A. Marieke Oudelaar

This paper identifies senescence-induced CTCF clusters (SICCs) and shows they sustain the senescence splicing program by repurposing nuclear speckle components.

The paper identifies RNA helicase partners of G-patch proteins and reveals distinct regulatory mechanisms by which they influence mRNA maturation.

The paper introduces mwMCC, a method to detect multi-way chromatin interactions at sub-nucleosome resolution, revealing synergistic nano-scale interactions within super-enhancers and their role in gene regulation.

This study reconstitutes Drosophila chromatin architecture in a cell-free system, revealing spontaneous formation of long-range interactions and TADs.

The paper uses super-resolution microscopy to measure enhancer-promoter distances during pluripotency exit, finding minimal changes despite large transcriptional changes.

This study shows translocations can drive widespread gene expression changes across entire chromosome arms in MCL by altering chromatin organization and regulatory loops.

The paper uses synthetic enhancer engineering in mESCs to show that enhancer clusters increase transcriptionally productive enhancer-gene contacts through enhanced RNA Polymerase II pause release.

The paper shows that active enhancers recruit cohesin to form cell-specific chromatin domains, using the alpha globin cluster as a model.

The paper shows that CTCF depletion disrupts chromatin hub formation but not enhancer-promoter interactions, which still drive gene expression during differentiation.

This study reconstitutes chromatin domains in vitro using S. cerevisiae and shows that nucleosome positioning alone is sufficient for domain formation.

This study shows that the Mediator complex is essential for enhancer-promoter interactions, as its depletion reduces interaction frequencies and gene expression, while increasing CTCF-binding site interactions and altering Cohesin distribution.

This study identifies higher-order coordination of DNA repair proteins in single cells by analyzing their genome-wide localization using DamID and ChIC sequencing.

The paper shows that super-enhancers function directionally and orientation-dependently, unlike regular enhancers, by analyzing the β-globin super-enhancer.

The paper analyzes sub-kilobase chromatin topology to show that nano-scale regulatory interactions depend on CTCF but not cohesin, and that cohesin affects longer-range enhancer-promoter interactions.

The paper examines how dynamic chromatin boundaries around the Runx1 gene influence its expression during hematopoietic development in mice.

DeepC predicts chromatin interactions from DNA sequence using deep learning and transfer learning, generalizing across cell types and resolutions.

The paper studies chromatin architecture changes during mouse erythroid differentiation using Tiled-C and shows enhancer-promoter interactions form during differentiation, not before gene expression.

The paper introduces a new method, NuTi Capture-C, that improves high-resolution chromosome conformation capture by reducing noise and increasing sequencing content, enabling reproducible genome-wide interaction profiles.

CaptureCompendium provides software tools to simplify the design, analysis, and visualization of 3C experiments, addressing the need for specialized bioinformatics skills in genome folding studies.

The paper develops a platform combining ATAC-seq, DNaseI footprints, NG Capture-C, and machine learning to identify causal variants and genes for polygenic human traits.

The paper investigates promoter competition in the -globin domain using chromatin interaction data, finding that promoters interact simultaneously with a super-enhancer rather than competing.

This study shows that enhancers primarily regulate gene expression by promoting transcription initiation rather than by affecting RNA polymerase II pausing.

The paper identifies a distinct class of enhancers in leukemia cells that depend on H3K79 methylation and shows that DOT1L inhibition disrupts their function.

The paper develops Tri-C, a single-cell 3C method, to reveal dynamic chromatin interactions and regulatory hubs in mammalian cells.