DNA methylation and differential gene regulation in photoreceptor cell death.
DNA methylation and differential gene regulation in photoreceptor cell death.
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DOI：
10.1038/cddis.2014.512
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发表时间：
2014-12-04
影响因子：
9
通讯作者：
Ekström PA
中科院分区：
文献类型：
--
作者：
Farinelli P;Perera A;Arango-Gonzalez B;Trifunovic D;Wagner M;Carell T;Biel M;Zrenner E;Michalakis S;Paquet-Durand F;Ekström PA
视网膜色素变性(RP)是一组遗传性退行性视网膜疾病，导致光感受器进行性丧失。直到今天，RP仍然是不可治疗的，合理的治疗方法的发展需要彻底了解潜在的细胞死亡机制。DNA甲基转移酶(DNMT)对DNA碱基胞嘧啶进行甲基化，是调控基因表达、细胞分化、细胞死亡和存活的重要表观遗传因子。以前的研究表明，表观遗传机制参与了RP，在本研究中，在RP的Rd1、Rd2、P23H和S334ter啮齿动物模型中，死亡的光感受器中检测到胞嘧啶甲基化增加。Rd1小鼠RP模型光感受器核形态的超微结构分析显示，在视网膜变性过程中，染色质结构发生了严重变化，这与DNMT同工酶DNMT3a的表达增加相一致。为了在基因组水平上识别疾病特异性的差异甲基化DNA区域(DMRS)，我们免疫沉淀甲基化的DNA片段，然后用靶向微阵列分析它们。对Rd1和野生型视网膜的DMR进行全基因组比较，发现参与细胞死亡和生存以及细胞形态和神经系统发育的基因高度甲基化。当将DMRS与基因表达数据相关联时，我们发现在转录抑制的同时发生了高甲基化。基序分析一致地表明，在突变模型中，几个与视网膜生理有关的重要转录因子的结合部位发生了高甲基化，这也与它们各自靶基因的转录沉默有关。最后，使用地西他滨抑制Rd1器官型视网膜外植体中的DNMTs可显著减少光感受器细胞的死亡，提示抑制DNA甲基化是一种潜在的治疗RP的新方法。
Retinitis pigmentosa (RP) defines a group of inherited degenerative retinal diseases causing progressive loss of photoreceptors. To this day, RP is still untreatable and rational treatment development will require a thorough understanding of the underlying cell death mechanisms. Methylation of the DNA base cytosine by DNA methyltransferases (DNMTs) is an important epigenetic factor regulating gene expression, cell differentiation, cell death, and survival. Previous studies suggested an involvement of epigenetic mechanisms in RP, and in this study, increased cytosine methylation was detected in dying photoreceptors in the rd1, rd2, P23H, and S334ter rodent models for RP. Ultrastructural analysis of photoreceptor nuclear morphology in the rd1 mouse model for RP revealed a severely altered chromatin structure during retinal degeneration that coincided with an increased expression of the DNMT isozyme DNMT3a. To identify disease-specific differentially methylated DNA regions (DMRs) on a genomic level, we immunoprecipitated methylated DNA fragments and subsequently analyzed them with a targeted microarray. Genome-wide comparison of DMRs between rd1 and wild-type retina revealed hypermethylation of genes involved in cell death and survival as well as cell morphology and nervous system development. When correlating DMRs with gene expression data, we found that hypermethylation occurred alongside transcriptional repression. Consistently, motif analysis showed that binding sites of several important transcription factors for retinal physiology were hypermethylated in the mutant model, which also correlated with transcriptional silencing of their respective target genes. Finally, inhibition of DNMTs in rd1 organotypic retinal explants using decitabine resulted in a substantial reduction of photoreceptor cell death, suggesting inhibition of DNA methylation as a potential novel treatment in RP.