Genome-wide analyses of epigenomic and transcriptomic profiles provide extensive resources for discovering epigenetic regulatory mechanisms. However, the construction of functionally-relevant hypotheses from correlative patterns and the rigorous testing of these hypotheses can be challenging. We combined bioinformatics-driven hypothesis building with mutant analyses to identify potential epigenetic mechanisms using the model plant Arabidopsis thaliana. Genome-wide maps of 9 histone modifications were produced by ChIP-seq together with a strand-specific RNA-seq dataset to profile the epigenome and transcriptome of Arabidopsis. Combinatorial chromatin patterns were described by the delineation of 42 major chromatin states and biochemical validation of selected states with the re-ChIP assay. The functional relevance of chromatin modifications were analyzed with ANCORP and newly developed State-Specific Effects Analysis (SSEA) methods, which interrogates individual chromatin marks in the context of combinatorial chromatin states. Based on results from these approaches, we proposed the hypothesis that DNA methylation (5mC) and H3K36me may synergistically repress the production of Natural Antisense Transcripts (NATs) in the context of actively expressed genes. Mutant analyses supported this proposed model at a significant portion of the tested loci. We further identified Polymerase Associated Factors (PAF) as a potential repressor for NAT abundance. Although the majority of tested NATs were found to localize to the nucleus, we also found evidence for cytoplasmically-partitioned NATs. The significance of subcellular localization of NATs and their biological functions remain to be defined.
© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd