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Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
Published on: April 21, 2023
3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D
Xianfu Yi1,2, Menghan Luo1, Xiangling Feng1
1Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
Abstract:
Precise identification of context-specific transcriptional regulators (TRs) cooperation facilitates the understanding of complex gene regulation. However, previous methods are highly reliant on the availability of ChIPped TRs. Here, we provide a protocol for running 3DCoop, a pipeline for computational inference of cell type-specific TR cooperation in 3D chromatin by integrating TR motifs, open chromatin profiles, gene expression, and chromatin loops. 3DCoop provides a feasible solution to study the potential interplay among TRs across multiple human or mouse tissue/cell types. For complete details on the use and execution of this protocol, please refer to Yi et al. (2021).
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