Identification of genetic elements that autonomously determine DNA methylation states
F Lienert, C Wirbelauer, I Som, A Dean, F Mohn… - Nature …, 2011 - nature.com
… DNA methylation states, we used mouse embryonic stem cells as a cellular model. The
methylation … epiblast cells, with established genome-wide methylation outside of CpG islands 24 . …
methylation … epiblast cells, with established genome-wide methylation outside of CpG islands 24 . …
Cross-talk between site-specific transcription factors and DNA methylation states
A Blattler, PJ Farnham - Journal of Biological Chemistry, 2013 - ASBMB
… acquisition of DNA methylation upon binding of a TF to unmethylated DNA, (b) promotion of
DNA methylation upon binding of a TF to unmethylated DNA, (c) reversal of DNA methylation …
DNA methylation upon binding of a TF to unmethylated DNA, (c) reversal of DNA methylation …
DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning
… methylation states and compared the model to existing imputation strategies for DNA
methylation … , we considered local averaging of the observed methylation states, either in 3-kbp …
methylation … , we considered local averaging of the observed methylation states, either in 3-kbp …
Function and information content of DNA methylation
D Schübeler - Nature, 2015 - nature.com
… Interestingly, CGIs marked by H3K27me3 are nevertheless more susceptible to DNA
methylation during differentiation and in disease states such as cancer 46,47 . Furthermore, CGIs …
methylation during differentiation and in disease states such as cancer 46,47 . Furthermore, CGIs …
New concepts in DNA methylation
A Jeltsch, RZ Jurkowska - Trends in biochemical sciences, 2014 - cell.com
… Although of vital importance for the DNA methylation process in cells, this preference is by
far not enough to copy faithfully and site specifically the methylation state of the ∼56 million …
far not enough to copy faithfully and site specifically the methylation state of the ∼56 million …
DNA methylation: bisulphite modification and analysis
… Since that time, bisulphite genomic sequencing has become the standard for DNA methylation
analysis, as this method defines the methylation state of every cytosine residue in the …
analysis, as this method defines the methylation state of every cytosine residue in the …
DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning
… To further evaluate the effectiveness of DeepSignal for predicting DNA methylation state,
we compare it with the results of bisulfite sequencing of two H. sapiens samples: HX1 and …
we compare it with the results of bisulfite sequencing of two H. sapiens samples: HX1 and …
A multistep epigenetic switch enables the stable inheritance of DNA methylation states
HN Lim, A Van Oudenaarden - Nature genetics, 2007 - nature.com
… , DNA methylation at cis-regulatory sequences determines whether gene expression is on or
off. Stable inheritance of these expression states is … the stability of these states by using the …
off. Stable inheritance of these expression states is … the stability of these states by using the …
MethylMix: an R package for identifying DNA methylation-driven genes
O Gevaert - Bioinformatics, 2015 - academic.oup.com
… MethylMix requires a large cohort to identify methylation states and capture DNA methylation
heterogeneity present in a particular disease. We used MethylMix and their associated DM-…
heterogeneity present in a particular disease. We used MethylMix and their associated DM-…
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states
… , the inheritance of these DNA methylation states has been … methylation state of a single
CpG site (12,13). Because unmethylated cytosine is inserted into the new strands during DNA …
CpG site (12,13). Because unmethylated cytosine is inserted into the new strands during DNA …