Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD

To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer–promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds to chromatin for minutes, decompacts chromatin structure and increases enhancer dynamics. We also uncovered a rare fast-diffusing state of enhancers and found that NuRD restricts the time spent in this state. Hi-C and Cut&Run experiments revealed that NuRD modulates enhancer–promoter interactions in active chromatin, allowing them to contact each other over longer distances. Furthermore, NuRD leads to a marked redistribution of CTCF and, in particular, cohesin. We propose that NuRD promotes a decondensed chromatin environment, where enhancers and promoters can contact each other over longer distances, and where the resetting of enhancer–promoter interactions brought about by the fast decondensed chromatin motions is reduced, leading to more stable, long-lived enhancer–promoter relationships

Publisher Correction: Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD

Correction to: Nature Structural & Molecular Biology, published online 28 September 2023. In the version of the article initially published there were some errors in the affiliations. A. Ponjavic’s second and third affiliations have been corrected to Present address: School of Physics and Astronomy, University of Leeds, Leeds, UK and Present address: School of Food Science and Nutrition, University of Leeds, Leeds, UK; and L. Morey now has only two affiliations: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain and Present address: Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, USA. Additionally, the received date has been corrected to 14 April 2020 from 26 October 2021. These errors have been corrected in the HTML and PDF versions of the article

Structure of the small G protein Cdc42 bound to the GTpasebinding domain of ACK

10.1038/20732Nature3996734384-388NATU

High-resolution heteronuclear multidimensional NMR of proteins in living insect cells using a baculovirus protein expression system

Recent developments in in-cell NMR techniques have allowed us to study proteins in detail inside living eukaryotic cells. In order to complement the existing protocols, and to extend the range of possible applications, we introduce a novel approach for observing in-cell NMR spectra using the sf9 cell/baculovirus system. High-resolution 2D 1H–15N correlation spectra were observed for four model proteins expressed in sf9 cells. Furthermore, 3D triple-resonance NMR spectra of the Streptococcus protein G B1 domain were observed in sf9 cells by using nonlinear sampling to overcome the short lifetime of the samples and the low abundance of the labeled protein. The data were processed with a quantitative maximum entropy algorithm. These were assigned ab initio, yielding approximately 80% of the expected backbone NMR resonances. Well-resolved NOE cross peaks could be identified in the 3D 15N-separated NOESY spectrum, suggesting that structural analysis of this size of protein will be feasible in sf9 cells

Soft x-ray magnetic scattering study of thin films and multilayers

A brief discussion of the resonant magnetic scattering process is given. Results from recent studies of thin Fe films and Fe/Gd multilayers are used as examples to demonstrate the information can be obtained and the unique features of this techniques: large resonant enhancement, sensitivity to magnitization, elemental specificity, and tunability of the penetration depth. Comparison is made with related techniques: magneto-optical Kerr effect, Faraday effect, and magnetic circular dichroism. 9 refs., 4 figs