Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes

A Blattler, L Yao, H Witt, Y Guo, CM Nicolet, BP Berman… - Genome biology, 2014 - Springer
Background Gene expression is epigenetically regulated by a combination of histone
modifications and methylation of CpG dinucleotides in promoters. In normal cells, CpG-rich …

Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer

H Heyn, E Vidal, HJ Ferreira, M Vizoso, S Sayols… - Genome biology, 2016 - Springer
Background One of the hallmarks of cancer is the disruption of gene expression patterns.
Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA …

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

D Aran, S Sabato, A Hellman - Genome biology, 2013 - Springer
Background Abnormal epigenetic marking is well documented in gene promoters of cancer
cells, but the study of distal regulatory siteshas lagged behind. We performed a systematic …

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

BP Berman, DJ Weisenberger, JF Aman, T Hinoue… - Nature …, 2012 - nature.com
Extensive changes in DNA methylation are common in cancer and may contribute to
oncogenesis through transcriptional silencing of tumor-suppressor genes. Genome-scale …

Defining a chromatin pattern that characterizes DNA-hypermethylated genes in colon cancer cells

KM McGarvey, L Van Neste, L Cope, JE Ohm… - Cancer research, 2008 - AACR
Epigenetic gene regulation is a key determinant of heritable gene expression patterns and is
critical for normal cellular function. Dysregulation of epigenetic transcriptional control is a …

Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

A de Mendoza, TV Nguyen, E Ford, D Poppe… - Genome Biology, 2022 - Springer
Background Cytosine DNA methylation is widely described as a transcriptional repressive
mark with the capacity to silence promoters. Epigenome engineering techniques enable …

DNA methylation of the first exon is tightly linked to transcriptional silencing

F Brenet, M Moh, P Funk, E Feierstein, AJ Viale… - PloS one, 2011 - journals.plos.org
Tissue specific patterns of methylated cytosine residues vary with age, can be altered by
environmental factors, and are often abnormal in human disease yet the cellular …

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation

S Lou, HM Lee, H Qin, JW Li, Z Gao, X Liu, LL Chan… - Genome biology, 2014 - Springer
Background DNA methylation is an important type of epigenetic modification involved in
gene regulation. Although strong DNA methylation at promoters is widely recognized to be …

A diverse epigenetic landscape at human exons with implication for expression

M Singer, I Kosti, L Pachter… - Nucleic acids …, 2015 - academic.oup.com
DNA methylation is an important epigenetic marker associated with gene expression
regulation in eukaryotes. While promoter methylation is relatively well characterized, the role …

Dynamic DNA methylation across diverse human cell lines and tissues

KE Varley, J Gertz, KM Bowling, SL Parker… - Genome …, 2013 - genome.cshlp.org
As studies of DNA methylation increase in scope, it has become evident that methylation has
a complex relationship with gene expression, plays an important role in defining cell types …