Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture

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.

Spatial relationship between chromosomal domains in diploid and autotetraploidArabidopsis thaliananuclei

“…Similar data were obtained using chromosome conformation capture technique, which demonstrated that the distal chromatin domains interact more frequently than proximal domains. 40,41 This suggests that distal chromatin domains might be privileged in terms of homologous association, which might be thus involved in regulating their activity.…”

Non-random chromosome arrangement in triploid endosperm nuclei

“…What emerged from these studies is that domains of low or high interaction frequency, i.e., loose or compacted structural domains, form locally on chromosome arms. These domains correlate with well-defined epigenetic indexing of chromatin, corresponding to distinct functional states with regard to, e.g., transcriptional competence, but are independent of CT organization (Feng et al 2014;Grob et al 2013Grob et al , 2014Wang et al 2015).…”

“…At a scale of ∼100 kb, the association frequency of homologous loci also follows a random spatial distribution (RSD) model (Pecinka et al 2004). Recently, chromosome configuration capture-based analyses (4C and Hi-C) of interacting domains confirmed a global chromatin folding according to a fractal globule model without a preferential association between homologous chromosomes (Feng et al 2014;Grob et al 2013Grob et al , 2014Wang et al 2015). What emerged from these studies is that domains of low or high interaction frequency, i.e., loose or compacted structural domains, form locally on chromosome arms.…”

Chromosome conformation capture technologies and their impact in understanding genome function

“…The first step of the method involves formaldehyde crosslinking of the cell population. The percentage of formaldehyde varies in different applications, for mammalian and yeast cell fixation with 1 % formaldehyde for 10 min is preferred, whereas up to 3 % for 30 min has been used for Drosophila cells, and 2 % for 5 min were used in Arabidopsis cells (Comet et al 2011;Duan et al 2012;Grob et al 2013;Hagege et al 2007), but we note that an extensive Fig. 1 Timeline showing the major steps that lead to the view of chromatin organization and ultimately to the development of chromosome conformation capture assays.…”