Z-matrix template-based substitution approach for enumeration of 3D molecular structures.
Ontology highlight
ABSTRACT:
SUBMITTER: Lorpaiboon W
PROVIDER: S-EPMC8374508 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:MotivationIn contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the 3D structures of chromosomes based on single-cell Hi-C data.ResultsWe developed single-cell lattice (SCL), a computational method to reconstruct 3D structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2 D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3 D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used to simulate the structure and minimize the loss function. We evaluated the SCL-inferred 3 D structures (at both 500 and 50 kb resolutions) using multiple criteria and compared them with the ones generated by another modeling software program. The results indicate that the 3 D structures generated by SCL closely fit single-cell Hi-C data. We also found similar patterns of trans-chromosomal contact beads, Lamin-B1 enriched topologically associating domains (TADs), and H3K4me3 enriched TADs by mapping data from previous studies onto the SCL-inferred 3 D structures.Availability and implementationThe C++ source code of SCL is freely available at http://dna.cs.miami.edu/SCL/.Supplementary informationSupplementary data are available at Bioinformatics online.
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