Hennig, Lars
- Department of Plant Biology, Swedish University of Agricultural Sciences
- Swiss Federal Institute of Technology (ETH Zürich)
- Uppsala University
Abstract
DNA accessibility is an important layer of regulation of DNA-dependent processes. Methods that measure DNA accessibility at local and genome-wide scales have facilitated a rapid increase in the knowledge of chromatin architecture in animal and yeast systems. In contrast, much less is known about chromatin organization in plants. We developed a robust DNase I-polymerase chain reaction (PCR) protocol for the model plant Arabidopsis (Arabidopsis thaliana). DNA accessibility is probed by digesting nuclei with a gradient of DNase I followed by locus-specific PCR. The reduction in PCR product formation along the gradient of increasing DNase I concentrations is used to determine the accessibility of the chromatin DNA. We explain a strategy to calculate the decay constant of such signal reduction as a function of increasing DNase I concentration. This allows describing DNA accessibility using a single variable: the decay constant. We also used the protocol together with AGRONOMICS1 DNA tiling microarrays to establish genome-wide DNase I sensitivity landscapes.
Published in
Plant Physiology
2013, volume: 162, number: 4, pages: 1794-1801
Publisher: AMER SOC PLANT BIOLOGISTS
SLU Authors
UKÄ Subject classification
Developmental Biology
Plant Biotechnology
Publication identifier
- DOI: https://doi.org/10.1104/pp.113.220400
Permanent link to this page (URI)
https://res.slu.se/id/publ/52588