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Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs
- Source :
- Cell. 176:520-534.e25
- Publication Year :
- 2019
- Publisher :
- Elsevier BV, 2019.
-
Abstract
- Elucidating the global and local rules that govern genome-wide, hierarchical chromatin architecture remains a critical challenge. Current high-throughput chromosome conformation capture (Hi-C) technologies have identified large-scale chromatin structural motifs, such as topologically associating domains and looping. However, structural rules at the smallest or nucleosome scale remain poorly understood. Here, we coupled nucleosome-resolved Hi-C technology with simulated annealing-molecular dynamics (SA-MD) simulation to reveal 3D spatial distributions of nucleosomes and their genome-wide orientation in chromatin. Our method, called Hi-CO, revealed distinct nucleosome folding motifs across the yeast genome. Our results uncovered two types of basic secondary structural motifs in nucleosome folding: α-tetrahedron and β-rhombus analogous to α helix and β sheet motifs in protein folding. Using mutants and cell-cycle-synchronized cells, we further uncovered motifs with specific nucleosome positioning and orientation coupled to epigenetic features at individual loci. By illuminating molecular-level structure-function relationships in eukaryotic chromatin, our findings establish organizational principles of nucleosome folding.
- Subjects :
- 0303 health sciences
Saccharomyces cerevisiae Proteins
Beta sheet
Saccharomyces cerevisiae
Computational biology
Biology
Chromatin Assembly and Disassembly
Chromatin
Chromosomes
General Biochemistry, Genetics and Molecular Biology
Nucleosomes
Chromosome conformation capture
Folding (chemistry)
03 medical and health sciences
0302 clinical medicine
Nucleosome
Protein folding
Epigenetics
Transcription Initiation Site
Structural motif
030217 neurology & neurosurgery
030304 developmental biology
Subjects
Details
- ISSN :
- 00928674
- Volume :
- 176
- Database :
- OpenAIRE
- Journal :
- Cell
- Accession number :
- edsair.doi.dedup.....d5d135becf5fd858693e5728a4c33eaf