Normal chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora crassa

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 113; no. 52; pp. 15048 - 15053
• Main Authors: Klocko, Andrew D., Ormsby, Tereza, Galazka, Jonathan M., Leggett, Neena A., Uesaka, Miki, Honda, Shinji, Freitag, Michael, Selker, Eric U.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 27.12.2016
• Series: From the Cover
• Subjects: Biological Sciences; Chromosomes; Genomes; Heterochromatin; Mutation; Neurospora crassa; Proteins; facultative heterochromatin; Neurospora crassa; H3K27me2/3; PRC2; Hi-C
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1615546113

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.