title: Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize.
abstract: The eukaryotic genome is organized into nucleosomes, the fundamental units of chromatin. The positions of nucleosomes on DNA regulate protein-DNA interactions and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in gene expression relate to changes in nucleosome position is poorly understood. We show that in nucleosome occupancy mapping experiments in maize (Zea mays), particular genomic regions are highly susceptible to variation introduced by differences in the extent to which chromatin is digested with micrococcal nuclease (MNase). We exploited this digestion-linked variation to identify protein footprints that are hypersensitive to MNase digestion, an approach we term differential nuclease sensitivity profiling (DNS-chip). Hypersensitive footprints were enriched at the 5' and 3' ends of genes, associated with gene expression levels, and significantly overlapped with conserved noncoding sequences and the binding sites of the transcription factor KNOTTED1. We also found that the tissue-specific regulation of gene expression was linked to tissue-specific hypersensitive footprints. These results reveal biochemical features of nucleosome organization that correlate with gene expression levels and colocalize with functional DNA elements. This approach to chromatin profiling should be broadly applicable to other species and should shed light on the relationships among chromatin organization, protein-DNA interactions, and genome regulation.
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295.
authors.forename: Daniel L
authors.identifier: http://orcid.org/0000-0003-2202-7397
authors.initials: DL
authors.lastname: Vera
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295.
authors.forename: Thelma F
authors.initials: TF
authors.lastname: Madzima
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Labonne
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295.
authors.forename: Mohammad P
authors.initials: MP
authors.lastname: Alam
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295.
authors.forename: Gregg G
authors.initials: GG
authors.lastname: Hoffman
authors.affiliation: Department of Statistics, Florida State University, Tallahassee, Florida 32306.
authors.forename: S B
authors.initials: SB
authors.lastname: Girimurugan
authors.affiliation: Department of Statistics, Florida State University, Tallahassee, Florida 32306.
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295.
authors.forename: Karen M
authors.initials: KM
authors.lastname: McGinnis
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295.
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Dennis
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295 bass@bio.fsu.edu.
authors.forename: Hank W
authors.identifier: http://orcid.org/0000-0003-0522-0881
authors.initials: HW
authors.lastname: Bass
mesh_terms: D001665:Binding Sites / Q000235:genetics; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D018983:DNA Footprinting / Q000379:methods; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D008836:Micrococcal Nuclease / Q000378:metabolism*; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D018744:DNA, Plant; D018398:Homeodomain Proteins; C095848:Kn1 protein, plant; D009707:Nucleosomes; D010940:Plant Proteins; D008836:Micrococcal Nuclease