Leveraging transcription factor physical proximity for enhancing gene regulation inference

TL;DR

This paper introduces GRIP, a new method for gene regulation inference that considers the physical proximity of transcription factors in a protein–protein interaction network.

Contribution

GRIP introduces a novel Boolean convex program and algorithm that improves gene regulation inference by incorporating TF physical proximity.

Findings

GRIP outperforms existing methods in predicting cell-type-specific gene regulation.

The inferred transcription factors are physically closer in the PPI network.

GRIP's results align better with PCHiC data than other methods.

Abstract

Gene regulation inference, a key challenge in systems biology, is crucial for understanding cell function, as it governs processes such as differentiation, cell state maintenance, signal transduction, and stress response. Leading methods utilize gene expression, chromatin accessibility, transcription factor (TF) DNA binding motifs, and prior knowledge. However, they overlook the fact that TFs must be in physical proximity to facilitate transcriptional gene regulation.

To fill the gap, we develop GRIP—Gene Regulation Inference by considering TF Proximity—a gene regulation inference method that directly considers the physical proximity between regulating TFs. Specifically, we use the distance in a protein–protein interaction (PPI) network to estimate the physical proximity between TFs. We design a novel Boolean convex program, which can identify TFs that not only can explain the gene expression of target genes (TGs) but also stay close in the PPI network. We propose an efficient algorithm to solve the Boolean relaxation of the proposed model with a theoretical tightness guarantee. We compare our GRIP with state-of-the-art methods (SCENIC+, DirectNet, Pando, and CellOracle) on inferring cell-type-specific (CD4, CD8, and CD 14) gene regulation using the PBMC 3k scMultiome-seq data and demonstrate its out-performance in terms of the predictive power of the inferred TFs, the physical distance between the inferred TFs, and the agreement between the inferred gene regulation and PCHiC data.

https://github.com/EJIUB/GRIP.

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