Neurospora chromosomes are organized by blocs of importin alpha-dependent heterochromatin that are largely independent of H3K9me3
- Jonathan M Galazka1,
- Andrew D Klocko2,
- Miki Uesake3,
- Shinji Honda3,
- Eric U Selker2 and
- Michael Freitag4,5
- 1 NASA Ames Research Center;
- 2 University of Oregon;
- 3 University of Fukui, Japan;
- 4 Oregon State University
- ↵* Corresponding author; email: freitagm{at}cgrb.oregonstate.edu
Abstract
Eukaryotic genomes are organized into chromatin domains with three-dimensional arrangements that presumably result from interactions between the chromatin constituents -proteins, DNA, and RNA- within the physical constraints of the nucleus. We used chromosome conformation capture (3C) followed by high-throughput sequencing (Hi- C) with wild-type and mutant strains of Neurospora crassa to gain insights into the role of heterochromatin in the organization and function of the genome. We tested the role of three proteins thought to be important for establishment of heterochromatin, namely the histone H3 lysine 9 methyltransferase DIM-5, Heterochromatin Protein 1 (HP1), which specifically binds to the product of DIM-5 (trimethylated H3 lysine 9; H3K9me3), and DIM- 3 (importin alpha), which is involved in DIM-5 localization. The average genome configuration of the wild type revealed strong intra- and inter-chromosomal associations between both constitutive and facultative heterochromatic domains, with the strongest interactions among the centromeres, subtelomeres, and interspersed heterochromatin. Surprisingly, loss of either H3K9me3 or HP1 had only mild effects on heterochromatin compaction whereas dim-3 caused more drastic changes, specifically decreasing interactions between constitutive heterochromatic domains. Thus, associations between heterochromatic regions are a major component of the chromosome conformation in Neurospora but two widely studied key heterochromatin proteins are not necessary, implying that undefined protein factors play key roles in maintaining overall chromosome organization.
- Received December 10, 2015.
- Accepted June 2, 2016.
- Published by Cold Spring Harbor Laboratory Press
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
