Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression

Using a ChIP-Seq data set of 20 histone lysine and arginine methylations and histone variant H2A.Z in human CD4+ T-cells, we built predictive models of gene expression as a function of histone modification/variant levels using Multilinear (ML) Regression and Multivariate Adaptive Regression Splines (MARS). Along with extensive crosstalk among the 20 histone methylations, we found H4R3me2 was the most and second most globally repressive histone methylation among the 20 studied in the ML and MARS models, respectively. In support of our finding, a number of experimental studies show that PRMT5-catalyzed symmetric dimethylation of H4R3 is associated with repression of gene expression. This includes a recent study, which demonstrated that H4R3me2 is required for DNMT3A-mediated DNA methylation--a known global repressor of gene expression.In stark contrast to univariate analysis of the relationship between H4R3me2 and gene expression levels, our study showed that the regulatory role of some modifications like H4R3me2 is masked by confounding variables, but can be elucidated by multivariate/systems-level approaches.Histones are subjected to numerous modifications, including methylation, acetylation and phosphorylation. Over 60 different amino acid residues of the histones, detected by specific antibodies or mass spectrometry, can be modified. They regulate a number of important processes on DNA, including transcription [1,2]. Extensive studies comparing histone modification and transcription levels have established that histone methylation is associated with either transcriptional repression or activation. A number of marks have been classified as "activating" transcription including H3 lysine 4 tri-methyl (H3K4me3) and H3 lysine 36 tri-methyl (H3K36me3) and "repressing" transcription including H3 lysine 27 tri-methyl (H3K27me3) [1,2]. These modifications can be recognized by chromatin remodeling proteins (readers), which render chromatin in either "open", transcriptionall