ArticleNucleic acids research2016
Categorical spectral analysis of periodicity in nucleosomal DNA.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 32 citations in OpenAlex.
- Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome.Biology · 2023Article
- Chromatin structure and context-dependent sequence features control prime editing efficiency.bioRxiv : the preprint server for biology · 2023Article
- Chromatin structure and context-dependent sequence features control prime editing efficiency.Frontiers in genetics · 2023Article
- Base-resolution models of transcription-factor binding reveal soft motif syntax.Nature genetics · 2021Article
- Measuring DNA mechanics on the genome scale.Nature · 2021Article
- Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members.Nucleic acids research · 2020Article
- Article
- A degeneration-reducing criterion for optimal digital mapping of genetic codes.Computational and structural biotechnology journal · 2019Article
- A unified computational framework for modeling genome-wide nucleosome landscape.Physical biology · 2018Article
- Maximum entropy methods for extracting the learned features of deep neural networks.PLoS computational biology · 2017Article
- Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping.Trends in genetics : TIG · 2017Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA helical twist imposes geometric constraints on the location of histone-DNA interaction sites along nucleosomal DNA. Certain 10.5-bp periodic nucleotides in phase with these geometric constraints have been suggested to facilitate nucleosome positioning. However, the extent of nucleotide periodicity in nucleosomal DNA and its significance in directing nucleosome positioning still remain unclear. We clarify these issues by applying categorical spectral analysis to high-resolution nucleosome maps in two yeast species. We find that only a small fraction of nucleosomal sequences contain significant 10.5-bp periodicity. We further develop a spectral decomposition method to show that the previously observed periodicity in aligned nucleosomal sequences mainly results from proper phasing among nucleosomal sequences, and not from a preponderant occurrence of periodicity within individual sequences. Importantly, we show that this phasing may arise from the histones' proclivity for putting preferred nucleotides at some of the evenly spaced histone-DNA contact points with respect to the dyad axis. We demonstrate that 10.5-bp periodicity, when present, significantly facilitates rotational, but not translational, nucleosome positioning. Finally, although periodicity only moderately affects nucleosome occupancy genome wide, reduced periodicity is an evolutionarily conserved signature of nucleosome-depleted regions around transcription start/termination sites.
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