Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production

Abstract

SUMMARYGenome-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 may 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 nine histone modifications produced by ChIP-seq were used together with a strand-specific RNA-seq dataset to profile the epigenome and transcriptome of Arabidopsis. Combinatorial chromatin patterns were described by 42 major chromatin states with selected states validated using the re-ChIP assay. The functional relevance of chromatin modifications was analyzed using the ANchored CORrelative Pattern (ANCORP) method and a newly developed state-specific effects analysis (SSEA) method, which interrogates individual chromatin marks in the context of combinatorial chromatin states. Based on results from these approaches, we propose the hypothesis that cytosine methylation (5mC) and histone methylation H3K36me may synergistically repress production of natural antisense transcripts (NATs) in the context of actively expressed genes. Mutant analyses supported this proposed model at a significant proportion of the tested loci. We further identified polymerase-associated factor 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 the subcellular localization of NATs and their biological functions remain to be defined.

Dicer-independent RNA-directed DNA methylation in Arabidopsis

“…We also examined specific histone modifications associated with the three types of RdDM loci using publicly available data [41]. We found that the ID and PD loci npg www.cell-research.com | Cell Research have significantly higher levels of two heterochromatin marks, H3K9me2 and H3K27me1 than the FD loci (Figure 5C and Supplementary information, Table S3).…”

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

“…H4K16ac is positively correlated with active marks (H3K9ac, H3K18ac, H3K4me2/3 and H3K36me2/3 15,[42][43][44] ) and anti-correlated with repressive modifications (H3K27me1 and H3K9me2 15,45 ) and histone variants H3.1 and H2A.W, which are required for heterochromatin condensation ( Fig. 2A).…”

“…The histone modification ChIPsequencing datasets were obtained from previously published papers. 43,46,47,70 Pairwise association analysis between histone modification marks was calculated by Pearson correlation method. The P values was calculated by a Student t-test.…”

Mobile small RNAs and their role in regulating cytosine methylation of DNA

“…The antagonistic relationship between H3K36me3 and H3K27me3 has been previously noted within genes, together with the hypothesis that natural antisense transcript (NAT) production is repressed by a combination of cytosine methylation and H3K36me3. 55 In combination with our data, this may suggest that either NATs have an increased tendency to generate mobile sRNAs, or that this is a more general result applying to some subset of mobile sRNA loci.…”

“…We further investigated differentiation between sRNA-methylome interaction classes through comparisons with the histone modification data of Luo et al 55 Peaks for 9 histone modifications were identified using the MACS2 pipeline 56 ; where data from multiple samples was available this was merged using DiffBind. 57 Overlaps between the locus classes and regions of histone modification (Fig.…”