Genome-wide analysis of local chromatin packing in Arabidopsis thaliana (original) (raw)

  1. Chang Liu1,3,
  2. Damian Roqueiro2,
  3. Dominik Grimm2,
  4. Rebecca Schwab1,
  5. Claude Becker1,
  6. Christa Lanz1 and
  7. Detlef Weigel1
  8. 1Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
  9. 2Machine Learning and Computational Biology Research Group, Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany
  10. Corresponding authors: chang.liu{at}tuebingen.mpg.de, weigel{at}weigelworld.org
  11. ↵3 These authors contributed equally to this work.

Abstract

The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.

Footnotes

This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0.