Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

Makowski, Matthew; Gräwe, Cathrin; Foster, Benjamin M.; Nguyen, Nhuong V.; Bartke, Till; Vermeulen, Michiel

doi:10.1038/s41467-018-04084-0

Cited by 61 publications

(75 citation statements)

References 57 publications

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“…In a recent study, a series of protein affinity pull-downs from nuclear lysates with oligonucleotide baits at different concentrations was combined with isobaric tandem-mass-tag labelling and mass spectrometry. This revealed apparent dissociation constants and binding profiles towards different G4 and transcription factor consensus sequences for hundreds of nuclear proteins in parallel [69].…”

Section: Natural G4-binding Proteinsmentioning

confidence: 97%

“…Furthermore, various epigenetic and chromatin remodelling enzymes selectively bind DNA G4 oligomers [69] . Genomic binding sites of the chromatin remodelling protein ATR-X are enriched at GC-rich tandem repeats and CpG islands with the potential to fold G4 structures, and ATR-X loss is implicated with G4-dependent replication stress, DNA damage, and copy number alterations 53 , 82 .…”

Section: Natural G4-binding Proteinsmentioning

confidence: 99%

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The Structure and Function of DNA G-Quadruplexes

Spiegel

Adhikari

Balasubramanian

2020

Trends in Chemistry

639

568

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Guanine-rich DNA sequences can fold into four-stranded, noncanonical secondary structures called G-quadruplexes (G4s). G4s were initially considered a structural curiosity, but recent evidence suggests their involvement in key genome functions such as transcription, replication, genome stability, and epigenetic regulation, together with numerous connections to cancer biology. Collectively, these advances have stimulated research probing G4 mechanisms and consequent opportunities for therapeutic intervention. Here, we provide a perspective on the structure and function of G4s with an emphasis on key molecules and methodological advances that enable the study of G4 structures in human cells. We also critically examine recent mechanistic insights into G4 biology and protein interaction partners and highlight opportunities for drug discovery. Beyond the DNA Double HelixA chemist's perspective on the function of a molecule, or a system of molecules, is typically led by a consideration of how molecular structure dictates function. The most widely recognised DNA structure is that of the classical DNA double helix [1], which defines a structural basis for the genetic code via defined base-pairing. Yet, it is evident that DNA is structurally dynamic and capable of adopting alternative secondary structures. One such class of DNA secondary structure is the four-stranded Gquadruplex (G4). Herein, we discuss some of the key scientific history that has shaped our understanding of this structural motif, its probable functions in biology, and major unanswered questions that remain to be solved.

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Section: Natural G4-binding Proteinsmentioning

confidence: 97%

Section: Natural G4-binding Proteinsmentioning

confidence: 99%

The Structure and Function of DNA G-Quadruplexes

Spiegel

Adhikari

Balasubramanian

2020

Trends in Chemistry

639

568

View full text Add to dashboard Cite

show abstract

“…Top protein hits included mediators of histone modification, HMG chromatin architectural proteins, and histone chaperones (Box ). The same year, a new quantitative method for proteome‐wide profiling of DNA–protein and nucleosome–protein interactions was employed to identify the binding partners of the c‐Myc promoter G4 . Top protein hits included SMARCB1—a subunit of the chromatin remodeling complex SWI/SNF, enhancer of zeste homolog 2 and embryonic ectoderm development—subunits of the PRC2, and GATAD2B, a subunit of NuRD .…”

Section: G4s Might Directly Engage Architectural Chromatin Proteins mentioning

confidence: 99%

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

2019

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Here, the emerging data on DNA G‐quadruplexes (G4s) as epigenetic modulators are reviewed and integrated. This concept has appeared and evolved substantially in recent years. First, persistent G4s (e.g., those stabilized by exogenous ligands) were linked to the loss of the histone code. More recently, transient G4s (i.e., those formed upon replication or transcription and unfolded rapidly by helicases) were implicated in CpG island methylation maintenance and de novo CpG methylation control. The most recent data indicate that there are direct interactions between G4s and chromatin remodeling factors. Finally, multiple findings support the indirect participation of G4s in chromatin reshaping via interactions with remodeling‐related transcription factors (TFs) or damage responders. Here, the links between the above processes are analyzed; also, how further elucidation of these processes may stimulate the progress of epigenetic therapy is discussed, and the remaining open questions are highlighted.

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“…These assays frequently use crude nuclear extracts, followed by either affinity purification of a TF of interest using antibodies or introduced protein tags such as GFP (8). Alternatively, nuclear extracts can be incubated with histone tails carrying a specific modification (34), reconstituted (un)modified nucleosomes (35), or a DNA sequence harbouring a specific DNA motif to identify the TFs that associate with this sequence (36)(37)(38). While these assays are informative to obtain DNA-binding specificity, histone (modification) binding potential, or to identify protein interaction partners, these assays have their limitations.…”

Section: Enrichment Of Localized Chromatin Compartmentsmentioning

confidence: 99%

Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities

Mierlo

Vermeulen

2021

Molecular & Cellular Proteomics

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Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. Mass spectrometry-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in their in vivo chromatin-bound context. Total chromatin isolated from cells can be directly analysed using mass spectrometry or further fractionated into transcriptionally active and inactive chromatin prior to MS-based analysis. Newly formed chromatin that is assembled during DNA replication can also be specifically isolated and analysed. Furthermore, capturing specific chromatin domains facilitates the identification of previously unknown transcription factors interacting with these domains. Finally, in recent years, advances have been made towards identifying proteins that interact with a single genomic locus of interest. In this review, we highlight the power of chromatin proteomics approaches and how these provide complementary alternatives compared to conventional affinity purification methods. Furthermore, we discuss the biochemical challenges that should be addressed to consolidate and expand the role of chromatin proteomics as a key technology in the context of gene expression regulation and epigenetics research in health and disease.

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Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

Cited by 61 publications

References 57 publications

The Structure and Function of DNA G-Quadruplexes

The Structure and Function of DNA G-Quadruplexes

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities

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