Job Dekker

This study shows that SA1/2 are not essential for V(D)J recombination in G0/G1-arrested cells, but their absence disrupts chromatin loops and long-range Igh recombination, while Ig{kappa} recombination remains functional.

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

This study shows cohesin suppresses unequal sister chromatid exchange by maintaining arm cohesion and limiting distal repeat interactions in yeast.

The paper identifies RNA as the molecular glue forming a stable chromatin compartment associated with nuclear speckles, independent of speckles themselves.

This study shows histone hyperacetylation disrupts TAD intra-interactions but preserves CTCF-CTCF loops, revealing distinct cohesin populations with different sensitivity to acetylation.

UnionLoops improves chromatin loop detection across related Hi-C datasets by integrating information to enhance specificity, precision, and sensitivity.

This study investigates the roles of esBAF and INO80C in shaping 3D genome organization in mouse embryonic stem cells, finding they influence subcompartment identity and enhancer-promoter interactions.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper identifies a spatial coordination between mRNA initiation and termination sites, proposing a 'Positional Initiation-Termination Axis' that influences isoform diversity.

The paper examines changes in chromosome conformation, nuclear organization, and transcription during motor neuron maturation in control and ALS C9orf72 mutant cells, finding delayed maturation in disease models.

In DT40 cells, condensins displace extrusive cohesin, bypass cohesive cohesin and stall against each other while extruding ~1-3 kb/sec, yielding irregular helical chromatids of consecutive loops.

The paper uses polymer physics models to simulate and analyze the 3D structure of the LTN1 gene region, comparing results with Hi-C data to predict structural features for microscopy experiments.

The paper investigates how interphase chromosome conformation is re-established after mitosis by distinguishing between chromosome-intrinsic and cytoplasmic inheritance mechanisms.

The paper shows mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two-stage process during mitotic exit.

The paper investigates mitotic chromosome architecture across species and cell types, finding species-specific loop sizes but no cell type differences, and links loop size to chromosome arm compaction.

The paper uses multi-omics analysis to compare malignant and normal uveal melanocytes, identifying genomic instability and a BAP1 promoter deletion as key features of uveal melanoma.

The paper develops Indel-Seq to study insertion mechanisms at DNA double-strand breaks, finding insertions arise from transcription and require DNA-PK and ssDNA overhangs.

This study shows Prmt5 regulates gene expression and chromatin organization during adipogenesis by modulating TAD boundaries and chromatin loop anchors.

The paper reanalyzes sperm chromatin structure in mice, finding that prior studies were contaminated by cell-free chromatin, and identifies open loci associated with early development.

The paper shows that ARP2/3-dependent nuclear actin polymerization and DNA end-resection coordinate genome reorganization to facilitate homology-directed repair and prevent translocations.

The paper identifies three inactive chromatin states in HCT116 cells and shows how H3K9me3-HP1/β heterochromatin influences genome compartmentalization and loop extrusion barriers through DNA methylation.

The paper identifies three types of chromatin boundaries that regulate cohesin traffic, which guides enhancer-promoter interactions and affects gene regulation.

This study shows that cohesin-mediated loops in G1 phase determine the genomic location of replication origins in S phase by anchoring replication initiation zones.

The paper generates chromosome-level reference genomes for two C. briggsae strains, improving genomic resources for comparative genomics in the Caenorhabditis genus.

This study evaluates 3C-based assays to understand how experimental parameters affect chromatin interaction detection and quantification, leading to the development of Hi-C 3.0.

This study identifies biochemically distinct cohesin complexes that mediate different types of chromatin loops based on genomic context.

The paper investigates how genome structure responds to nuclear swelling, finding that global topology remains elastic and robust despite dramatic volume changes.

The paper presents a chromosome-level genome assembly of the Atlantic silverside and reports high heterozygosity and extensive structural variation linked to local adaptation.

This study introduces liquid chromatin Hi-C to analyze chromatin interaction dynamics and finds that compartmentalization stability varies with chromatin domain type and fragment size.

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.