Abstract
BackgroundThe packaging of long chromatin fibers in the nucleus poses a major challenge, as it must fulfill both physical and functional requirements. Until recently, insights into the chromosomal architecture of plants were mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation capture technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalized description of nuclear organization.ResultsEmploying circular chromosome conformation capture, this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organization of chromosomes is reflected in the genome-wide interactome. In addition, we study the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 maintains a pericentromere-like interaction profile and interactome despite its euchromatic surrounding.ConclusionDespite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: heterochromatin and euchromatin represent two distinct interactomes; interactions between chromosomes correlate with the linear position on the chromosome arm; and distal chromosome regions have a higher potential to interact with other chromosomes.
Highlights
The packaging of long chromatin fibers in the nucleus poses a major challenge, as it must fulfill both physical and functional requirements
The current knowledge on chromosomal architecture in Arabidopsis is largely based on microscopic observations
We aimed to gain insights into higher-order chromatin organization based on Circular chromosome conformation capture (4C) technology, which promises to complement previously published fluorescence in situ hybridization (FISH) experiments, and to reveal novel mechanisms governing chromosomal architecture
Summary
The packaging of long chromatin fibers in the nucleus poses a major challenge, as it must fulfill both physical and functional requirements. Insights into the chromosomal architecture of plants were mainly provided by cytogenetic studies. Over the past 15 years, the field of epigenetics has grown rapidly, addressing basic questions about the long-term regulation of genes, and how diverse cell types reach their differentiated states. These studies have provided insights into the mechanisms that enable cells to differentiate into diverse cell types with distinct phenotypes, despite sharing exactly the same genotype
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