Identifying Positioned Nucleosomes with Epigenetic Marks in Humans
Author Information
Author(s): Zhang Yong, Shin Hyunjin, Song Jun S, Lei Ying, Liu X Shirley
Primary Institution: Dana-Farber Cancer Institute, Harvard School of Public Health
Hypothesis
How can we efficiently identify positioned nucleosomes and their histone modification profiles from ChIP-Seq data?
Conclusion
The study developed a computational framework that identified over 438,000 positioned nucleosomes in functionally important regions of the human genome.
Supporting Evidence
- Over 438,000 positioned nucleosomes were identified.
- 22% of the identified nucleosomes were found in promoters within 2.5 kb of transcription start sites.
- 76% of distal positioned nucleosomes contained transcriptional promoter signatures.
- Modified positioned nucleosomes were detected in 45% of all DNase HS regions.
Takeaway
The researchers found a lot of special DNA packages called nucleosomes that help control how genes work in humans.
Methodology
The study combined ChIP-Seq tags from various histone modifications, extended them, and used signal processing techniques to identify nucleosome positions.
Potential Biases
Potential biases from unannotated repetitive sequences and Solexa sequencing bias were noted.
Limitations
The study may miss nucleosomes that lack the specific histone modifications investigated and did not include a proper control sample.
Participant Demographics
Human CD4+ T cells were used for the study.
Statistical Information
P-Value
p<0.05
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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