Deciphering molecular interactions by proximity labeling

W Qin, KF Cho, PE Cavanagh, AY Ting - Nature methods, 2021 - nature.com
Many biological processes are executed and regulated through the molecular interactions of
proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the …

Regulation, functions and transmission of bivalent chromatin during mammalian development

TA Macrae, J Fothergill-Robinson… - … reviews Molecular cell …, 2023 - nature.com
Cells differentiate and progress through development guided by a dynamic chromatin
landscape that mediates gene expression programmes. During development, mammalian …

[HTML][HTML] CLIP and complementary methods

M Hafner, M Katsantoni, T Köster, J Marks… - Nature Reviews …, 2021 - nature.com
RNA molecules start assembling into ribonucleoprotein (RNP) complexes during
transcription. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA …

The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes

TH Beacon, GP Delcuve, C López, G Nardocci… - Clinical …, 2021 - Springer
Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4
(H3K4me3) located after first exons and around transcription start sites. This epigenetic mark …

Tracking chromatin state changes using nanoscale photo-proximity labelling

CP Seath, AJ Burton, X Sun, G Lee, RE Kleiner… - Nature, 2023 - nature.com
Interactions between biomolecules underlie all cellular processes and ultimately control cell
fate. Perturbation of native interactions through mutation, changes in expression levels or …

Manipulating cation− π interactions of reader proteins in living cells with genetic code expansion

H Zhao, L Tang, Y Fang, C Liu, W Ding… - Journal of the …, 2023 - ACS Publications
Despite tremendous success in understanding the chemical nature and the importance of
cation− π interactions in a range of biological processes, particularly in epigenetic …

A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution

X Grau-Bové, C Navarrete, C Chiva… - Nature ecology & …, 2022 - nature.com
Histones and associated chromatin proteins have essential functions in eukaryotic genome
organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack …

Genetically encoded bioorthogonal tryptophan decaging in living cells

Y Zhu, W Ding, Y Chen, Y Shan, C Liu, X Fan, S Lin… - Nature Chemistry, 2024 - nature.com
Tryptophan (Trp) plays a critical role in the regulation of protein structure, interactions and
functions through its π system and indole N–H group. A generalizable method for blocking …

Real-time single-molecule imaging of transcriptional regulatory networks in living cells

DW Hwang, A Maekiniemi, RH Singer… - Nature Reviews …, 2024 - nature.com
Gene regulatory networks drive the specific transcriptional programmes responsible for the
diversification of cell types during the development of multicellular organisms. Although our …

Interrogating epigenetic mechanisms with chemically customized chromatin

N Hananya, S Koren, TW Muir - Nature Reviews Genetics, 2024 - nature.com
Genetic and genomic techniques have proven incredibly powerful for identifying and
studying molecular players implicated in the epigenetic regulation of DNA-templated …