ReviewBiophysical journal2017
Contributions of Sequence to the Higher-Order Structures of DNA.
Review in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 27 citations in OpenAlex.
- The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.Biophysical journal · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Article
- DNA simulation benchmarks revealed with the accumulation of high-resolution structures.Biophysical reviews · 2024Review
- emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.Journal of molecular biology · 2022Article
- The 3D Genome: From Structure to Function.International journal of molecular sciences · 2021Review
- The "Genomic Code": DNA Pervasively Moulds Chromatin Structures Leaving no Room for "Junk".Life (Basel, Switzerland) · 2021Review
- Topological polymorphism of nucleosome fibers and folding of chromatin.Biophysical journal · 2021Review
- Biophysical Reviews' "Meet the Editors Series"-a profile of Wilma K. Olson.Biophysical reviews · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Modelling and DNA topology of compact 2-start and 1-start chromatin fibres.Nucleic acids research · 2019Article
- G4Hunter web application: a web server for G-quadruplex prediction.Bioinformatics (Oxford, England) · 2019Article
- Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation.The journal of physical chemistry. B · 2019Article
- The Oligomerization Landscape of Histones.Biophysical journal · 2019Article
- The formation of chromatin domains involves a primary step based on the 3-D structure of DNA.Scientific reports · 2018Article
- Chromosomal organization of transcription: in a nutshell.Current genetics · 2018Review
- Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates.Biophysical journal · 2018Article
- Article
- Towards quantitative analysis of gene regulation by enhancers.Epigenomics · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very-long-chain molecules. The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of double helices with hundreds of basepairs. These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers. Like the patterns of basepair association within DNA, the arrangements of nucleosomes in chromatin modulate the properties of longer polymers. The intrachromosomal loops detected in genomic studies contain hundreds of nucleosomes, and given that the simulated configurations of chromatin depend on the lengths of linker DNA, the formation of these loops may reflect sequence-dependent information encoded within the positioning of the nucleosomes. With knowledge of the positions of nucleosomes on a given genome, methods are now at hand to estimate the looping propensities of chromatin in terms of the spacing of nucleosomes and to make a direct connection between the DNA base sequence and larger-scale chromatin folding.
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What OpenQuestion holds
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.