ArticleBMC genomics2011
Nucleosome DNA sequence structure of isochores.
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 5 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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Who cites it
5 citing papers in PubMed, 21 citations in OpenAlex.
- Mutational Analysis of Ionizing Radiation Induced Neoplasms.Cell reports · 2015Article
- Chromosome Architecture and Genome Organization.PloS one · 2015Article
- Segmenting the Human Genome into Isochores.Evolutionary bioinformatics online · 2015Article
- The influence of DNA sequence on epigenome-induced pathologies.Epigenetics & chromatin · 2012Article
- Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes.BMC genomics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSignificant differences in G+C content between different isochore types suggest that the nucleosome positioning patterns in DNA of the isochores should be different as well.
resultsExtraction of the patterns from the isochore DNA sequences by Shannon N-gram extension reveals that while the general motif YRRRRRYYYYYR is characteristic for all isochore types, the dominant positioning patterns of the isochores vary between TAAAAATTTTTA and CGGGGGCCCCCG due to the large differences in G+C composition. This is observed in human, mouse and chicken isochores, demonstrating that the variations of the positioning patterns are largely G+C dependent rather than species-specific. The species-specificity of nucleosome positioning patterns is revealed by dinucleotide periodicity analyses in isochore sequences. While human sequences are showing CG periodicity, chicken isochores display AG (CT) periodicity. Mouse isochores show very weak CG periodicity only.
conclusionsNucleosome positioning pattern as revealed by Shannon N-gram extension is strongly dependent on G+C content and different in different isochores. Species-specificity of the pattern is subtle. It is reflected in the choice of preferentially periodical dinucleotides.
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Registered trials
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