Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

Abstract

Chromosomes are folded, spatially organized, and regulated by epigenetic marks. How chromosomal architecture is connected to the epigenome is not well understood. We show that chromosomal architecture of Arabidopsis is tightly linked to the epigenetic state. Furthermore, we show how physical constraints, such as nuclear size, correlate with the folding principles of chromatin. We also describe a nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes interact. These KNOT ENGAGED ELEMENT (KEE) regions represent heterochromatic islands within euchromatin. Similar to PIWI-interacting RNA clusters, such as flamenco in Drosophila, KEEs represent preferred landing sites for transposable elements, which may be part of a transposon defense mechanism in the Arabidopsis nucleus.

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

“…However, additional categories are likely to be discovered, and this may shed light on how the cell dictates which TEs are subject to each silencing mechanism. For example, recent investigation of the three-dimensional chromosomal structure identified TE island (nonpericentromeric) regions of all five Arabidopsis chromosomes that consistently interact (Grob et al, 2014). The function and mechanism of this trans-chromosome TE interaction, termed the "KNOT," is currently not understood.…”

The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants

“…For example, in the model species Arabidopsis thaliana hypocotyls and trichomes (Traas et al, 1998), root hairs (Sugimoto-Shirasu et al, 2005) and pollen tubes (Dittmer et al, 2007;Grob et al, 2014;Wang et al, 2013) have been used to illustrate variations in cell and nuclear morphogenesis. Here, we chose three different cell types displaying distinct nuclear features to characterise their nuclear shapes and chromatin organisation (Fig.…”

FISH Is in the Limelight Again As More Than a Cytogenetical Technique for Metaphase Chromosomes

“…In particular, a chromosome conformation capture technique in combination with deep sequencing, Hi-C, can reveal the spatial genome organization in the whole genome through the frequency of the DNA interaction with each other. This genome organization has been confirmed by 3D-FISH (Markenscoff-Papadimitriou et al 2014, Feng et al 2014, Grob et al 2014. Chromosome conformation capture techniques also proposed a chromosomal module at sub-Mb scale, which is termed a topologically associated domain (TAD) ( Fig.…”