This study investigates how B cell stimulation affects the structure and organization of the inactive X chromosome, revealing dynamic changes in TAD boundaries and Xi compaction.

Cell Reports · Feb 26, 2025Peer-reviewedGenetics

Combinatorial single-cell profiling of all major chromatin types with MAbID

Silke J. A. Lochs, Robin H. van der Weide, Kim L. de Luca, Tessy Korthout, Ramada E. van Beek, Hiroshi Kimurâ, Jop Kind

MAbID enables simultaneous profiling of multiple chromatin states in single cells, revealing multifactorial chromatin state changes during neural differentiation.

Nature Methods · Dec 4, 2023Peer-reviewedGenomics

Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction

Emilia Dimitrova, Angelika Feldmann, Robin H. van der Weide, Koen D. Flach, Anna Lastuvkova, Elzo de Wit, Robert J. Klose

The paper investigates the role of CDK-Mediator in gene regulation, finding it essential for Polycomb-dependent chromosomal interactions and gene priming during differentiation through distinct mechanisms.

bioRxiv · Nov 4, 2021 · PreprintMolecular Biology

Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance

Ruben Schep, Eva Karina Brinkman, Christ Leemans, Xabier Vergara, Robin H. van der Weide, Ben Morris, Tom van Schaik, Stefano Giustino Manzo, Daniel Peric‐Hupkes, Jeroen van den Berg, Roderick L. Beijersbergen, René H. Medema, Bas van Steensel

The paper measures how chromatin context influences the balance between DNA repair pathways after Cas9-induced breaks in over 1,000 genomic locations.

Molecular Cell · Apr 13, 2021Peer-reviewedMolecular Biology

Hi-C Analyses with GENOVA: a case study with cohesin variants

Robin H. van der Weide, Teun van den Brand, Judith H.I. Haarhuis, Hans Teunissen, Benjamin D. Rowland, Elzo de Wit

GENOVA is an R-package for analysing Hi-C data, demonstrating that cohesin subunits SA1 and SA2 differentially affect loop formation and genome compartmentalisation.

NAR Genomics and Bioinformatics · Apr 9, 2021Peer-reviewedGenomics

Condensin’s ATPase Machinery Drives and Dampens Mitotic Chromosome Condensation

Ahmed M.O. Elbatsh, Eugene Kim, Jorine M. Eeftens, Jonne A. Raaijmakers, Robin H. van der Weide, Alberto García-Nieto, Sol Bravo, Mahipal Ganji, Jelmi uit de Bos, Hans Teunissen, René H. Medema, Elzo de Wit, Christian H. Haering, Cees Dekker, Benjamin D. Rowland

This study shows that condensin complexes use opposing ATPase sites to drive and dampen chromosome condensation, with condensin II playing a key role in decatenation and axis formation.

Molecular Cell · Oct 16, 2019Peer-reviewedMolecular Biology

Systematic identification of human SNPs affecting regulatory element activity

Joris van Arensbergen, Ludo Pagie, Vincent FitzPatrick, Marcel de Haas, Marijke P. A. Baltissen, Federico Comoglio, Robin H. van der Weide, Hans Teunissen, Urmo Võsa, Lude Franke, Elzo de Wit, Michiel Vermeulen, Harmen J. Bussemaker, Bas van Steensel

The paper identifies over 30,000 SNPs affecting regulatory element activity using SuRE reporter technology, linking them to gene regulation and potential human traits.

Nature Genetics · Jun 28, 2019Peer-reviewedGenomics