ArticleNature2006
A genomic code for nucleosome positioning.
Article in Nature, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 794 papers.
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Who cites it
794 citing papers in PubMed, 1,520 citations in OpenAlex.
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- DNA Sequence and Histone Variant H2A.Z Jointly Govern Nucleosome Unwrapping Pathways.bioRxiv : the preprint server for biology · 2026Article
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- Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models.Nature communications · 2026Article
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
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- Gene expression is stable despite widespread cis and trans regulatory divergence inbioRxiv : the preprint server for biology · 2026Article
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- Searching for sequence features that control DNA cyclizability.PNAS nexus · 2026Article
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
- Subtle-seq reveals frequent ageing-associated chromosome fragmentation on nucleosome core DNA.Nucleic acids research · 2026Article
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.Genome research · 2026Article
- What makes genes burst.Trends in cell biology · 2026Review
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- DNA breathing and shape encode distinct mechanisms of transcription factor binding.Bioinformatics advances · 2026Article
- Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications.eLife · 2025Article
734 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome-DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain approximately 50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.
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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.