Putting a modern twist on the holiday spirit, researchers from the University of Zurich (Switzerland) gift a new piece of chromatin architecture that welcomes each and every chromosome to its party. And it comes from a surprisingly festive plant; Arabidopsis.
On a Hi-C run surveying chromatin architecture, the touring researchers encountered a number of landmarks. At first they came across the standard sights:
- Chromatin domains of each shape and size, but generally ranging several Mb.
- Not so surprisingly, the observation that the chromatin architecture is ‘linked to the epigenetic landscape’.
- A better correlation of nuclear size with long distance trans interactions than local cis interactions.
But then their journey took a turn most strange, when they encountered a delightful new structure that just couldn’t get enough chromosome. Termed KNOT, it:
- Interacts with genomic regions of all five Arabidopsis chromosomes.
- Has preferred bedfellows, termed KNOT ENGAGED ELEMENT (KEE) regions.
- KEE regions are found in heterochormatic islands that pop up in euchromatin and are associated with distinct epigenetic marks.
When it comes to biological function, the authors hypothesize that KNOT is tangled in the messy business of being a transposon trap. KEEs are similar to PIWI-interacting RNA (piRNA) clusters in that they represent the preferred landing sites of transposable elements.
Interestingly, the authors parallel KNOT to the flamenco locus of Drosophila, which also serves as a transposable element trap. This cross-species similarity leaves the authors hypothesizing that KNOT could be a conserved nuclear structure, with analogues in other eukaryotes.
Go see how the genome likes to place ancient epigenetic traps in Molecular Cell, December 2014