Deciphering multi-way interactions in the human genome
Abstract
Chromatin architecture, a key regulator of gene expression, can be inferred using chromatin contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does not preserve multi-way contacts. Here we use long sequencing reads to map genome-wide multi-way contacts and investigate higher order chromatin organization in the human genome. We use hypergraph theory for data representation and analysis, and quantify higher order structures in neonatal fibroblasts, biopsied adult fibroblasts, and B lymphocytes. By integrating multi-way contacts with chromatin accessibility, gene expression, and transcription factor binding, we introduce a data-driven method to identify cell type-specific transcription clusters. We provide transcription factor-mediated functional building blocks for cell identity that serve as a global signature for cell types.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Sep 20, 2022
- Source ID
- 10.1038/s41467-022-32980-z
Entities
People
- Amit Surana
- Anthony Cicalo
- Can Chen
- Charles J Ryan
- Cooper Stansbury
- Gabrielle A Dotson
- Indika Rajapakse
- Joshua Pickard
- Lindsey A. Muir
- Max S. Wicha
- Nicholas Beckloff
- Sam Dilworth
- Sivakumar Jeyarajan
- Stephen Lindsly
- Walter Meixner
Organizations
- Air Force Office of Scientific Research
- National Human Genome Research Institute
- National Science Foundation
- United States Department of Defense