ArticleEpigenetics & chromatin2010
Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae.
Article in Epigenetics & chromatin, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 21 citations in OpenAlex.
- Distinct chromosomal "niches" in the genome ofNAR genomics and bioinformatics · 2022Article
- iNuc-ext-PseTNC: an efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou's PseAAC to pseudo-tri-nucleotide composition.Molecular genetics and genomics : MGG · 2019Article
- Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.Nucleic acids research · 2018Article
- Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition.Bioinformatics (Oxford, England) · 2017Article
- Topoisomerase II regulates yeast genes with singular chromatin architectures.Nucleic acids research · 2013Article
- DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure.Genome research · 2013Article
- Evolutionary constraints in the β-globin cluster: the signature of purifying selection at the δ-globin (HBD) locus and its role in developmental gene regulation.Genome biology and evolution · 2013Article
- Codons support the maintenance of intrinsic DNA polymer flexibility over evolutionary timescales.Genome biology and evolution · 2012Article
- Nucleosome positioning in a model of active chromatin remodeling enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards providing a better understanding of the process of nucleosome positioning, for which several models have been suggested. Nevertheless, questions regarding the sequence constraints of nucleosomal DNA and how they may have been shaped through evolution remain open. In this paper, we analyze in detail different experimental nucleosome datasets with the aim of providing a hypothesis for the emergence of nucleosome-forming sequences.
resultsWe compared the complete sets of nucleosome positions for the budding yeast (Saccharomyces cerevisiae) as defined in the output of two independent experiments with the use of two different experimental techniques. We found that < 10% of the experimentally defined nucleosome positions were consistently positioned in both datasets. This subset of well-positioned nucleosomes, when compared with the bulk, was shown to have particular properties at both sequence and structural levels. Consistently positioned nucleosomes were also shown to occur preferentially in pairs of dinucleosomes, and to be surprisingly less conserved compared with their adjacent nucleosome-free linkers.
conclusionOur findings may be combined into a hypothesis for the emergence of a weak nucleosome-positioning code. According to this hypothesis, consistent nucleosomes may be partly guided by nearby nucleosome-free regions through statistical positioning. Once established, a set of well-positioned consistent nucleosomes may impose secondary constraints that further shape the structure of the underlying DNA. We were able to capture these constraints through the application of a recently introduced structural property that is related to the symmetry of DNA curvature. Furthermore, we found that both consistently positioned nucleosomes and their adjacent nucleosome-free regions show an increased tendency towards conservation of this structural feature.
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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.