ArticleThe Plant cell2014
Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 91 citations in OpenAlex.
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- The chromatin accessibility landscape during early maize seed development.The Plant journal : for cell and molecular biology · 2025Article
- ZmHsp18 screened from the ZmHsp20 gene family confers thermotolerance in maize.BMC plant biology · 2024Article
- Functional Characterization of Accessible Chromatin in Common Wheat.International journal of molecular sciences · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- MNase-Seq Analysis for Identifying Stress-Altered Nucleosome Occupancy in Plants.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Epigenetic Landscape Is Largely Shaped by Diversiform Transposons inInternational journal of molecular sciences · 2023Article
- Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei.BMC plant biology · 2023Article
- The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells.BMC genomics · 2023Article
- Phosphorylation of the FACT histone chaperone subunit SPT16 affects chromatin at RNA polymerase II transcriptional start sites in Arabidopsis.Nucleic acids research · 2022Article
- Mapping open chromatin by ATAC-seq in bread wheat.Frontiers in plant science · 2022Article
- Selection on Accessible Chromatin Regions in Capsella grandiflora.Molecular biology and evolution · 2021Article
- The native cistrome and sequence motif families of the maize ear.PLoS genetics · 2021Article
- Differential nuclease sensitivity profiling uncovers a drought responsive change in maize leaf chromatin structure for two large retrotransposon derivatives,Plant direct · 2021Article
- Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells.Nature communications · 2021Article
- Chromatin dynamics: Nucleosome occupancy and sensitivity as determinants of gene expression and cell fate.Journal of cancer biology · 2021Article
- Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes.Genome biology · 2020Article
- MNase Profiling of Promoter Chromatin inG3 (Bethesda, Md.) · 2020Article
- The regulatory landscape of early maize inflorescence development.Genome biology · 2020Article
- Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin.Plant physiology · 2020Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.