ArticleBiophysical journal2009
DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
37 citing papers in PubMed, 68 citations in OpenAlex.
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- An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays.Nucleic acids research · 2022Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- Biophysical Reviews' "Meet the Editors Series"-a profile of Wilma K. Olson.Biophysical reviews · 2020Article
- Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4.Nucleic acids research · 2019Article
- Article
- Parallels between DNA and collagen - comparing elastic models of the double and triple helix.Scientific reports · 2017Article
- Contributions of Sequence to the Higher-Order Structures of DNA.Biophysical journal · 2017Review
- High-resolution biophysical analysis of the dynamics of nucleosome formation.Scientific reports · 2016Article
- X-ray structure of the MMTV-A nucleosome core.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.PloS one · 2016Article
- DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity.PloS one · 2015Article
- DNA methylation effects on tetra-nucleosome compaction and aggregation.Biophysical journal · 2014Article
- Triple helical DNA in a duplex context and base pair opening.Nucleic acids research · 2014Article
- Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy.BMC bioinformatics · 2014Article
- Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.Nucleic acids research · 2014Article
- Can nucleosomal DNA be described by an elastic model?: comment on "Sequence-dependent collective properties of DNAs and their role in biological systems" by Pasquale De Santis and Anita Scipioni.Physics of life reviews · 2013Article
- Article
- Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The folding of DNA on the nucleosome core particle governs many fundamental issues in eukaryotic molecular biology. In this study, an updated set of sequence-dependent empirical "energy" functions, derived from the structures of other protein-bound DNA molecules, is used to investigate the extent to which the architecture of nucleosomal DNA is dictated by its underlying sequence. The potentials are used to estimate the cost of deforming a collection of sequences known to bind or resist uptake in nucleosomes along various left-handed superhelical pathways and to deduce the features of sequence contributing to a particular structural form. The deformation scores reflect the choice of template, the deviations of structural parameters at each step of the nucleosome-bound DNA from their intrinsic values, and the sequence-dependent "deformability" of a given dimer. The correspondence between the computed scores and binding propensities points to a subtle interplay between DNA sequence and nucleosomal folding, e.g., sequences with periodically spaced pyrimidine-purine steps deform at low cost along a kinked template whereas sequences that resist deformation prefer a smoother spatial pathway. Successful prediction of the known settings of some of the best-resolved nucleosome-positioning sequences, however, requires a template with "kink-and-slide" steps like those found in high-resolution nucleosome structures.
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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.