Predicting chromatin organization using histone marks |
| |
Authors: | Jialiang Huang Eugenio Marco Luca Pinello Guo-Cheng Yuan |
| |
Affiliation: | Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215 USA ;Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA ;Harvard Stem Cell Institute, Cambridge, MA 02138 USA ;Present Address: Editas Medicine, Cambridge, MA 02138 USA |
| |
Abstract: | Genome-wide mapping of three dimensional chromatin organization is an important yet technically challenging task. To aid experimental effort and to understand the determinants of long-range chromatin interactions, we have developed a computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD) boundaries. Our model accurately and robustly predicts these features across datasets and cell types. Cell-type specific histone mark information is required for prediction of chromatin interaction hubs but not for TAD boundaries. Our predictions provide a useful guide for the exploration of chromatin organization.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0740-z) contains supplementary material, which is available to authorized users. |
| |
Keywords: | |
|
|