Daan Noordermeer

Genomic imprinting of the metabolic regulator gene Klf14 is regulated by a paternal sub-TAD anchored at Mest and a shared enhancer in mice.

This paper identifies a paternal sub-TAD and shared enhancer that regulate Klf14 genomic imprinting in mice, revealing a mechanism involving Mest and allele-specific CTCF binding.

A segmental duplication-mediated deletion leads to neocentromere formation in orangutans

The paper identifies a segmental duplication-mediated deletion causing neocentromere formation in orangutans by analyzing structural and epigenetic variation.

Phase transition of spindle pole localized protein orchestrates nuclear organization at mitotic exit

The paper shows that Aurora A regulates NuMA's phase state at spindle poles, affecting nuclear organization during mitotic exit.

Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms

The paper investigates how TAD boundary width influences insulation between adjacent TADs, showing that wider boundaries reduce inter-TAD contacts and enhance insulation.

Identification and copy number variant analysis of enhancer regions of genes causing spinocerebellar ataxia

The paper identifies enhancer regions of SCA genes in human cerebellum and screens for copy number variants in undiagnosed patients, finding one potential CNV of unknown significance.

The embryonic DNA methylation program modulates the cis-regulatory landscape via CTCF antagonism

This study shows that DNA methylation affects CTCF binding and 3D chromatin structure during mouse embryonic differentiation.

A complex CTCF binding code defines TAD boundary structure and function

The paper reveals that CTCF binding at TAD boundaries is modular and clustered, challenging existing models of loop extrusion blocking and highlighting a complex code for TAD structure and function.

The Drosophila Fab-7 boundary element modulates Abd-B gene activity in the genital disc by guiding an inversion of collinear chromatin organization and alternative promoter use

The paper investigates how the Fab-7 boundary element influences Abd-B gene activity in Drosophila genital discs by altering chromatin organization and promoting alternative promoter use.

ATM-dependent formation of a novel chromatin compartment regulates the Response to DNA Double Strand Breaks and the biogenesis of translocations

The paper identifies a novel chromatin compartment formed by ATM-dependent clustering of damaged TADs, which enhances DNA damage response but increases translocations.

Loss of Polycomb Protein EZH2 causes major depletion of H3K27 and H3K9 tri-methylation and developmental defects in the fungus Podospora anserina

The paper investigates the role of H3K27me3 and H3K9me3 histone modifications in the fungus Podospora anserina, showing their distinct functions in development and gene silencing.

Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation

The paper identifies TADs as functional units in DDR, showing cohesin-mediated loop extrusion contributes to {gamma}H2AX/53BP1 domain formation during DSB repair.

CTCF controls imprinted gene activity at the mouse Dlk1-Dio3 and Igf2- H19 domains by modulating allele-specific sub-TAD structure

The paper investigates how CTCF modulates sub-TAD structure at imprinted domains in mice, affecting gene activity through allele-specific binding.

Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers

The paper develops a polymer model to analyze chromatin organization changes during differentiation, finding synchronous compaction/decompaction of TADs and secondary structures in 5C data.

Dynamic enhancer partitioning instructs activation of a growth regulator during exit from naïve pluripotency

The paper shows that CTCF-mediated enhancer partitioning controls the promoter switch of Zdbf2 during exit from naïve pluripotency, independent of polycomb and DNA methylation.

LARGE-SCALE GENOMIC REORGANIZATIONS OF TOPOLOGICAL DOMAINS (TADs) AT THE HoxD LOCUS

The paper investigates how genomic rearrangements affect TAD structures at the HoxD locus by analyzing long-range chromatin interactions and boundary selection mechanisms.