Linking chromatin acylation mark-defined proteome and genome in living cells

Qin, Fangfei; Li, Boyuan; Wang, Hui; Ma, Sihui; Li, Jiaofeng; Liu, Shanglin; Kong, Linghao; Zheng, Huangtao; Zhu, Rongfeng; Han, Yu; Yang, Mingdong; Li, Kai; Xiong, Ji; Chen, Peng R.

doi:10.1016/j.cell.2023.02.007

Cited by 20 publications

(22 citation statements)

References 147 publications

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“…Environmental chemicals and their endogenous active metabolites can covalently attach to the nucleophilic sites of proteins, like amines, thiols, carboxylates, and alcohols, and form protein adducts to trigger various toxicities, as exemplified by cellular metabolite modifications on histone acylations. 29 For example, fluorotelomer unsaturated aldehydes were found to have covalent interactions with proteins in rat liver microsomes and bovine blood plasma, in which, the levels of covalent modification ranged from 20.1 (±2.8)% to 71.3 (±19.5)% and 24.0 (±1.5)% to 82.5 (±14.0)%, respectively. 30 In such cases, by identifying the covalent chemical modifications of chemicals across the proteome enables systematic target protein determination and thus helps get a better understanding of pollutant-induced toxicities.…”

Section: Compound-centric Methods To Identify Target Protein(s) Of En...mentioning

confidence: 99%

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Li,

Lyu,

Wang

et al. 2023

Chem. Res. Toxicol.

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Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinitydriven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.

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Section: Compound-centric Methods To Identify Target Protein(s) Of En...mentioning

confidence: 99%

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Li,

Lyu,

Wang

et al. 2023

Chem. Res. Toxicol.

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show abstract

“…Remarkably, a powerful single‐site‐resolved multi‐omics (SiTomics) strategy has recently been developed by utilizing the bifunctional UAAs containing both lysine acylation (post‐translational modifications) and diazirine (photocrosslinker). In this study, it was found that these UAAs can be site‐specifically incorporated into the histones on the chromatin and serve as the in situ crosslinker to capture the interacting protein that could recognize the specific acylated lysine in native cellular chromatin, leading to the identification of GLYR1 as a distinct interacting protein in modulating H3K56cr's gene body localization [125] . However, it should be noted that these activated photocatalytic intermediates are not amino acid‐specific, which may result in higher background values and complicate mass spectrometry analysis and data interpretation.…”

Section: Mass Spectrometry (Ms) Based Proximity Labeling Strategies F...mentioning

confidence: 99%

Chemical and Biological Strategies for Profiling Protein‐Protein Interactions in Living Cells

Wang

et al. 2023

Chemistry An Asian Journal

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Protein-protein interactions (PPIs) play critical roles in almost all cellular signal transduction events. Characterization of PPIs without interfering with the functions of intact cells is very important for basic biology study and drug developments. However, the ability to profile PPIs especially those weak/transient interactions in their native states remains quite challenging. To this end, many endeavors are being made in developing new methods with high efficiency and strong operability. By coupling with advanced fluorescent microscopy and mass spectroscopy techniques, these strategies not only allow us to visualize the subcellular locations and monitor the functions of protein of interest (POI) in real time, but also enable the profiling and identification of potential unknown interacting partners in high-throughput manner, which greatly facilitates the elucidation of molecular mechanisms underlying numerous pathophysiological processes. In this review, we will summarize the typical methods for PPIs identification in living cells and their principles, advantages and limitations will also be discussed in detail.

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“…Most technologies can hardly decipher endogenous proteins that transit between specific organelles or cells. Professor Alice Y. Ting from Stanford University recently developed a novel technique called TransitID, and this technique can be expanded to several new applications, especially in neuroscience [1] …”

Section: Figurementioning

confidence: 99%

TurboID coupled with APEX2: Application prospects for deciphering proteome trafficking and interactions in neuroscience

Zhu,

Wang

2023

Brain-X

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Linking chromatin acylation mark-defined proteome and genome in living cells

Cited by 20 publications

References 147 publications

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions

Chemical and Biological Strategies for Profiling Protein‐Protein Interactions in Living Cells

TurboID coupled with APEX2: Application prospects for deciphering proteome trafficking and interactions in neuroscience

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