At. Histone modifications
Histone modifications of Arabidopsis thaliana (aerial tissue)
Bioinformatics powered correlative analysis of epigenomic patterns is an effective method to help derive biological hypotheses that can be tested genetically or biochemically. To accommodate the variety and complexity of epigenomic and transcriptomic patterns, ANchored COrrelative Patterns (ANCORP) was developed as a platform to integrate and intuitively visualize a large number of genome-wide profiles. With global profiles of 9 histone modifications mapped by ChIP-seq and a strand-specific RNA-seq dataset, we have applied the ANCORP-genetics pipeline for hypothesis building and testing in order to understand how global transcription may be regulated by epigenetic pathways such as histone modifications. It was found that intragenic antisense RNAs are depleted from genes with strong gene-body H3K36me2 mark and cytosine methylation enrichments but are significantly overrepresented in H3K4me3/H3K27me3 bivalent genes. Moreover, gene body H3K36me2 and DNA methylation anti-correlate with multiple active chromatin marks including H3K4me2/3, H3K9Ac and H3K18Ac. These observations lead us to hypothesize that H3K36me2 and DNA methylation may synergistically repress active chromatin marks in gene bodies and subsequently inhibit transcription of the antisense strand. This hypothesis was tested with mutants deficient in DNA methylation (met1-1), H3K36me (sdg8-2 and elf8-1) or both (met1-1/sdg8-2). We found evidence that H3K36me2 but not DNA methylation is involved in the repression of intragenic antisense RNA production. Interestingly, the activation of antisense RNA in sdg8-2 or elf8-1 mutants does not associate with any increase of histone marks in gene bodies that are known to correlate with gene activation, suggesting a fundamental difference with sense transcription pathways. Our results suggest that ANCORP-genetics is an effective approach to uncover epigenetic regulatory mechanisms by leveraging on the rapid advances in sequencing technologies and the resultant wealth of genome-wide information.