title: Hydroxymethyl cytosine marks in the human mitochondrial genome are dynamic in nature.
abstract: Apart from DNA methylation, hydroxymethylation has increasingly been studied as an important epigenetic mark. 5- hydroxymethylcytosines, though initially were thought to be an intermediary product of demethylation, recent studies suggest this to be a highly regulated process and modulated by the TET family of enzymes. Recent genome wide studies have shown that hydroxymethylcytosine marks are closely associated with the regulation of important biological processes like transcription and embryonic development. It is also known that aberrant hydroxymethylation marks have been associated with diseases like cancer. The presence of hydroxymethylcytosines in the mitochondrial genome has been earlier suggested, though the genome-scale map has not been laid out. In this present study, we have mapped and analyzed the hydroxymethylcytosine marks in the mitochondrial genome using 23 different publicly available datasets. We cross validated our data by checking for consistency across a subset of genomic regions previously annotated to hydroxymethylcytosines and show good consistency. We observe a dynamic distribution of hydroxymethylation marks in the mitochondrial genome. Unlike the methylcytosine marks, hydroxymethylcytosine marks are characterized by the lack of conservation across the samples considered, though similar cell types shared the pattern. We additionally observed that the hydroxymethylation marks are enriched in the upstream of GSS (gene start site) regions and in gene body as similar as nuclear genes. To the best of our knowledge, this is the first genome-scale map of hydroxymethyl cytosines in the human mitochondrial genome.
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India.
authors.forename: Sourav
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India. Electronic address: shantanus@igib.res.in.
authors.forename: Shantanu
authors.initials: S
authors.lastname: Sengupta
authors.affiliation: GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India. Electronic address: vinods@igib.in.
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis; D004272:DNA, Mitochondrial / Q000737:chemistry*; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D054629:Genome, Mitochondrial; D006801:Humans
chemical_list: D004272:DNA, Mitochondrial; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine
keywords: 5-Hydroxymethylcytosine; Epigenome; Mitochondria