SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data.

ABSTRACT:

Motivation

In 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.

Results

We 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-inferre

SUBMITTER: Zhu H 

PROVIDER: S-EPMC6792089 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature