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

Cross-linking mass spectrometry (XLMS) allows mapping of protein-protein and protein-RNA interactions, but the analysis of protein-DNA complexes remains challenging. Here, the authors develop a UV light-based XLMS workflow to determine protein-DNA interfaces in reconstituted chromatin and isolated nuclei.

Alexandra Stützer
Luisa M. Welp
Henning Urlaub
ResearchOpen Access16 Oct 2020
Nature Communications

Volume: 11, P: 1-12
Defining the RBPome of primary T helper cells to elucidate higher-order Roquin-mediated mRNA regulation

An extensive RNA binding protein atlas (RBPome) for primary T cells would be a useful resource. Here the authors use two different methods to characterise the mouse and human T cell RBPome and show regulation of Roquin-1/2 dependent and independent pathways.

Kai P. Hoefig
Alexander Reim
Vigo Heissmeyer
ResearchOpen Access01 Sept 2021
Nature Communications

Volume: 12, P: 1-18
Functional identity of hypothalamic melanocortin neurons depends on Tbx3

Hypothalamic melanocortin neurons control energy homoeostasis by modulating appetite. Here, the authors reveal a role for the transcription factor Tbx3 as a regulator of the peptidergic identity and function of immature and mature mouse melanocortin neurons.

Carmelo Quarta
Alexandre Fisette
Matthias H. Tschöp
Research28 Jan 2019
Nature Metabolism

Volume: 1, P: 222-235
Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry

Cross-linking mass spectrometry (MS) is an important tool in structural biology, but its application to protein-DNA complexes has been hampered by low cross-linking efficiency. Here, the authors develop a femtosecond UV-laser induced cross-linking MS workflow to map protein-DNA interactions in vitro and in cells.

Alexander Reim
Roland Ackermann
Michael Wierer
ResearchOpen Access15 Jun 2020
Nature Communications

Volume: 11, P: 1-14
A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition

The fungal plant pathogen Zymoseptoria tritici is a major threat to wheat yield. Here Seybold et al. show that Z. tritici can suppress immune responses not only in infected tissue but also on other leaves, a phenomenon termed “systemic induced susceptibility” that is correlated with systemic changes in metabolite accumulation.

Heike Seybold
Tobias J. Demetrowitsch
Eva H. Stukenbrock
ResearchOpen Access20 Apr 2020
Nature Communications

Volume: 11, P: 1-12
The H2A.Z and NuRD associated protein HMG20A controls early head and heart developmental transcription programs

How the histone variant H2A.Z controls cell fate remains unclear. Here, the authors reveal that the H2A.Z interacting partner HMG20A plays a key role in regulating transcription during early head and heart development.

Andreas Herchenröther
Stefanie Gossen
Sandra B. Hake
ResearchOpen Access28 Jan 2023
Nature Communications

Volume: 14, P: 1-20
NUDT2 initiates viral RNA degradation by removal of 5′-phosphates

RNA of some viruses is protected from degradation by a 5′ triphosphate group. Here the authors identify nudix hydrolase 2 (NUDT2) as novel antiviral defense protein that dephosphorylates viral RNA and thereby enables its degradation.

Beatrice T. Laudenbach
Karsten Krey
Andreas Pichlmair
ResearchOpen Access25 Nov 2021
Nature Communications

Volume: 12, P: 1-13
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

Single-cell analysis of Drosophila development with Hi-M suggests that physical proximity between regulatory regions does not necessarily instruct transcriptional states. Multi-way analyses identify the existence of regulatory hubs that emerge before topologically associating domains.

Sergio Martin Espinola
Markus Götz
Marcelo Nollmann
Research01 Apr 2021
Nature Genetics

Volume: 53, P: 477-486
Efficient production of multi-modified pigs for xenotransplantation by ‘combineering’, gene stacking and gene editing

Konrad Fischer
Simone Kraner-Scheiber
Angelika Schnieke
ResearchOpen Access29 Jun 2016
Scientific Reports

Volume: 6, P: 1-11

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

Defining the RBPome of primary T helper cells to elucidate higher-order Roquin-mediated mRNA regulation

Functional identity of hypothalamic melanocortin neurons depends on Tbx3

Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry

A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition

The H2A.Z and NuRD associated protein HMG20A controls early head and heart developmental transcription programs

NUDT2 initiates viral RNA degradation by removal of 5′-phosphates

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

Efficient production of multi-modified pigs for xenotransplantation by ‘combineering’, gene stacking and gene editing

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