Abstract Background Defining histone modification at single-nucleosome resolution provides accurate epigenomic information in individual nucleosomes. However, most of histone modification data deposited in current databases, such as ENCODE and Roadmap, have low resolution with peaks of several kilo-base pairs (kb), which due to the technical defects of regular ChIP-Seq technology. Results To generate histone modification data at single-nucleosome resolution, we developed a novel approach, NUCLIZE, using synergistic analyses of histone modification data from ChIP-Seq and high-resolution nucleosome mapping data from native MNase-Seq. With this approach, we generated quantitative epigenomics data of single and multivalent histone modification marks in each nucleosome. We found that the dominant trivalent histone mark (H3K4me3/H3K9ac/H3K27ac) and others showed defined and specific patterns near each TSS, indicating potential epigenetic codes regulating gene transcription. Conclusions Single-nucleosome histone modification data render epigenomic data become quantitative, which is essential for investigating dynamic changes of epigenetic regulation in the biological process or for functional epigenomics studies. Thus, NUCLIZE turns current epigenomic mapping studies into genuine functional epigenomics studies with quantitative epigenomic data.

+More

dynamic changes of epigenetic regulation in the biological process approach nuclize quantitative epigenomics data histone modification marks trivalent histone mark highresolution nucleosome mapping data synergistic epigenetic codes regulating gene transcription regular chipseq epigenomic mapping studies functional epigenomics studies thus

Daoshan Zheng,Justyna Trynda,Zhifu Sun,Zhaoyu Li,.NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions. 20 (1),.

Daoshan Zheng,Justyna Trynda,Zhifu Sun,Zhaoyu Li,"NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions" 20

Daoshan Zheng,Justyna Trynda,Zhifu Sun,Zhaoyu Li,"NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions"