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Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in Fragile X syndrome

Brasa, Sarah and Sebastien, Jacquemont and Hahne, Florian and Rozenberg, Izabela and Peters, Thomas and He, Yunsheng and Mccormack, Christine and Gasparini, Fabrizio and Chibout, Salah-Dine and Grenet, Olivier and Moggs, Jonathan and Gomez-Mancilla, Baltazar and Terranova, Remi (2016) Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in Fragile X syndrome. Clinical Epigenetics (http://www.clinicalepigeneticsjournal.com/).

Abstract

Background. The molecular pathways associated with FMR1 epigenetic silencing in Fragile X syndrome (FXS) patients 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.
Results. Here we have deployed customized epigenomic profiling assays on blood-derived samples from FXS patients and healthy volunteers to comprehensively map the FMR1 locus chromatin landscape. Using a methylated DNA immunocapture (MeDIP) assay combined with DNA microarrays covering the entire FMR1 locus, we identified novel regions of altered DNA methylation (5-methylcytosine, 5mC) within FXS patients. Changes in 5mC were accompanied by unprecedented, reciprocal, changes in DNA hydroxymethylation (5-hydroxymethylcytosine, 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 locus histone post-translational epigenetic marks, together DNA methylation and gene expression analyses, support a functional relationship between 5hmC levels and FMR1 transcriptional activation and reveal cell-type specific differences in FMR1 gene body 5hmC levels. 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.
Conclusions. We identify novel FMR1 locus-specific and cell-type specific epigenetic marks in FXS patient cells and propose that the combined profiling of 5mC and 5hmC may enhance the molecular and functional characterization and clinical stratification of FXS patients.

Item Type: Article
Keywords: Fragile X syndrome (FXS); Chromatin profiling; Epigenetic silencing, FMR1; 5-hydroxymethylation (5hmC); Clinical Biomarker
Date Deposited: 26 Apr 2016 23:45
Last Modified: 26 Apr 2016 23:45
URI: https://oak.novartis.com/id/eprint/25822

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