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The extent to which physical properties and intranuclear locations of chromatin can influence transcription output remains unclear and poorly quantified. Because the scale and resolution at which structural parameters can be queried are usually so different from the scale that transcription outputs are measured, the integration of these data is often indirect. To overcome this limitation in quantifying chromatin structural parameters at different locations in the genome, a Chromatin Charting collection with 277 transposon-tagged
Arabidopsis
lines has been established in order to discover correlations between gene expression and the physical properties of chromatin loci within the nuclei.In these lines, dispersed loci in the
Arabidopsis
genome are tagged with an identical transgene cassette containing a luciferase gene reporter, which permits the quantification of gene expressions in real time, and an ∼2 kb
LacO
repeat that acts as a “chromatin beacon” to facilitate the visual tracking of a tagged locus in living plants via the expression of LacI–GFP fusion proteins in
trans
. In this chapter, we describe the methods for visualizing and tracking these insertion loci in vivo and illustrate the potential of using this approach to correlate chromatin mobility with gene expression in living plants.
