Huang, JialiangMarco, EugenioPinello, LucaYuan, Guo-Cheng2015-09-012015Huang, Jialiang, Eugenio Marco, Luca Pinello, and Guo-Cheng Yuan. 2015. “Predicting chromatin organization using histone marks.” Genome Biology 16 (1): 162. doi:10.1186/s13059-015-0740-z. http://dx.doi.org/10.1186/s13059-015-0740-z.1474-7596http://nrs.harvard.edu/urn-3:HUL.InstRepos:21459760Genome-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 material The online version of this article (doi:10.1186/s13059-015-0740-z) contains supplementary material, which is available to authorized users.en-USJournal Article2015-09-0110.1186/s13059-015-0740-z