title: Normal chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora crassa.
abstract: High-throughput chromosome conformation capture (Hi-C) analyses revealed that the 3D structure of the Neurospora crassa genome is dominated by intra- and interchromosomal links between regions of heterochromatin, especially constitutive heterochromatin. Elimination of trimethylation of lysine 9 on histone H3 (H3K9me3) or its binding partner Heterochromatin Protein 1 (HP1)-both prominent features of constitutive heterochromatin-have little effect on the Hi-C pattern. It remained possible that di- or trimethylation of lysine 27 on histone H3 (H3K27me2/3), which becomes localized in regions of constitutive heterochromatin when H3K9me3 or HP1 are lost, plays a critical role in the 3D structure of the genome. We found that H3K27me2/3, catalyzed by the Polycomb Repressive Complex 2 (PRC2) member SET-7 (SET domain protein-7), does indeed play a prominent role in the Hi-C pattern of WT, but that its presence in regions normally occupied by H3K9me3 is not responsible for maintenance of the genome architecture when H3K9me3 is lost. The Hi-C pattern of a mutant defective in the PRC2 member N. crassa p55 (NPF), which is predominantly required for subtelomeric H3K27me2/3, was equivalent to that of the set-7 deletion strain, suggesting that subtelomeric facultative heterochromatin is paramount for normal chromosome conformation. Both PRC2 mutants showed decreased heterochromatin-heterochromatin contacts and increased euchromatin-heterochromatin contacts. Cytological observations suggested elimination of H3K27me2/3 leads to partial displacement of telomere clusters from the nuclear periphery. Transcriptional profiling of Δdim-5, Δset-7, Δset-7; Δdim-5, and Δnpf strains detailed anticipated changes in gene expression but did not support the idea that global changes in genome architecture, per se, led to altered transcription.
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, OR 97403.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Klocko
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, OR 97403.
authors.forename: Tereza
authors.initials: T
authors.lastname: Ormsby
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Galazka
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, OR 97403.
authors.forename: Neena A
authors.initials: NA
authors.lastname: Leggett
authors.affiliation: Division of Chromosome Biology, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan.
authors.forename: Miki
authors.initials: M
authors.lastname: Uesaka
authors.affiliation: Division of Chromosome Biology, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan.
authors.forename: Shinji
authors.initials: S
authors.lastname: Honda
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331.
authors.forename: Michael
authors.initials: M
authors.lastname: Freitag
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, OR 97403; selker@uoregon.edu.
authors.forename: Eric U
authors.initials: EU
authors.lastname: Selker
mesh_terms: D000090266:Chromobox Protein Homolog 5; D002868:Chromosomal Proteins, Non-Histone; D002875:Chromosomes / Q000648:ultrastructure*; D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation; D004271:DNA, Fungal / Q000235:genetics; D005656:Fungal Proteins / Q000378:metabolism; D020869:Gene Expression Profiling; D020868:Gene Silencing; D016681:Genome, Fungal; D006570:Heterochromatin / Q000737:chemistry*; D006657:Histones / Q000378:metabolism; D008239:Lysine / Q000378:metabolism; D008968:Molecular Conformation; D009492:Neurospora crassa / Q000235:genetics / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D017423:Sequence Analysis, RNA; D016615:Telomere / Q000648:ultrastructure
chemical_list: D002868:Chromosomal Proteins, Non-Histone; D004271:DNA, Fungal; D005656:Fungal Proteins; D006570:Heterochromatin; D006657:Histones; D000090266:Chromobox Protein Homolog 5; D003596:Cytosine; D008239:Lysine
keywords: H3K27me2/3; Hi-C; Neurospora crassa; PRC2; facultative heterochromatin