Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions.

ABSTRACT: The epigenetic control of gene expression is highly cell-type and context specific. Yet, despite its complexity, gene regulatory logic can be broken down into modular components consisting of a transcription factor (TF) activating or repressing the target gene expression through its binding to a cis-regulatory region. We propose a nonparametric approach, TRIPOD, to detect and characterize the three-way relationships between a TF, its target gene, and the accessibility of the TF's binding site using single-cell RNA and ATAC multiomic data. We apply TRIPOD to interrogate the cell-type-specific regulatory logic in peripheral blood mononuclear cells and contrast our results to detections from enhancer databases, cis-eQTL studies, ChIP-seq experiments, and TF knockdown/knockout studies. We then

SUBMITTER: Jiang Y 

PROVIDER: S-EPMC9509445 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature