Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5CReport as inadecuate




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BMC Medical Genomics

, 6:1

Functional and structural genomics

Abstract

BackgroundA number of neurodevelopmental syndromes are caused by mutations in genes encoding proteins that normally function in epigenetic regulation. Identification of epigenetic alterations occurring in these disorders could shed light on molecular pathways relevant to neurodevelopment.

ResultsUsing a genome-wide approach, we identified genes with significant loss of DNA methylation in blood of males with intellectual disability and mutations in the X-linked KDM5C gene, encoding a histone H3 lysine 4 demethylase, in comparison to age-sex matched controls. Loss of DNA methylation in such individuals is consistent with known interactions between DNA methylation and H3 lysine 4 methylation. Further, loss of DNA methylation at the promoters of the three top candidate genes FBXL5, SCMH1, CACYBP was not observed in more than 900 population controls. We also found that DNA methylation at these three genes in blood correlated with dosage of KDM5C and its Y-linked homologue KDM5D. In addition, parallel sex-specific DNA methylation profiles in brain samples from control males and females were observed at FBXL5 and CACYBP.

ConclusionsWe have, for the first time, identified epigenetic alterations in patient samples carrying a mutation in a gene involved in the regulation of histone modifications. These data support the concept that DNA methylation and H3 lysine 4 methylation are functionally interdependent. The data provide new insights into the molecular pathogenesis of intellectual disability. Further, our data suggest that some DNA methylation marks identified in blood can serve as biomarkers of epigenetic status in the brain.

KeywordsKDM5C DNA methylation H3K4 methylation Intellectual disability AbbreviationsIDIntellectual disability

XLIDX-linked intellectual disability

H3K4Histone H3 Lysine 4

ESembryonic stem

AMLacute myeloid leukemia.

Electronic supplementary materialThe online version of this article doi:10.1186-1755-8794-6-1 contains supplementary material, which is available to authorized users.

Daria Grafodatskaya, Barian HY Chung contributed equally to this work.

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Author: Daria Grafodatskaya - Barian HY Chung - Darci T Butcher - Andrei L Turinsky - Sarah J Goodman - Sana Choufani - Yi-An C

Source: https://link.springer.com/



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