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Summary Eukaryotic DNA wraps around histone octamers forming nucleosomes, which modulate genome function by defining chromatin environments with distinct accessibility. These well-conserved properties allowed “humanization” of the nucleosome core particle (NCP) inSaccharomyces cerevisiaeat high fitness costs. Here we studied nucleosome-humanized yeast-genomes to understand how species-specific chromatin affects nuclear organization and function. We found a size increase in human-NCP, linked to shorter free linker DNA, supporting decreased chromatin accessibility. 3-D humanized-genome maps showed increased chromatin compaction and defective centromere clustering, correlated with high chromosomal aneuploidy rate. Site-specific chromatin alterations were associated with lack of initiation of early origins of replication and dysregulation of the ribosomal (rDNA and rRNA) metabolism. This latter led to nucleolar fragmentation and rDNA-array instability, through a non-coding RNA dependent mechanism, leading to its extraordinary, but entirely reversible, intra-chromosomal expansion. Overall, our results reveal species-specific properties of the NCP that define epigenome function across vast evolutionary distances. HighlightsHumanized nucleosomes wrap 10 additional nucleotides, shortening free linker lengthHistone-humanized nucleosomes have increased occupancy for DNAHumanized nucleosomes potentially decrease chromatin accessibility by blocking-out free linker DNANucleosome humanization impedes DNA replication by affecting chromatin structure at originsHumanized nucleosomes reversibly destabilize the ribosomal DNA array and leads to massive intrachromosomal rDNA locus expansionHistone humanization disrupts rDNA silencing and leads to nucleolar fragmentation
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Nucleosome placement and polymer mechanics explain genomic contacts on 100 kb scales
Abstract The 3D organization of the genome—in particular, which two regions of DNA are in contact with each other—plays a role in regulating gene expression. Several factors influence genome 3D organization. Nucleosomes (where ∼100 base pairs of DNA wrap around histone proteins) bend, twist, and compactify chromosomal DNA, altering its polymer mechanics. How much does the positioning of nucleosomes between gene loci influence contacts between those gene loci? And to what extent are polymer mechanics responsible for this? To address this question, we combine a stochastic polymer mechanics model of chromosomal DNA including twists and wrapping induced by nucleosomes with two data-driven pipelines. The first estimates nucleosome positioning from ATAC-seq data in regions of high accessibility. Most of the genome is low accessibility, so we combine this with a novel image analysis method that estimates the distribution of nucleosome spacing from electron microscopy data. There are no fit parameters in the biophysical model. We apply this method to IL-6, IL-15, CXCL9, and CXCL10, inflammatory marker genes in macrophages, before and after inflammatory stimulation, and compare the predictions with contacts measured by conformation capture experiments (4C-seq). We find that within a 500-kb genomic region, polymer mechanics with nucleosomes can explain 71% of close contacts. These results suggest that, while genome contacts on 100 kb scales are multifactorial, they may be amenable to mechanistic, physical explanation. Our work also highlights the role of nucleosomes, not just at the loci of interest, but between them, and not just the total number of nucleosomes, but their specific placement. The method generalizes to other genes, and can be used to address whether a contact is under active regulation by the cell (e.g. a macrophage during inflammatory stimulation).
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- Award ID(s):
- 2022182
- PAR ID:
- 10618110
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Nucleic Acids Research
- Volume:
- 53
- Issue:
- 14
- ISSN:
- 0305-1048
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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