Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands.

PloS One
Clemens WrzodekAndreas Zell

Abstract

DNA methylation of CpG islands plays a crucial role in the regulation of gene expression. More than half of all human promoters contain CpG islands with a tissue-specific methylation pattern in differentiated cells. Still today, the whole process of how DNA methyltransferases determine which region should be methylated is not completely revealed. There are many hypotheses of which genomic features are correlated to the epigenome that have not yet been evaluated. Furthermore, many explorative approaches of measuring DNA methylation are limited to a subset of the genome and thus, cannot be employed, e.g., for genome-wide biomarker prediction methods. In this study, we evaluated the correlation of genetic, epigenetic and hypothesis-driven features to DNA methylation of CpG islands. To this end, various binary classifiers were trained and evaluated by cross-validation on a dataset comprising DNA methylation data for 190 CpG islands in HEPG2, HEK293, fibroblasts and leukocytes. We achieved an accuracy of up to 91% with an MCC of 0.8 using ten-fold cross-validation and ten repetitions. With these models, we extended the existing dataset to the whole genome and thus, predicted the methylation landscape for the given cell types. The me...Continue Reading

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Citations

Dec 27, 2013·BMC Systems Biology·Meeta P PradhanMathew J Palakal
Apr 10, 2013·Epigenomics·Jerome D Boyd-KirkupJing-Dong J Han
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Dec 26, 2012·Trends in Molecular Medicine·Alasdair MacKenzieScott Davidson
Apr 26, 2015·Genome Research·Irene M KaplowHunter B Fraser

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
subclone sequencing
MethylSeq

Software Mentioned

PhastCon
ModuleMaster
UCSC genome browser
PhastCons
Ensembl
LIBSVM svm - predict
professional
SpliceDB
NUBIScan
TRANSFAC

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