ArticleBMC genomics2011
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 40 citations in OpenAlex.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- Initiation of base excision repair is modulated by nucleosome occupancy modifying sequences.DNA repair · 2025Article
- Synthetic gene circuits in plants: recent advances and challenges.Quantitative plant biology · 2025Review
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- An integrated machine-learning model to predict nucleosome architecture.Nucleic acids research · 2024Article
- A commentary on the ABC consortium and its impact on the development of mesoscopic models of DNA.Biophysical reviews · 2024Article
- A study of strong nucleosomes in the human genome.iScience · 2022Article
- DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.Nucleic acids research · 2021Article
- A deformation energy model reveals sequence-dependent property of nucleosome positioning.Chromosoma · 2021Article
- Genetic circuit design automation for yeast.Nature microbiology · 2020Article
- Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning.Nucleic acids research · 2019Article
- DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region.Nucleic acids research · 2019Article
- Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.Epigenetics & chromatin · 2017Article
- DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.Nucleic acids research · 2017Article
- Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Histone Chaperone Nap1 Is a Major Regulator of Histone H2A-H2B Dynamics at the Inducible GAL Locus.Molecular and cellular biology · 2016Article
- Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.Nucleic acids research · 2016Article
- Nucleosome architecture throughout the cell cycle.Scientific reports · 2016Article
- Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.PloS one · 2015Article
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive.
resultsNaked (histone-free) and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase) and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions.
conclusionsOur experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site) and TTS (Transcription Termination Site) (at least in yeast) is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression.
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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.