Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

ABSTRACT: Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes. We apply Cicero to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of Cicero-linked regulatory elements meet criteria of "chromatin hubs"-they are enriched for physical proximity, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of changes in gene expression. Pseudotemporal analysis revealed that most DNA elements remain in chro

SUBMITTER: Pliner HA 

PROVIDER: S-EPMC6582963 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature