Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

Abstract

DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

“…WGBS and RNA-seq data for B73 shoot apex, immature ear and anther tissue, H3K4me3 ChIP-seq for B73 seedling leaf tissue, RNA-seq data for mop1, mop3, and wild-type siblings earshoot/seedling leaf, and WGBS data for PH207 seedling leaf were generated for experiments described in this paper. In addition the analyses in this study used previously published WGBS data for B73 seedling leaf and RNA-seq data for B73, Mo17, Oh43, Tx303, and CML322 seedling leaf from Eichten et al (16), H3K9me2 ChIP-seq data for B73 seedling from West et al (10), WGBS data for Mo17, Oh43, Tx303, and CML322 seedling leaf from Li et al (19), WGBS data for mop1 earshoot and targeted bisulfite sequencing data for mop1 earshoot, B73, mop2, and mop3 seedling leaf from Li et al (22), and chromatin accessibility data for B73 earshoot from Gent et al (13).…”

“…The maize genome is much more complex, with the majority (85.5%) of genes positioned within 1 kb of transposons. In both species, transposons tend to have quite high levels of CG and CHG methylation whereas genes have much lower levels (10). mCHH is often thought to provide an important component for silencing transposons, yet the maize genome has relatively low levels of mCHH despite the high transposon context (11).…”

“…Genomic profiles of mCHH in maize revealed that this modification is often found near genes (termed mCHH islands) and is dependent upon RdDM activity (12)(13)(14). This elevation of mCHH in regions surrounding genes is much less prevalent in Arabidopsis (10). A recent study showed that high mCHH can also be induced near genes that are up-regulated in plants subjected to phosphate starvation (15).…”

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

“…TEs, which typically contain high levels of DNA methylation and the repressive histone modification H3K9me2 in maize (Eichten et al, 2012;Regulski et al, 2013;West et al, 2014), are traditionally thought of as silenced chromatin. Specifically, all of the six most abundant LTR-retro families that we investigated exhibit high overall levels of internal DNA methylation and H3K9me2 in B73 aerial tissues, as well as spreading of these heterochromatic modifications into adjacent regions of ;1 to 2 kb (Eichten et al, 2012).…”

Genetic Perturbation of the Maize Methylome

“…The maize genome is larger than that of Arabidopsis (2500 Mb versus 125 Mb) and contains substantially more transposable elements (Baucom et al, 2009;Schnable et al, 2009). While most Arabidopsis genes are adjacent to other genes, many maize genes are flanked by heavily methylated transposons (West et al, 2014). There are also several differences in the genome-wide distribution of DNA methylation in maize relative to Arabidopsis.…”