![alignment of the ten tec triton iv timebase alignment of the ten tec triton iv timebase](https://www.qsl.net/tentec/large/555.jpg)
It consists of a low density of expressed genes but a high density of repeats derived from pericentromeric regions 10. The knob hk4s in Arabidopsis, which is cytogenetically discernable, is about hundreds of kilobases close to the pericentromere on the left (top/short) arm of chromosome 4 9, 10. The knob, first discovered in maize 8, is another conspicuous chromatin structure in Arabidopsis 9. A recent study indicates that KNOT can interact with invasive DNA elements, such as transgenes, and the interaction frequency is positively correlated with transgene silencing this noncanonical silencing mechanism has been designated as KNOT-linked silencing 7.
![alignment of the ten tec triton iv timebase alignment of the ten tec triton iv timebase](https://www.qsl.net/tentec/specs/545b.jpg)
TEs are preferentially integrated into KEEs, suggesting a role of the KNOT in TE defense 4. Intriguingly, KEEs in euchromatic arms are enriched with the repressive histone mark H3K27me1 and small RNAs for gene silencing. KEEs have either short- or long-range intrachromosomal and interchromosomal interactions 4, 5 and can also interact with telomeres 4, 5. The KNOT is formed by ten KNOT engaged elements (KEEs), or interactive heterochromatic islands, which are similar in interaction patterns to Piwi-interacting RNA clusters, the major controllers of transposable element (TE) silencing in Drosophila 4, 5, 6. Notably, genome annotation shows that these two chromatin compartments are largely in accordance with the euchromatin/heterochromatin landscapes in Arabidopsis 4.īoth Hi-C and fluorescence in situ hybridization (FISH) studies have identified a chromatin structure, the KNOT, in Arabidopsis 4, 5. The Arabidopsis chromosomes, like mammalian chromosomes 1, are organized into A and B compartments 3, 4. Recently, Hi-C technology 1, which couples proximity ligation-based chromosome conformation capture (3C) 2, and next generation sequencing has revealed multifaceted and hierarchical 3D genome organization in microbes, animals, and plants (reviewed in ref. The three-dimensional (3D) configuration of genome is dynamic and can regulate gene expression. Together, our results provide insights into the relationship between TE activation and 3D genome reorganization. Furthermore, heat activation of TEs exhibits a high correlation with the reduction of chromosomal interactions involving pericentromeres, the KNOT, the knob, and the upstream and downstream flanking regions of the activated TEs. Many inter-chromosomal interactions, including those within the KNOT, are also reduced. However, interactions within pericentromeres and those between distal intra-chromosomal regions are decreased. Contacts between pericentromeric regions and distal chromosome arms, as well as proximal intra-chromosomal interactions along the chromosomes, are enhanced. By comparing genome-wide high-resolution chromatin packing patterns under normal or heat conditions obtained through Hi-C analysis, we show here that heat stress causes global rearrangement of the 3D genome in Arabidopsis thaliana.
![alignment of the ten tec triton iv timebase alignment of the ten tec triton iv timebase](https://i2.wp.com/jimkerkhoff.com/wp-content/uploads/2020/07/The-Ten-Tec-Century-21.jpeg)
But, the silencing of certain heterochromatin-associated TEs is disrupted by heat stress. In higher eukaryotes, heterochromatin is mainly composed of transposable elements (TEs) silenced by epigenetic mechanisms.