ArticlePloS one2010
Prediction of nucleosome positioning based on transcription factor binding sites.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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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, 10 citations in OpenAlex.
- Initiation of base excision repair is modulated by nucleosome occupancy modifying sequences.DNA repair · 2025Article
- MACE: model based analysis of ChIP-exo.Nucleic acids research · 2014Article
- Training-free atomistic prediction of nucleosome occupancy.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Identifying cooperative transcription factors in yeast using multiple data sources.BMC systems biology · 2014Article
- Nucleosome Positioning with Set of Key Positions and Nucleosome Affinity.The open biomedical engineering journal · 2014Article
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs) have been suggested to play a role in nucleosome positioning in vivo. PRINCIPAL
findingsHere, the minimum redundancy maximum relevance (mRMR) feature selection algorithm, the nearest neighbor algorithm (NNA), and the incremental feature selection (IFS) method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs) in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test.
conclusionsOur results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.
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