Distinct modes of DNA accessibility in plant chromatin

Abstract

The accessibility of DNA to regulatory proteins is a major property of the chromatin environment that favours or hinders transcription. Recent studies in flies reported that H3K9me2-marked heterochromatin is accessible while H3K27me3-marked chromatin forms extensive domains of low accessibility. Here we show that plants regulate DNA accessibility differently. H3K9me2-marked heterochromatin is the least accessible in the Arabidopsis thaliana genome, and H3K27me3-marked chromatin also has low accessibility. We see that very long genes without H3K9me2 or H3K27me3 are often inaccessible and generated significantly lower amounts of antisense transcripts than other genes, suggesting that reduced accessibility is associated with reduced recognition of alternative promoters. Low accessibility of H3K9me2-marked heterochromatin and long genes depend on cytosine methylation, explaining why chromatin accessibility differs between plants and flies. Together, we conclude that restriction of DNA accessibility is a local property of chromatin and not necessarily a consequence of microscopically visible compaction.

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

“…For the chromatin digestion, PCR signals of the two heterochromatic TE genes remained nearly constant while PCR signals of the two active genes dropped rapidly, confirming our hypothesis of differences between heterochromatin regions and active genes. This is in agreement with genome-wide profiles (Shu et al, 2012) and establishes these regions as insensitive and sensitive controls for future assays. Interestingly, the sensitivity of the two PcG-targeted genes AG and FT seemed to be between the TE genes and the active genes.…”

“…As an example, the chromatin sensitivity was analyzed for two silent transposable element (TE) genes (Ta2 and Cinful-like) and two active genes (GAPDHa and ACTIN7 [ACT7]) in Arabidopsis. We and others have shown that transcription is generally associated with accessible chromatin (Weil et al, 2004;Boyle et al, 2008;Bell et al, 2010;Shu et al, 2012;Zhang et al, 2012). Thus, we predict that the two TE genes should be much less sensitive to DNase I than the two active genes and, therefore, can be used as insensitive and sensitive controls in future assays.…”

“…Thus, we predict that the two TE genes should be much less sensitive to DNase I than the two active genes and, therefore, can be used as insensitive and sensitive controls in future assays. Reduced DNA accessibility is now also considered a silencing mechanisms established by Polycomb group (PcG) proteins in animals (Bell et al, 2010;Eskeland et al, 2010;Naughton et al, 2010;Bantignies et al, 2011) and plants (Shu et al, 2012). Therefore, two Arabidopsis PcG target genes (AG and FT) were included in the assays.…”

“…7, left three columns). Isolated DNA can be labeled and hybridized to genomic DNA tiling arrays (Shu et al, 2012). Alternatively, isolated DNA can be subjected to next-generation sequencing.…”

“…The technique used in these reports was exclusively DNase I treatment and analysis of accessibility using Southern blotting. More recently, we have combined the DNase I sensitivity assay with whole-genome tiling arrays in Arabidopsis to generate a genome-wide chromatin accessibility profile (Shu et al, 2012).…”