Differential Nuclease Sensitivity Profiling of Chromatin Reveals Biochemical Footprints Coupled to Gene Expression and Functional DNA Elements in Maize[W][OPEN]
| Autor: | Jinfeng Zhang, Hank W. Bass, Gregg G. Hoffman, Jonathan D J Labonne, S.B. Girimurugan, Karen M. McGinnis, Thelma F. Madzima, Mohammad Parwez Alam, Jonathan H. Dennis, Daniel L. Vera |
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| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Nucleosome organization
DNA Plant DNA Footprinting Plant Science Computational biology Biology Zea mays Gene Expression Regulation Plant Nucleosome Micrococcal Nuclease Large-Scale Biology Article Scaffold/matrix attachment region skin and connective tissue diseases Gene ChIA-PET Oligonucleotide Array Sequence Analysis Plant Proteins Genetics Regulation of gene expression Homeodomain Proteins Binding Sites High-Throughput Nucleotide Sequencing Cell Biology Chromatin Nucleosomes biology.protein sense organs Genome Plant Micrococcal nuclease Protein Binding |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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