Abstract
BackgroundNucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public data sets.ResultsThe NUCOME is a database focused on filtering qualified nucleosome organization referenced landscapes covering various cell types in human and mouse based on QC metrics. The filtering strategy guarantees the quality of nucleosome organization referenced landscapes and exempts users from redundant data set selection and processing. The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci.ConclusionsThe NUCOME provides valuable data resources for integrative analyses focus on nucleosome organization. The NUCOME is freely available at http://compbio-zhanglab.org/NUCOME.
Highlights
Nucleosome organization is involved in many regulatory activities in various organisms
Nucleosome-free regions (NFR) and regularly spaced nucleosome arrays are strongly associated with transcription initiation [1,2,3,4]
All data was processed with a standardized analysis pipeline named CAM, which we developed previously [18], accompanying with quality control (QC) measurements specific for MNaseseq data
Summary
Nucleosome organization is involved in many regulatory activities in various organisms. Results: The NUCOME is a database focused on filtering qualified nucleosome organization referenced landscapes covering various cell types in human and mouse based on QC metrics. The filtering strategy guarantees the quality of nucleosome organization referenced landscapes and exempts users from redundant data set selection and processing. The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci. The nucleosome is the fundamental unit of eukaryotic chromatin and is involved in regulatory activities through interactions with DNA binding proteins, including regulatory factors, chromatin remodelers, histone chaperones and polymerases [1]. Nucleosomes act as barriers to transcription factors (TFs) interacting with cis-regulatory elements.
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