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Nucleic Acids Res. 2019 Jan 8;47(D1):D163-D169. doi: 10.1093/nar/gky980.

NucMap: a database of genome-wide nucleosome positioning map across species.

Zhao Y1, Wang J2,3,4, Liang F2, Liu Y2,3,4, Wang Q2,3,4, Zhang H2,3,4, Jiang M2,3, Zhang Z2,3, Zhao W2,3, Bao Y2,3, Zhang Z2,3,5, Wu J3, Asmann YW1, Li R2, Xiao J2,3,4,5.

Author information

1
Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA.
2
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
3
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
4
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
5
Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China.

Abstract

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, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation.

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