Genome-wide identification of Polycomb target genes in human embryonic stem cells

Polycomb group (PcG) proteins are epigenetic regulators that are essential for stem cell differentiation. Identifying PcG binding profiles is important for understanding the mechanisms of PcG-mediated repression in mammals. We used a mapping-convergence (M-C) algorithm using support vector machine (SVM) technology for genome-wide identification of PcG target genes in human embryonic stem cells. The method combined histone modifications and transcription factor binding motifs, eliminating the need for negative training samples as in traditional SVM. Good prediction accuracy comprising 3-fold cross-validation was obtained. In the analysis of 3133 PcG target genes identified by the model, PcG proteins were observed to suppress gene expression during differentiation. The results suggested that PcG and DNA methylation non-redundantly repress gene expression during differentiation. The genome-wide identification of PcG target genes will aid the further analysis of PcG mechanisms.

► We applied a mapping-convergence algorithm using SVM to predict PcG target genes.
► PcG proteins suppress gene expression during differentiation.
► PcG target genes tend to interact with more proteins in PPIN.