Abstract
BackgroundOur understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome.ResultsAlthough open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs’ chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin.ConclusionsChromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.
Highlights
Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited
These trends correlate with a slightly higher proportion of genes showing D-genome biased expression [30]. To investigate whether these patterns of epigenomic and gene expression variation are reflected in the level of chromatin accessibility, we assessed wheat chromatin states using digestion with different concentrations of micrococcal nuclease (MNase)
Segmentation of the wheat genome based on the distribution of differential nuclease sensitivity (DNS) scores was performed using the iSeg program [36], which identifies outlier regions (> 1.5 standard deviations of the genome-wide DNS score) corresponding to either MNase hyper-sensitive footprints (MSFs) or MNase hyperresistant footprints (MRFs)
Summary
Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. In contrast to heterochromatic regions, nucleosomes in promoters and enhancers were shown to dynamically change between accessible and inaccessible configurations in response to developmental and environmental signals activating or suppressing gene expression [1, 3, 4]. These changes in chromatin states are associated with posttranscriptional histone modifications mediated by a large number of chromatin-associated proteins. Transition from open to closed chromatin, accompanying transcriptional suppression, could be promoted by Polycomb protein complexes [5, 6], which could be involved in long-range interactions with distant cis-regulatory elements [7]. Open chromatin states reflect the regulatory potential of a genomic region and their characterization helps to accurately identify promoters, enhancers, and transcription factor binding sites
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