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Open AccessRibosomal DNA copy number is associated with body mass in humans and other mammals
Body mass results from a complex interplay between genetics and environment. Previous studies of the genetic contribution to body mass have excluded repetitive regions due to the technical limitations of platf...
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Open AccessAuthor Correction: The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans
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Article
A stochastic basis for metabolic phenotypes
It has long been recognized that some phenotypic variation in mammals cannot be explained by known genetic or environmental variables. Here, the authors show that the absence of Nnat expression is associated with...
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Article
Open AccessGenetic variation at mouse and human ribosomal DNA influences associated epigenetic states
Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far no...
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Article
Open AccessDNA methylation aging clocks: challenges and recommendations
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other v...
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Open AccessEarly life diet conditions the molecular response to post-weaning protein restriction in the mouse
Environmental influences fluctuate throughout the life course of an organism. It is therefore important to understand how the timing of exposure impacts molecular responses. Herein, we examine the responses of...
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Open AccessAgeing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species
Mammalian species exhibit a wide range of lifespans. To date, a robust and dynamic molecular readout of these lifespan differences has not yet been identified. Recent studies have established the existence of ...
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Open AccessIncreased DNA methylation variability in type 1 diabetes across three immune effector cell types
The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epige...
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Open AccessCorrelation of an epigenetic mitotic clock with cancer risk
Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be...
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Open AccessA donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation
Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematological conditions. Acute graft-versus-host disease (aGVHD) is a prevalent immune-mediated complication followin...
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Open AccessThe senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans
Cellular senescence is a stable arrest of proliferation and is considered a key component of processes associated with carcinogenesis and other ageing-related phenotypes. Here, we perform methylome analysis of...
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Open AccessSexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development
As sex determines mammalian development, understanding the nature and developmental dynamics of the sexually dimorphic transcriptome is important. To explore this, we generated 76 genome-wide RNA-seq profiles ...
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Open AccessCorrecting for cell-type composition bias in epigenome-wide association studies
Recent epigenome-wide association studies have indicated a potential role for epigenetic variation in the etiology of complex human diseases. However, one major challenge is to distinguish true epigenetic vari...
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Article
Open AccessMarmal-aid - a database for Infinium HumanMethylation450
DNA methylation is indispensible for normal human genome function. Currently there is an increasingly large number of DNA methylomic data being released in the public domain allowing for an opportunity to inve...
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Article
Open AccessInactive or moderately active human promoters are enriched for inter-individual epialleles
Inter-individual epigenetic variation, due to genetic, environmental or random influences, is observed in many eukaryotic species. In mammals, however, the molecular nature of epiallelic variation has been poo...
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Epigenome-wide association studies for common human diseases
Epigenetic variation affects genome function and hence can contribute to common disease. To establish a possible link requires systematic studies, such as the ...
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Open AccessGenome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus
Diabetic nephropathy is a serious complication of diabetes mellitus and is associated with considerable morbidity and high mortality. There is increasing evidence to suggest that dysregulation of the epigenome...
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A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
An inability to estimate absolute DNA methylation levels has slowed progress in understanding the role of this epigenetic modification in health and disease. Down et al. describe an algorithm for analyzing methyl...
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Open AccessGeneration of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many d...
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DNA methylation profiling of human chromosomes 6, 20 and 22
DNA methylation is the most stable type of epigenetic modification modulating the transcriptional plasticity of mammalian genomes. Using bisulfite DNA sequencing, we report high-resolution methylation profiles...
