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Series GSE232933 Query DataSets for GSE232933
Status Public on Jul 03, 2023
Title Histone deacetylation and cytosine methylation are required for the normal compartmentalization of heterochromatin in the genome organization of Neurospora crassa [ChIP-Seq]
Organism Neurospora crassa
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes: in the fungus Neurospora crassa, chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures that are anchored by heterochromatic region aggregates. However, insufficient information exists on how histone post-translational modifications, including acetylation, impact genome organization. In Neurospora, the HCHC (HDA-1, CDP-2, HP1, CHAP) complex deacetylates heterochromatic regions including centromeres: loss of individual HCHC members increases centromeric acetylation and cytosine methylation. Here, we evaluate the role of the HCHC complex on genome organization using chromosome conformation capture with high-throughput sequencing (Hi-C) in Δcdp-2 or Δchap deletion strains. CDP-2 loss increases interactions between intra- and inter-chromosomal heterochromatic regions, while removal of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different histone PTM patterns genome-wide: in Dcdp-2, heterochromatic H4K16 acetylation is increased, yet some heterochromatic regions lose H3K9 trimethylation, which locally increases inter-heterochromatin contacts; CHAP loss produces minimal acetylation changes but increases H3K9me3 enrichment in heterochromatin. Furthermore, deletion of the DIM-2 DNA methyltransferase in a Δcdp-2 background causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how enhanced cytosine methylation ensures heterochromatic compartmentalization when silenced regions are acetylated.
Overall design We analyzed genome organization of mutants of a heterochromatin-specific histone deacetylase complex (the HCHC complex) found in the filamentous fungus Neurospora crassa by chromosome conformation capture by paired-end high-throughput sequencing (Hi-C); Hi-C libraries were generated with the four-base cutters DpnII and MseI, which monitor euchromatic and heterochromatic regions of the Neurospora genome, respectively, due to the location of the recognition sequences of these restriction enzymes. All HCHC mutant Hi-C data was compared to wild type Hi-C data, previously reported in Rodriguez et al. (Pubmed ID: 35244156). We also examined the histone post-translational modification enrichment of wild type and HCHC mutant strains, specifically looking at the acetylation of lysine 9 on histone H3, the acetylation of lysine 16 on histone H4, and the trimethylation of lysine 9 on histone H3.
Contributor(s) Scadden AW, Graybill A, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD
Citation(s) 37461718
Submission date May 19, 2023
Last update date Sep 12, 2023
Contact name Andrew David Klocko
Phone 719-255-3255
Organization name University of Colorado Colorado Springs
Department Chemistry and Biochemistry
Lab Klocko
Street address 278 Centennial Hall, 1420 Austin Bluffs Pkwy
City Colorado Springs
State/province Colorado
ZIP/Postal code 80918
Country USA
Platforms (1)
GPL26551 Illumina NovaSeq 6000 (Neurospora crassa)
Samples (19)
GSM7394478 N150_WT_ChIPseq-H4K16ac_rep1
GSM7394479 N3752_WT_ChIPseq-H4K16ac_rep2
GSM7394480 N150_WT_ChIPseq-H3K9me3_rep1
This SubSeries is part of SuperSeries:
GSE232935 Histone deacetylation and cytosine methylation are required for the normal compartmentalization of heterochromatin in the genome organization of Neurospora crassa
BioProject PRJNA974448

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Supplementary file Size Download File type/resource 9.7 Mb (ftp)(http) BW
GSE232933_N150_WT_H3K9ac_merged_nc14_R1_25bins_normRPKM.bigwig.gz 9.9 Mb (ftp)(http) BIGWIG 8.7 Mb (ftp)(http) BW 9.5 Mb (ftp)(http) BW 9.8 Mb (ftp)(http) BW 9.6 Mb (ftp)(http) BW 9.2 Mb (ftp)(http) BW 8.6 Mb (ftp)(http) BW 10.1 Mb (ftp)(http) BW
GSE232933_RAW.tar 169.4 Mb (http)(custom) TAR (of BEDGRAPH, BIGWIG, BW)
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Raw data are available in SRA
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