Space-time resolves protein-DNA interactions globally

On April 27, 2023, Beijing time, Chen Xiaohua’s research group of Shanghai Institute of Materia Medica, Chinese Academy of Sciences and Tan Minjia’s research group published a report entitled “Spatiotemporal and global profiling of DNA–protein interactions enables discovery of low-affinity transcription” in the journal Nature Chemistry factors”.

The study reports a new method for resolving protein-DNA interactions (Light-Induced Lysine (K) Enabled Crosslinking, or for shortLIKE-XL), combined with mass spectrometry analysis, transcription factors interacting with DNA probes can be found, and transcription factors with low affinity can be resolved and resolved in time and space; Then, the dynamic interaction between related transcription factors and specific sequence DNA probes under different conditions can be solved, which provides a new method for the global analysis of protein-DNA dynamic interaction.

Researcher Chen Xiaohua and researcher Tan Minjia of Shanghai Institute of Materia Medica, are the corresponding authors of this paper; Guo Andi, Yan Kenian and Hu Hao are the co-first authors of this paper.

The interaction of proteins with DNA plays a key role in biological processes. Accurate elucidation of protein-DNA interactions can reveal mutual recognition mechanisms and dynamic changes, which is essential for a deeper understanding of gene regulation under physiological and pathological conditions. Although existing research methods have made great progress in characterizing the recognition and mechanism of action of high-affinity DNA-proteins, especially transcription factors, the analysis of low-abundance proteins in biological systems and dynamic and weak protein-DNA complexes is still extremely challenging.

In order to realize the panoramic analysis of protein-DNA interaction in spatiotemporal dynamics, Chen Xiaohua’s research group and Tan Minjia’s research group of Shanghai Institute of Materia Medica, Chinese Academy of Sciences collaborated to develop light induction in the early stagePANACLight click on the basis of chemistry (Nat. Commun. 2020, 11, 5472; Chem 2019, 5, 2955-2968), developed a protein-DNA crosslinking method with lysine-selective (Light-induced Lysine (K) Enabled CrosslinkingLIKE-XL), combined with the team’s rich experience and technical advantages in deep quantitative proteomics analysis, the in-depth analysis of protein-DNA dynamic interactions, including transcription factors-DNA spatiotemporal dynamics with weak interactions, was achieved (Figure 1).

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Figure 1: Schematic diagram of the LIKE-XL method to globally resolve protein-DNA spatiotemporal dynamic interactions

The researchers first designed and synthesized a DNA probe containing a photocrosslinked group that can efficiently crosslink interacting proteins at low concentrations (micromolar concentrations) and in short periods of time (5-10 minutes). Combined with quantitative proteomics technology based on mass spectrometry, the LIKE-XL global analytical method far exceeds the non-covalent interaction technology in identifying the number of interacting proteins. Showed better efficiency and higher sensitivity than non-specific crosslinking methods. The LIKE-XL strategy not only successfully identified transcription factor-DNA interactions with expected low affinity, but also discovered novel transcription factors and binding sites on target DNA sequences. Further, by integrating cross-linking sites, structural biology information, and molecular docking, the study discovered a new mode of action for transcription factors with weak binding capacity to bind to DNA. With LIKE-XL technology, researchers have revealed a dynamic panorama of the time-resolved downstream transcription factor interaction network of epigenetic drugs such as the deacetylase inhibitor SAHA.

This study provides a new method for the global in-depth analysis of the spatiotemporal dynamic interaction of protein-DNA, and the interaction protein binding activity analysis strategy using specific DNA sequences as probes is expected to be used to analyze the interaction between different base modifications and proteins in target DNA sequences, and provide new chemical biology tools for DNA and epigenetic related research.

This work has been supported by the National Natural Science Foundation of China “Dynamic Modification and Chemical Intervention of Biomacromolecules” major research program, the Ministry of Science and Technology Key Research and Development Program and other projects. This work has received great help and support from Professor Zhang Jian of Shanghai Jiaotong University School of Medicine, Researcher Zhao Dongxin, Researcher Lu Xiaojie and Researcher Xu Yechun of Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Professor Xu Yongjiang of Jiangnan University, and Professor Liu Wei of Shanghai Medical College of Fudan University. (Source: Science Network)

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