Elzo de Wit

The paper shows that SMARCB1 loss disrupts TF-dependent chromatin priming, revealing lineage-specific regulatory output of BAF complexes is constrained by TF repertoire in ATRT tumors.

This study shows CTCF has dual roles in early mammalian development: promoting morphogenesis through promoter binding early on and enabling correct development via looping later.

The paper investigates how CTCF binding sites affect the regulatory landscape of the mouse Sox2 locus by relocating them and measuring their impact on gene expression.

This study shows that DOT1L maintains CD8 T cell identity and restricts their cytotoxic potential by preventing NK-cell features and enhancing anti-tumor reactivity.

The paper identifies TOP2B as a regulator of genome-nuclear lamina interactions, showing its role in partitioning genomic regions between the nuclear lamina and interior, with LBR playing a complementary role.

The paper relocates promoter-reporter constructs to study the positional relationship between the Sox2 gene and its enhancer, revealing gene-mediated confinement of enhancer activity.

The paper investigates how genomic regions called LADs interact with the nuclear lamina, finding that these interactions are multivalent and cooperative, with some subregions having stronger affinity and influencing neighboring sequences.

This study shows that cohesin accumulates at CTCF-bound loop anchors after WAPL depletion, and active genes form long-range clusters independent of cohesin.

The paper introduces IDLI, a method to map nucleosome structures and distortion patterns in mammalian chromatin, revealing widespread and regulated DNA accessibility across cell types.

This study shows ZNF143 regulates nuclear-encoded mitochondrial genes and is essential for development, without affecting chromatin looping or CTCF interactions.

This study shows that cohesin is not always necessary for enhancer function, as some enhancers can act independently through synergy or insulators.

The paper shows that disrupting nuclear lamina association promotes ABCB1 gene derepression and taxol resistance in RPE cells.

The paper identifies that SOX2 maintains chromatin accessibility at regulatory sites that drive gene expression, distinguishing them from non-activating binding sites.

This study uses TACL to analyze individual cohesin loop extrusion trajectories in vivo, revealing new roles for cohesin subunits and their interactions with CTCF and chromatin structure.

The paper identifies cross-lineage dependencies in gastruloid development by analyzing single-cell chromatin accessibility, showing that paraxial mesoderm is required for spinal cord formation through cell-cell interactions.

The paper investigates Ki67's role in chromatin organization by analyzing its genomic interactions and dynamics during the cell cycle in human cells.

The paper investigates the role of CTCF and cohesin in LAD positioning, finding they reinforce borders but do not position LADs, and mediate fine-tuning of nuclear lamina interactions.

This study reports that lentiviral-based CRISPR-Cas9 vectors can integrate into the target genomic location, unexpectedly activating the target gene.

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.

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

This study shows WAPL maintains dynamic cohesin at lineage-specific regulatory regions in mouse embryonic stem cells, which is essential for gene expression and pluripotency.

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.

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

The paper introduces a new 3C method, MC-4C, to study multi-way DNA conformations and reveals cooperative and competitive chromatin interactions, including enhancer hubs and loop collisions.