ArticleGenome research2011
Variety of genomic DNA patterns for nucleosome positioning.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
41 citing papers in PubMed, 64 citations in OpenAlex.
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions.Nature communications · 2026Article
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation.Nucleic acids research · 2025Article
- The gap-free genome ofHorticulture research · 2024Article
- Interpretable deep residual network uncovers nucleosome positioning and associated features.Nucleic acids research · 2024Article
- Non-B-form DNA tends to form in centromeric regions and has undergone changes in polyploid oat subgenomes.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Distinct chromosomal "niches" in the genome ofNAR genomics and bioinformatics · 2022Article
- DeepNup: Prediction of Nucleosome Positioning from DNA Sequences Using Deep Neural Network.Genes · 2022Article
- Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.International journal of molecular sciences · 2022Article
- Distinctive regulatory architectures of germline-active and somatic genes inGenome research · 2020Article
- Nucleosome positioning sequence patterns as packing or regulatory.PLoS computational biology · 2020Article
- The DNA-binding protein HTa fromeLife · 2019Article
- Chromatinization ofeLife · 2019Article
- The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes.Nucleic acids research · 2019Article
- Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes.The Plant cell · 2019Article
- Conservation, Divergence, and Functions of Centromeric Satellite DNA Families in the Bovidae.Genome biology and evolution · 2019Article
- Nucleosome positions establish an extended mutation signature in melanoma.PLoS genetics · 2018Article
- LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks.Bioinformatics (Oxford, England) · 2018Article
- Nucleosomal organization and DNA base composition patterns.Nucleus (Austin, Tex.) · 2017Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Precise positioning of nucleosomes along DNA is important for a variety of gene regulatory processes. Among the factors directing nucleosome positioning, the DNA sequence is highly important. Two main classes of nucleosome positioning sequence (NPS) patterns have previously been described. In the first class, AA, TT, and other WW dinucleotides (where W is A or T) tend to occur together (in-phase) in the major groove of DNA closest to the histone octamer surface, while SS dinucleotides (where S is G or C) are predominantly positioned in the major groove facing outward. In the second class, AA and TT are structurally separated (AA backbone near the histone octamer, and TT backbone further away), but grouped with other RR (where R is purine A or G) and YY (where Y is pyrimidine C or T) dinucleotides. As a result, the RR/YY pattern includes counter-phase AA/TT distributions. We describe here anti-NPS patterns, which are inverse to the conventional NPS patterns: WW runs inverse to SS, and RR inverse to YY. Evidence for the biological relevance of anti-NPS patterns is presented.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.