Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

W Zhang, TD Spector, P Deloukas, JT Bell… - Genome biology, 2015 - Springer
Background Recent assays for individual-specific genome-wide DNA methylation profiles
have enabled epigenome-wide association studies to identify specific CpG sites associated …

Genetics meets DNA methylation in rare diseases

G Velasco, C Francastel - Clinical genetics, 2019 - Wiley Online Library
Alterations in epigenetic landscapes are hallmarks of many complex human diseases, yet, it
is often challenging to assess the underlying mechanisms and causal link with clinical …

[HTML][HTML] AutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assay

LM Butcher, S Beck - Methods, 2010 - Elsevier
DNA methylation is an epigenetic mark linking DNA sequence and transcription regulation,
and therefore plays an important role in phenotypic plasticity. The ideal whole genome …

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal …

SS Nair, MW Coolen, C Stirzaker, JZ Song… - Epigenetics, 2011 - Taylor & Francis
DNA methylation primarily occurs at CpG dinucleotides in mammals and is a common
epigenetic mark that plays a critical role in the regulation of gene expression. Profiling DNA …

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types

MJ Ziller, F Müller, J Liao, Y Zhang, H Gu, C Bock… - PLoS …, 2011 - journals.plos.org
DNA methylation plays an important role in development and disease. The primary sites of
DNA methylation in vertebrates are cytosines in the CpG dinucleotide context, which …

Comprehensive DNA methylation analysis of human peripheral blood leukocytes and lymphoblastoid cell lines

H Sugawara, K Iwamoto, M Bundo, J Ueda… - Epigenetics, 2011 - Taylor & Francis
DNA methylation is involved in development and in human diseases. Genomic DNA derived
from lymphoblastoid cell lines (LCLs) is commonly used to study DNA methylation. There …

An integrated-omics analysis of the epigenetic landscape of gene expression in human blood cells

EM Kennedy, GN Goehring, MH Nichols, C Robins… - BMC genomics, 2018 - Springer
Background Gene expression can be influenced by DNA methylation 1) distally, at
regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current …

Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns

W Qu, S Hashimoto, A Shimada, Y Nakatani… - Genome …, 2012 - genome.cshlp.org
5-methyl-cytosines at CpG sites frequently mutate into thymines, accounting for a large
proportion of spontaneous point mutations. The repair system would leave substantial …

Extensive sequence-influenced DNA methylation polymorphism in the human genome

A Hellman, A Chess - Epigenetics & chromatin, 2010 - Springer
Background Epigenetic polymorphisms are a potential source of human diversity, but their
frequency and relationship to genetic polymorphisms are unclear. DNA methylation, an …

Quantifying the role of transcript levels in mediating DNA methylation effects on complex traits and diseases

MC Sadler, C Auwerx, K Lepik, E Porcu… - Nature …, 2022 - nature.com
High-dimensional omics datasets provide valuable resources to determine the causal role of
molecular traits in mediating the path from genotype to phenotype. Making use of molecular …