Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome.
Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome.
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DOI：
10.1186/s13148-016-0181-x
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发表时间：
2016
影响因子：
5.7
通讯作者：
Terranova R
中科院分区：
文献类型：
--
作者：
Brasa S;Mueller A;Jacquemont S;Hahne F;Rozenberg I;Peters T;He Y;McCormack C;Gasparini F;Chibout SD;Grenet O;Moggs J;Gomez-Mancilla B;Terranova R
脆性X综合征（FXS）是遗传性智力残疾最常见的形式，由脆性X智力发育迟滞1 （FMR1）基因功能丧失引起。与FMR1表观遗传沉默相关的分子途径仍然难以捉摸，它们的表征可能会促进新的治疗靶点的发现以及疾病状态的新型临床生物标志物的开发。我们采用定制的表观基因组分析方法，全面绘制了来自8名FXS患者的外周单核血细胞（PBMCs）和来自3名FXS患者的成纤维细胞系的FMR1位点染色质图谱。脱氧核糖核酸（DNA）甲基化（5-甲基胞嘧啶（5mC））和羟甲基化（5-羟甲基胞嘧啶（5hmC））分析使用甲基化DNA免疫沉淀（MeDIP）结合定制的FMR1微阵列鉴定FMR1基因体内以及近侧区域DNA（羟基）甲基化变化的新区域。在FMR1转录起始位点周围的区域，5mC水平升高与5hmC的相互变化相关，这代表了FXS疾病的一个新的分子特征。FMR1 5mC和5hmC变化的基因座特异性验证强调了个体间差异，这可能解释了FXS患者中FMR1基因座观察到的预期DNA甲基化嵌合体。FMR1组蛋白修饰的染色质免疫沉淀（ChIP）分析，以及5mC/5hmC和基因表达分析，支持5hmC水平与FMR1转录激活之间的功能关系，并揭示了FMR1表观遗传调控的细胞类型特异性差异。此外，虽然5hmC FMR1水平与FXS疾病严重程度（异常行为的临床评分）呈正相关，但我们的数据首次揭示了5hmC FMR1水平与FXS疾病严重程度之间的负相关。我们在FXS患者细胞中发现了新的、细胞类型特异性的FMR1表观遗传变化区域，为FXS的分子机制提供了新的见解。我们提出，在FMR1位点的选定区域联合测量5mC和5hmC可能会显著增强FXS的临床诊断和患者分层。本文的在线版本（doi:10.1186/s13148-016-0181-x）包含补充材料，可供授权用户使用。
Fragile X syndrome (FXS) is the most common form of inherited intellectual disability, resulting from the loss of function of the fragile X mental retardation 1 (FMR1) gene. The molecular pathways associated with FMR1 epigenetic silencing are still elusive, and their characterization may enhance the discovery of novel therapeutic targets as well as the development of novel clinical biomarkers for disease status. We have deployed customized epigenomic profiling assays to comprehensively map the FMR1 locus chromatin landscape in peripheral mononuclear blood cells (PBMCs) from eight FXS patients and in fibroblast cell lines derived from three FXS patient. Deoxyribonucleic acid (DNA) methylation (5-methylcytosine (5mC)) and hydroxymethylation (5-hydroxymethylcytosine (5hmC)) profiling using methylated DNA immunoprecipitation (MeDIP) combined with a custom FMR1 microarray identifies novel regions of DNA (hydroxy)methylation changes within the FMR1 gene body as well as in proximal flanking regions. At the region surrounding the FMR1 transcriptional start sites, increased levels of 5mC were associated to reciprocal changes in 5hmC, representing a novel molecular feature of FXS disease. Locus-specific validation of FMR1 5mC and 5hmC changes highlighted inter-individual differences that may account for the expected DNA methylation mosaicism observed at the FMR1 locus in FXS patients. Chromatin immunoprecipitation (ChIP) profiling of FMR1 histone modifications, together with 5mC/5hmC and gene expression analyses, support a functional relationship between 5hmC levels and FMR1 transcriptional activation and reveal cell-type specific differences in FMR1 epigenetic regulation. Furthermore, whilst 5mC FMR1 levels positively correlated with FXS disease severity (clinical scores of aberrant behavior), our data reveal for the first time an inverse correlation between 5hmC FMR1 levels and FXS disease severity. We identify novel, cell-type specific, regions of FMR1 epigenetic changes in FXS patient cells, providing new insights into the molecular mechanisms of FXS. We propose that the combined measurement of 5mC and 5hmC at selected regions of the FMR1 locus may significantly enhance FXS clinical diagnostics and patient stratification. The online version of this article (doi:10.1186/s13148-016-0181-x) contains supplementary material, which is available to authorized users.