Publication

Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

current
   February 4th, 2019 at 6:38pm

Overview


Abstract

Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate twelve different single-cell combinatorial indexed Hi-C (sciHi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 25,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sciHi-C data in the form of "chromatin topics." We further show enrichment of particular compartment structures associated with locus pairs in these topics.

Authors

Hyeon-Jin Kim  •  Galip Gurkan Yardimici  •  Giancarlo Bonora  •  Vijay Ramani  •  Jie Liu  •  Ruolan Qiu  •  Choli Lee  •  Jennifer Hesson  •  Carol B. Ware  •  Jay Shendure  •  Zhijun Duan  •  William Stafford Noble

Link

https://www.biorxiv.org/content/10.1101/534800v1


Journal

bioRxiv

doi:10.1101/534800

Published

January 30th, 2019