Research

Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, Researchers from the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences developed NucMap, a database of genome-wide nucleosome positioning map across species. This work has been published online in Nucleic Acids Research on October 22. 

NucMap includes 798 experimental datasets from 477 samples across 15 species. All functionalities in NucMap are organized into four modules: search, browse, analysis and download.  

Sample-based search helps users to find the samples they are interested in. With hyperlinked sample ID, users can access more specific information for each sample, including original data source, original publication, all downloadable data for this sample and other related omics samples.  

Gene-based searching helps users to checkup nucleosome positioning at the promoter region of an individual gene. To facilitate browsing nucleosome profile at single-base resolution, NucMap has deployed a nucleosome browser based on the open source program JBrowser. Nucleosome browser can help users quickly make side-by-side comparison across multiple relevant genomic track files.  

The online analysis module can characterize nucleosome occupancy profile at all genomic regions. All processed nucleosome positioning data are freely available. 

Nucleosome positioning is one important type of chromatin state information. To deeply understand chromatin biology, we will make NucMap compatible to other public epigenomics databases, such as MethBank, Cistrome and ENCODE. Based on comprehensive analysis on cross-omics data, biologists will therefore learn more about chromatin regulation. 

This work is supported by National Key Research Program of China, Promoting Big Data Development Project, the National Development and Reform Commission of China and so on.