Publications associées à Mechanism of Chromatin Ubiquitination by PRC1 on the Single-Molecule Level

Publications associées (21)

Structural basis of SIRT7 nucleosome engagement and substrate specificity

Esther Calvino Sanles, Polina Nikolaeva Foteva, Henning Paul-Julius Stahlberg, Beat Fierz, Dongchun Ni, Babatunde Edukpe Ekundayo, Carlos Moreno Yruela

Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. SIRT7 is an NAD+-dependent deacylase often deregulated in cancer, which deacetylates either H3 lysine 36 (H3K36) or H3K18 with high specificity withi ...

NATURE PORTFOLIO2025

CircCDYL Association With hnRNPL Modulates CDYL Isoform Switching in Breast Cancer Cells

Isabella Tarulli

Circular RNAs (circRNAs) are covalently closed back‐splicing products involved in the regulation of different cellular processes, and their dysregulation has been frequently observed in cancer cells. CircCDYL, a circRNA derived from the back‐splicing of CD ...

Wiley2025

The Regulation of Transcription Factors Binding Site Occupancies by Their Concentrations

Romane Joséphine Madeleine Mizeret

The precise control of transcription factor (TF) concentrations is crucial for While TF concentration gradients are well-characterized in model organisms like Drosophila and Caenorhabditis elegans, their quantitative relationship with genomic occupancy in ...

EPFL2025

Oxidative stress at telomeres triggers internal DNA loops, TRF1 dissociation, and TRF2-dependent R-loops

Leona Brandl, Joachim Lingner, Wareed Ahmed, Eftychia Kyriacou, Thomas Frédéric Lunardi, Thu Trang Nguyen

Telomeres are the nucleoprotein structures at chromosome ends. Telomeres are particularly sensitive to oxidative stress, which can induce telomere damage, shortening, and premature cellular senescence. How oxidative damage influences telomere structure has ...

2025

Modelling the metabolism of the polyphosphate-accumulating organism Candidatus Accumulibacter

Pilar Natalia Rodilla Ramírez

Wastewater resulting from human activities must be treated to minimize the impact on the receiving ecosystems. One of such potential impacts in lakes and other water bodies is eutrophication, an excessive increase in their nitrogen and phosphorus content. ...

EPFL2025

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

David Michael Suter, Natalya Katanayeva, Haitham Ahmed Shaban Ahmed, Armelle Inge Marie Eleonore Tollenaere

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear ...

National Academy of Sciences2024

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Fides Zenk

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Nature Portfolio2024

DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen

Giovanna Ambrosini, Nicolas Jean Philippe Guex, Christian Iseli

The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-typ ...

OXFORD UNIV PRESS2024

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Chen Zhang

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

EPFL2024

Dissecting the epigenetic regulation of human brain organoid development in single cells

Fides Zenk

We present a developmental atlas that offers insight into sequential epigenetic changes underlying early human brain development modeled in organoids, which reconstructs the differentiation trajectories of all major CNS regions. It shows that epigenetic re ...

NATURE PORTFOLIO2024

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

A modular toolbox for the optogenetic deactivation of transcription

Matteo Fiumara, Johannes Gräff, Davide Martino Coda

Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high spatiotemporal precision. The vast majority of existing tools are, however, limited to light-triggered inducti ...

OXFORD UNIV PRESS2025

G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction

Matteo Dal Peraro

Protein–ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perf ...

2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

Doping In Vivo Alkylation in E. coli by Introducing the Direct Sulfurylation Pathway of S. cerevisiae

Patricia Bencic

Methylation and alkylation are important techniques used for the synthesis and derivatisation of small molecules and natural products. Application of S-adenosylmethionine (SAM)-dependent methyltransferases (MTs) in biotechnological hosts such as Escherichi ...

Wiley-VCH Verlag GmbH2024

A Versatile Method for Site-Specific Chemical Installation of Aromatic Posttranslational Modification Analogs into Proteins

Bouchra Bouri, Hilal Lashuel, Rajasekhar Kolla, Shaswati Mandal

Posttranslational modifications (PTMs) of proteins play central roles in regulating the protein structure, interactome, and functions. A notable modification site is the aromatic side chain of Tyr, which undergoes modifications such as phosphorylation and ...

2024

ERK signalling eliminates Nanog and maintains Oct4 to drive the formative pluripotency transition

David Michael Suter

Naïve epiblast cells in the embryo and pluripotent stem cells in vitro undergo developmental progression to a formative state competent for lineage specification. During this transition, transcription factors and chromatin are rewired to encode new functio ...

2024

ER remodelling by ER-phagy in neurogenesis

Maurizio Molinari

The endoplasmic reticulum (ER) controls the synthesis of lipids and proteins and Ca2+ homeostasis, as well as contacting other organelles and the plasma membrane. A study now looks at a process by which this compartment is remodelled in axons during neurog ...

NATURE PORTFOLIO2024

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Dariia Gudkova, Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Hüseyin Baris Atakan, Daniel Alpern, Mustafa Demir

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

Hydrophobic Interaction and its Small Molecule effect

Ting Mao

Protein stabilization has a crucial rule sustaining biological functionality, disease prevention, and pharmaceutical formulation stabilization, and yet its stabilization mechanism by small molecules such as amino acids is not fully understood. In this work ...

EPFL2024