Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

Stützer, Alexandra; Welp, Luisa M.; Raabe, Marco; Sachsenberg, Timo; Kappert, Christin; Wulf, Alexander; Lau, Andy M.; Chernev, Aleksandar; Kramer, Katharina; Politis, Argyris; Kohlbacher, Oliver; Fischle, Wolfgang; Urlaub, Henning

doi:10.1038/s41467-020-19047-7

Cited by 30 publications

(69 citation statements)

References 79 publications

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“…To understand the DNA-dependent processes, mapping of such protein–DNA interactions as well as identification of specific sites of interaction are required [ 139 ]. Many of the previously described CLMS workflows can be adopted to obtain such insights as has been recently demonstrated by Stützer et al [ 140 ], who performed mass spectrometric identification of proteins interacting directly with DNA in reconstituted and native chromatin after cross-linking by UV light. Analysis of contact interface at amino acid level was possible by this approach, and they also described the possible means to distinguish the protein–DNA and protein–RNA interactions by performing a single experiment [ 140 ].…”

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

“…Many of the previously described CLMS workflows can be adopted to obtain such insights as has been recently demonstrated by Stützer et al [ 140 ], who performed mass spectrometric identification of proteins interacting directly with DNA in reconstituted and native chromatin after cross-linking by UV light. Analysis of contact interface at amino acid level was possible by this approach, and they also described the possible means to distinguish the protein–DNA and protein–RNA interactions by performing a single experiment [ 140 ]. Chromatin is one of the most prominent protein–DNA complexes of a eukaryotic cell and in this, a core of eight histone proteins (2xH2A, 2xH2B, 2xH3, and 2xH4) associate with DNA in a repetitive manner to facilitate structural and functional organization of the genome [ 139 ].…”

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

“…Several studies described that RNA binding sites in proteins can be detected efficiently by using UV cross-linking combined with mass spectrometry [ 141 , 142 ]. Similarly for the cross-linking of protein and DNA components, a well established protein–DNA cross-links are induced in vivo after the exposure of cells to UV light, ionizing radiation or alkylating agents, in order that lead to bulky DNA lesions [ 140 , 143 ]. UV irradiation of DNA triggers a cellular cascade called DNA damage response, comprising a multitude of proteins and likewise, this UV irradiation has been successfully applied to cross-link single- and double- stranded DNA to proteins for analyzing chromatin dynamics [ 144 ].…”

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

“…UV irradiation of DNA triggers a cellular cascade called DNA damage response, comprising a multitude of proteins and likewise, this UV irradiation has been successfully applied to cross-link single- and double- stranded DNA to proteins for analyzing chromatin dynamics [ 144 ]. Accordingly, the UV cross-linking with mass spectrometry could be beneficial to explore structural and functional relations in protein–DNA systems [ 140 ].…”

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

“…Recently, Stützer et al adapted the established protein–RNA CLMS workflow for detecting protein–DNA cross-links [ 140 ]. In their initial experiments they showed that UV irradiation at 254 nm efficiently cross-link histone proteins to double stranded DNA.…”

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

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Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

et al. 2021

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The fundamentals of how protein–protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein–protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.

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Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

Section: Concept and Perspectives Of Cross-linking Mass Spectrometmentioning

confidence: 99%

See 3 more Smart Citations

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

et al. 2021

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A Paper‐Based Wearable Photodetector for Simultaneous UV Intensity and Dosage Measurement

Cai

Zuo

Zhang

et al. 2021

Adv Funct Materials

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Photodetectors, which convert the light signal into other forms of signal, have been under the spotlight of research for many years because they are widely applied in monitoring, communication, and imaging. Most of the currently available photodetectors can output electrical signals to indicate the transient light intensity, while some display color change to reveal the absorbed light dosage. However, there is no device that can tell the transient light intensity and accumulated light dosage at the same time. Here, a paper‐based wearable photodetector that can simultaneously measure transient light intensity and accumulated light dosage is reported. The phosphomolybdic acid/citric acid system, whose color change can be observed by the naked eye, is designed as the photochromic material to combine with photodetective materials (using 2D Sr2Nb3O10 and ZnO nanoparticle as examples) on paper. Such paper‐based photodetector fully utilizes natural hygroscopicity and softness of paper, showing decent flexibility. Its optoelectronic signal remains stable even after 1000 cycles of bending. To the best of one's knowledge, this is the first photodetector that can tell light intensity and dosage simultaneously. This work introduces a new type of wearable photodetector by structure design and material selection, shedding light on more novel works for convenient and practical photodetection.

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Photochromic Perovskite Nanocrystals for Ultraviolet Dosimetry

Chen,

Sun,

Zheng

et al. 2024

Small

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Excessive ultraviolet (UV) radiation has serious damage to human's health, therefore the development of visible, portable, and wearable sensor for monitoring UV radiation, especially the cumulative UV dosage, is highly desired but full of challenges. Herein, a wearable and flexible UV dosimeter based on photochromic perovskite nanocrystals (PNCs) is designed. The obtained CsPbCl3 PNCs dispersed in dibromomethane (PNCs‐DBM) undergo continuous, vivid, and multiple (from very weak purple to blue, cyan, and finally strong green) color change in response to UV radiation. It is demonstrated that the UV‐induced degradation of DBM and subsequent anion‐exchange reaction between CsPbCl3 and Br−, play a crucial role in the color change of PNCs‐DBM. The properties of continuous fluorescence color change and enhanced fluorescence intensity enable the construction of sensitive and visible UV dosimeter. Furthermore, by integrated photochromic PNCs with flexible bracelet or PDMS substrate, a wearable UV sensor or a multi‐indicator array for the detection of solar UV dosage is developed. This work may advance the fundamental understanding about photochromic perovskite, and show promising application of perovskite nanomaterials in easily fabricated, low‐cost, visualized, and wearable solar UV dosimeter.

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Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

Cited by 30 publications

References 79 publications

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)

A Paper‐Based Wearable Photodetector for Simultaneous UV Intensity and Dosage Measurement

Photochromic Perovskite Nanocrystals for Ultraviolet Dosimetry

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