Length-dependent gene misregulation in Rett syndrome (Dnmt3a)

Disruption of the MECP2 gene leads to Rett syndrome (RTT), a severe neurological disorder with features of autism. MECP2 encodes a methyl-DNA-binding protein that is proposed to function as a transcriptional repressor, but, despite numerous studies examining neuronal gene expression in MeCP2 mutants, no coherent model has emerged for how MeCP2 regulates transcription. Here we identify a genome-wide length-dependent increase in the expression of long genes in neurons lacking MeCP2. This gene misregulation occurs in human RTT brains and correlates with onset and severity of phenotypes in Mecp2 mutant mice, suggesting that the disruption of long gene expression contributes to RTT pathology. We present evidence that MeCP2 represses long genes by binding to brain-enriched, methylated CA dinucleotides within genes and show that loss of methylated CA in the brain recapitulates gene expression defects observed in MeCP2 mutants. We find that long genes encode proteins with neuronal functions, and overlap substantially with genes that have been implicated in autism and Fragile X syndrome. Reversing the overexpression of long genes in neurons lacking MeCP2 can improve some RTT-associated cellular deficits. These findings suggest that a function of MeCP2 in the mammalian brain is to temper the expression of genes in a length-dependent manner, and that mutations in MeCP2 and possibly other autism genes may cause neurological dysfunction by disrupting the expression of long genes in the brain. Total RNA was extracted from the cerebellum of 10-11 week old Dnmt3a conditional knockout and control animals. Gene expression was analyzed using the Affymetrix Mo_Exon ST 1.0 microarray platform.MECP2基因的功能缺失会引发雷特综合征（Rett syndrome, RTT）——一种兼具自闭症特征的重症神经系统疾病。MECP2编码一种甲基DNA结合蛋白，被推测可作为转录抑制因子；尽管已有诸多研究针对MeCP2突变体的神经元基因表达展开分析，但学界尚未形成一套连贯的模型，用以阐释MeCP2调控转录的具体机制。本研究在缺失MeCP2的神经元中，首次发现长链基因的表达呈现全基因组范围内的长度依赖性上调。该基因表达失调现象在人类雷特综合征患者的脑组织中同样存在，且与Mecp2突变小鼠的表型发病时机及严重程度显著相关，提示长链基因表达紊乱可能参与了雷特综合征的病理进程。我们的研究证据表明，MeCP2可通过结合脑组织富集的、基因内部的甲基化CA二核苷酸，实现对长链基因的转录抑制；同时证实，脑组织中甲基化CA位点的缺失，会复刻MeCP2突变体中观察到的基因表达异常。我们还发现，长链基因所编码的蛋白多参与神经元功能活动，且与自闭症及脆性X综合征（Fragile X syndrome）的相关基因存在大量重叠。在缺失MeCP2的神经元中逆转长链基因的过表达状态，可改善部分雷特综合征相关的细胞缺陷。上述研究结果提示，MeCP2在哺乳动物脑组织中的核心功能之一，是以长度依赖性方式调控基因表达水平；而MeCP2乃至其他自闭症相关基因的突变，可能通过破坏脑组织中长链基因的正常表达，进而引发神经系统功能异常。本研究从10至11周龄的Dnmt3a条件性敲除小鼠及对照小鼠的小脑组织中提取总RNA，采用Affymetrix Mo_Exon ST 1.0微阵列平台完成基因表达分析。