ArticleBMC genomics2017
An approach of identifying differential nucleosome regions in multiple samples.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 9 citations in OpenAlex.
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- Application of Next-Generation Sequencing in Neurodegenerative Diseases: Opportunities and Challenges.Neuromolecular medicine · 2021Review
- Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning.Nucleic acids research · 2019Article
- NucMap: a database of genome-wide nucleosome positioning map across species.Nucleic acids research · 2019Article
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNucleosome plays a role in transcriptional regulation through occluding the binding of proteins to DNA sites. Nucleosome occupancy varies among different cell types. Identification of such variation will help to understand regulation mechanism. The previous researches focused on the methods for two-sample comparison. However, a multiple-sample comparison (n ≥ 3) is necessary, especially in studying development and cancer.
methodsHere, we proposed a Chi-squared test-based approach, named as Dimnp, to identify differential nucleosome regions (DNRs) in multiple samples. Dimnp is designed for sequenced reads data and includes the modules of both calling nucleosome occupancy and identifying DNRs.
resultsWe validated Dimnp on dataset of the mutant strains in which the modifiable histone residues are mutated into alanine in Saccharomyces cerevisiae. Dimnp shows a good capacity (area under the curve > 0.87) compared with the manually identified DNRs. Just by one time, Dimnp is able to identify all the DNRs identified by two-sample method Danpos. Under a deviation of 40 bp, the matched DNRs are above 60% between Dimnp and Danpos. With Dimnp, we found that promoters and telomeres are highly dynamic upon mutating the modifiable histone residues.
conclusionsWe developed a tool of identifying the DNRs in multiple samples and cell types. The tool can be applied in studying nucleosome variation in gradual change in development and cancer.
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