title: 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.
authors.affiliation: Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Grob
authors.affiliation: Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland.
authors.forename: Marc W
authors.initials: MW
authors.lastname: Schmid
authors.affiliation: Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland. Electronic address: grossnik@botinst.uzh.ch.
authors.forename: Ueli
authors.initials: U
authors.lastname: Grossniklaus
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics; D002467:Cell Nucleus / Q000648:ultrastructure; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism* / Q000648:ultrastructure; D032461:Chromosomes, Plant / Q000737:chemistry / Q000378:metabolism* / Q000648:ultrastructure; D018744:DNA, Plant / Q000737:chemistry; D004330:Drosophila / Q000235:genetics* / Q000378:metabolism; D057890:Epigenomics / Q000379:methods; D017404:In Situ Hybridization, Fluorescence; D009690:Nucleic Acid Conformation; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D018744:DNA, Plant