Open chromatin reveals the functional maize genome

Abstract

Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome.

Keywords: biased gene conversion; chromatin; maize; recombination; variance partitioning.

Fig. 1.

The distribution of MNase HS regions in maize. (A) The frequency of MNase HS bases across the genome in 1-Mb windows, along with the recombination frequency. (B) The relationship between gene density and MNase HS density in 1-Mb windows. (C) The total sizes of MNase HS regions in the root and shoot and the intersection of the two tissues. (D) MNase HS base frequency within and surrounding protein coding genes. Genic elements were binned according to percentage of total element size, whereas upstream and downstream regions were binned in units of 10 bp. (E) The distribution of distances to the nearest gene boundary for intergenic MNase HS bases (blue) and for all intergenic bases (green).

Fig. 2.

MNase HS is associated with gene regulation. Mean MNase HS profiles in root (red) and shoot (green) for genes divided into tertiles according to expression levels within root and within shoot.

Fig. 3.

MNase HS regions are associated with DNA hypomethylation. Mean DNA methylation profiles within and surrounding MNase HS regions.

Fig. 4.

GC-biased gene conversion strongly affects coding sequence content surrounding MNase HS regions. (A) The frequency of G/C content and the histone modifications H3K9me2 and H3K4me3 surrounding and within MNase HS regions for coding and genic, noncoding (e.g., UTR, intron) sites. Base content for coding sites is divided into invariant and neutral sites. Base positions are plotted relative to the direction of transcription. (B) Mean ranges of GC-biased gene conversion probabilities within MNase HS regions and regions 1–2 kb from the nearest MNase HS region for both recombination hotspots and control regions flanking recombination hotspots. Ranges correspond to 95% credible intervals.

Fig. 5.

MNase HS marks known QTL. (A) Profile of shoot hypersensitivity in the tb1 region. Regions with a MNase HS Bayes factor above 1 are shown in red, and the opacity is proportional to the significance of the difference. The putative regulatory region containing the tourist and hopscotch TEs is enlarged. Regions without uniquely mapping reads are shown in gray. Regions covered by reads but without sufficient evidence for hypersensitivity are shown in blue. (B) Posterior distributions for the relative frequency of GWAS SNPs among total SNPs within 2 kb of a MNase HS region vs. control regions ≥2 kb from the nearest MNase HS region, directly flanking the MNase HS proximal regions.

Fig. 6.

MNase HS regions explain nearly half of quantitative trait variation. (A and B) The enrichments of variance in functional categories within (A) US-NAM and (B) Ames Diversity Panel (C and D) The average contributions of SNPs with the given annotations to heritable variance and the partitioning of variance to individual traits within (C) US-NAM and (D) Ames Diversity Panel. Exploded slices in the pie charts denote the MNase HS.