Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 31053705.
- Also identified by DOI 10.1038/s41467-019-10005-6 and PMC identifier 6499832.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
The new advances in various experimental techniques that provide complementary information about the spatial conformations of chromosomes have inspired researchers to develop computational methods to fully exploit the merits of individual data sources and combine them to improve the modeling of chromosome structure. Here we propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model. Comprehensive tests on a set of chromosomes, for which both Hi-C and FISH data are available, demonstrate that GEM-FISH can outperform previous chromosome structure modeling methods and accurately capture the higher order spatial features of chromosome conformations. Moreover, our reconstructed 3D models of chromosomes revealed interesting patterns of spatial distributions of super-enhancers which can provide useful insights into understanding the functional roles of these super-enhancers in gene regulation.
Medical subject headings
- Chromosomes
- Imaging, Three-Dimensional
- Models, Molecular
- Nucleic Acid Conformation