title: 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.
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; esb33@cornell.edu eli.rodgers-melnick@pioneer.com.
authors.forename: Eli
authors.initials: E
authors.lastname: Rodgers-Melnick
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL 32306;
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Vera
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295;
authors.forename: Hank W
authors.initials: HW
authors.lastname: Bass
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853 esb33@cornell.edu eli.rodgers-melnick@pioneer.com.
authors.forename: Edward S
authors.identifier: 0000-0002-3100-371X
authors.initials: ES
authors.lastname: Buckler
mesh_terms: D002843:Chromatin / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D005091:Exons / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008836:Micrococcal Nuclease / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D018744:DNA, Plant; D009707:Nucleosomes; D010940:Plant Proteins; D008836:Micrococcal Nuclease
keywords: biased gene conversion; chromatin; maize; recombination; variance partitioning