Predicting chromatin organization using histone marks.
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.
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. jhuang@jimmy.harvard.edu.|Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA. jhuang@jimmy.harvard.edu.
Jialiang
J
Huang
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. emarco@jimmy.harvard.edu.|Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA. emarco@jimmy.harvard.edu.|Present Address: Editas Medicine, Cambridge, MA, 02138, USA. emarco@jimmy.harvard.edu.
Eugenio
E
Marco
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. lpinello@jimmy.harvard.edu.|Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA. lpinello@jimmy.harvard.edu.
Luca
L
Pinello
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. gcyuan@jimmy.harvard.edu.|Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA. gcyuan@jimmy.harvard.edu.|Harvard Stem Cell Institute, Cambridge, MA, 02138, USA. gcyuan@jimmy.harvard.edu.
Guo-Cheng
GC
Yuan
D002460:Cell Line; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing; D042421:Histone Code; D006801:Humans; D012045:Regulatory Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA
D002843:Chromatin