Unmethylated Regions Encompass The Functional Space Within The Maize Genome

Abstract

Delineating the functional space within genomes has been a long-standing goal shared among geneticists, molecular biologists, and genome scientists. The genome of Zea mays (maize) has served as a model for locating functional elements within the gene-distal intergenic space. A recent development has been the discovery and use of accessible chromatin as a proxy for functional regulatory elements. However, the idea has recently arisen that DNA methylation data could supplement the use of accessible chromatin data for homing in on regulatory regions. Here, I test the robustness of using DNA methylation as a proxy for functional space. I find that CHG methylation can be non-arbitrarily partitioned into hypo-methylated and hyper-methylated regions. Hypo-methylated CHG regions are stable across development and contain nearly all accessible chromatin. Note: changes that will be made in version 2: expand introduction; expand discussion; add additional analyses; expand methods; link to github scripts.