RT Journal
A1 Szałaj, Przemysław
A1 Tang, Zhonghui
A1 Michalski, Paul
A1 Pietal, Michal J.
A1 Luo, Oscar J.
A1 Sadowski, Michał
A1 Li, Xingwang
A1 Radew, Kamen
A1 Ruan, Yijun
A1 Plewczynski, Dariusz
T1 An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization
JF Genome Research 
JO Genome Research 
YR 2016 
FD December 01 
VO 26 
IS 12 
SP 1697 
OP 1709 
DO 10.1101/gr.205062.116 
UL http://genome.cshlp.org/content/26/12/1697.abstract 
AB ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures.