Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.

Heng WANG; Ang WU; Meng-Chen YANG; Di ZHOU; Xiyang CHEN; Zhifei SHI; Yiqun ZHANG; Yu-Xin LIU; Kai CHEN; Xiaosong WANG; Xiao-Fang CHENG; Baodan HE; Yutao FU; Lan KANG; Yujun HOU; Kun CHEN; Shan BIAN; Juan TANG; Jianhuang XUE; Chenfei WANG; Xiaoyu LIU; Jiejun SHI; Shaorong GAO; Jia-Min ZHANG

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Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.

Author: Heng WANG ¹ ; Ang WU ¹ ; Meng-Chen YANG ¹ ; Di ZHOU ¹ ; Xiyang CHEN ² ; Zhifei SHI ² ; Yiqun ZHANG ¹ ; Yu-Xin LIU ¹ ; Kai CHEN ² ; Xiaosong WANG ¹ ; Xiao-Fang CHENG ¹ ; Baodan HE ¹ ; Yutao FU ¹ ; Lan KANG ³ ; Yujun HOU ³ ; Kun CHEN ³ ; Shan BIAN ³ ; Juan TANG ³ ; Jianhuang XUE ¹ ; Chenfei WANG ¹ ; Xiaoyu LIU ² ; Jiejun SHI ¹ ; Shaorong GAO ² ; Jia-Min ZHANG ¹
Author Information

1. Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China.
2. Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
3. Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Publication Type:Journal Article
Keywords: TF footprint; chromatin accessibility; chromatin landscape; chromatin remodeling; gene regulation; nucleosome position; transcription factor
MeSH: Transcription Factors/genetics*; Humans; Chromatin/genetics*; Animals; Binding Sites; Mice; DNA Footprinting/methods*
From: Protein & Cell 2025;16(11):932-952
CountryChina
Language:English
Abstract: Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.