛋白的基因下调相关。有趣的是，在病情日益严重的小鼠模型中，许多视杆富集基因的转录逐渐减少，而视锥富集基因的转录则逐渐增加。与下调基因不同，下调基因在正常视网膜中显示出高度的CRX结合和动态表观遗传图谱，上调的视锥富集基因与CRX的直接活性无关，而是可能反映了视杆细胞命运完整性的变化。此外，这些分析描述了微小基因表达变化对表型的影响，因为两个突变体显示出略有区别的表达模式，但存在巨大的表型差异，包括不同的视网膜变性机制。
我们的结果表明基因表达水平对光感受器功能和存活具有阈值效应，突出了CRX在光感受器亚型发育和维持中的重要性，并为CRX相关视网膜病变的表型变异性提供了分子基础。
