Regional differences in mitochondrial DNA methylation in human post-mortem brain tissue

Katie Lunnon,Aaron Jeffries,Matthew Devall,Leonard Schalkwyk,Eilis Hannon,Jonathan Mill,Michael Weedon,Matthew N. Davies,Rebecca G. Smith

doi:10.1186/s13148-017-0337-3

Abstract

BackgroundDNA methylation is an important epigenetic mechanism involved in gene regulation, with alterations in DNA methylation in the nuclear genome being linked to numerous complex diseases. Mitochondrial DNA methylation is a phenomenon that is receiving ever-increasing interest, particularly in diseases characterized by mitochondrial dysfunction; however, most studies have been limited to the investigation of specific target regions. Analyses spanning the entire mitochondrial genome have been limited, potentially due to the amount of input DNA required. Further, mitochondrial genetic studies have been previously confounded by nuclear-mitochondrial pseudogenes. Methylated DNA Immunoprecipitation Sequencing is a technique widely used to profile DNA methylation across the nuclear genome; however, reads mapped to mitochondrial DNA are often discarded. Here, we have developed an approach to control for nuclear-mitochondrial pseudogenes within Methylated DNA Immunoprecipitation Sequencing data. We highlight the utility of this approach in identifying differences in mitochondrial DNA methylation across regions of the human brain and pre-mortem blood.ResultsWe were able to correlate mitochondrial DNA methylation patterns between the cortex, cerebellum and blood. We identified 74 nominally significant differentially methylated regions (p < 0.05) in the mitochondrial genome, between anatomically separate cortical regions and the cerebellum in matched samples (N = 3 matched donors). Further analysis identified eight significant differentially methylated regions between the total cortex and cerebellum after correcting for multiple testing. Using unsupervised hierarchical clustering analysis of the mitochondrial DNA methylome, we were able to identify tissue-specific patterns of mitochondrial DNA methylation between blood, cerebellum and cortex.ConclusionsOur study represents a comprehensive analysis of the mitochondrial methylome using pre-existing Methylated DNA Immunoprecipitation Sequencing data to identify brain region-specific patterns of mitochondrial DNA methylation.

Highlights

Mitochondria are unique organelles in that they have their own circular genome, approximately 16.6 kb in size [1]
MtDNA methylation patterns are correlated between the cortex, cerebellum and blood To date, no study has investigated differences in Mitochondrial DNA (mtDNA) methylation across different matched regions of human brain and blood samples
Given that MeDIP-seq data has been generated from standardly extracted total genomic DNA and contains a mixture of Nuclear DNA (ncDNA) and mtDNA [36], we initially controlled for regions of high sequence homology between the two genomes within our data by realigning mtDNA reads to a series of custom reference genomes using an in-house pipeline to analyze mtDNA methylation (Fig. 1)

Summary

Introduction

Mitochondria are unique organelles in that they have their own circular genome, approximately 16.6 kb in size [1]. Most research is either focussed on low resolution, global DNA methylation, or candidate gene DNA methylation changes using techniques such as bisulfite pyrosequencing [20]. These recent publications have indicated that differences in mtDNA methylation are present in a variety of different phenotypes [24,25,26,27,28,29] and may have potential utility as a biomarker [30]. DNA methylation is an important epigenetic mechanism involved in gene regulation, with alterations in DNA methylation in the nuclear genome being linked to numerous complex diseases. We highlight the utility of this approach in identifying differences in mitochondrial DNA methylation across regions of the human brain and pre-mortem blood

Methods

Results

Discussion

Conclusion