Job Dekker

SisterC is a method to distinguish inter- and intra-sister chromatid interactions using BrdU labeling and Hi-C, revealing centromere alignment and cohesin-mediated loops.

The paper assembles the genome of Symbiodinium microadriaticum using Hi-C and describes its unique chromosomal structure and organization.

This study improves chromosome architecture mapping by using Micro-C to achieve nucleosome-resolution insights in human cells, revealing new looping interactions and structural patterns.

The paper uses multi-contact 3C data to show that chromosomes and compartment domains in the human genome are largely unentangled.

The paper shows that during telophase, condensin-mediated loops are replaced by cohesin-mediated loops and TADs, revealing telophase as a critical transition in chromosome folding.

A haplotype-resolved Hi-C approach reveals structured homolog pairing in early Drosophila embryos, correlated with Zelda-mediated chromatin accessibility.

The paper uses haplotype-resolved Hi-C to reveal structured homolog pairing and its global impact on gene activity in hybrid Drosophila cells.

The paper evaluates reproducibility and quality measures for Hi-C data using real and simulated datasets, showing that specialized methods outperform simple correlation analysis.

The paper shows Stag2 loss in HSPCs impairs B-cell lineage commitment by reducing chromatin accessibility, while Stag1 cannot restore this function despite rescuing topological domains.

The paper shows CTCF binding and nucleosome positioning at CTCF sites change during the cell cycle, with loss of binding in prometaphase and rearrangement of chromatin structure.

This study shows that SmcHD1 prevents TAD formation on the inactive X chromosome by altering chromatin structure and epigenetic marks.

This study develops a method to probe mRNA 3D structures and finds that pre-translational mRNPs form linear rod-like structures without strong end interactions.

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

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

C-BERST uses dCas9-APEX2 to map proteomes near genomic loci, identifying telomere and centromere-associated proteins.

The paper shows mitotic chromosomes form through condensin-mediated disassembly of interphase chromatin and helical winding of loop arrays during prophase and prometaphase.

This paper investigates the mechanism of nuclear inversion in rod photoreceptors by combining Hi-C, microscopy, and polymer modeling, revealing that heterochromatin interactions drive phase separation and that lamina interactions maintain conventional nuclear organization.

The paper investigates the HoxD cluster's role as a dynamic TAD boundary in limb development, showing its resilience and ability to maintain regulatory segregation.

The paper outlines the goals and structure of the 4D Nucleome Project, which aims to map the spatial and temporal dynamics of the genome in human and mouse cells.

This study investigates the roles of cohesin and condensin in mitotic chromosome organization in budding yeast using Hi-C and polymer modeling, revealing distinct functions for each complex.

This study investigates cell-to-cell and cell-intrinsic variability in genome organization using Hi-C and genome imaging in human fibroblasts, revealing extensive heterogeneity in chromatin conformations.

This study shows CTCF is essential for TAD organization but not for genome compartmentalization, revealing distinct mechanisms for chromatin folding and insulation.

Hi-C 2.0 improves Hi-C protocol to achieve high-resolution mapping of chromatin interactions with better resolution and reduced noise.