Nucleosomes with their associated modifications organize and regulate the genome. It is unclear how this is integrated with the requirement of replica…

High-dimensional data are visualized through representation on tree structures.

This study uses single-molecule footprinting to quantify chromatin accessibility at enhancers and promoters in mouse embryonic stem cells and to dissect the contributions of transcription factor bindi...

Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...

Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...

Mitglieder eines CDU-Verbandes in Brandenburg fordern in einem Antrag die Aufhebung des Unvereinbarkeitsbeschlusses der Union mit der AfD. Man könne nicht „Millionen von Bürgern” ausschließen.

Shah, Tortora, et al. show that cells can dial the rate of cohesin loop extrusion by balancing the relative dosage of NIPBL and PDS5. Their models provide a quantitative mechanistic basis for the gene...

CTCF is an essential DNA binding protein whose absence leads to embryonic lethality. CTCF is primarily known for its role in 3D genome organization where its N-terminal domain interacts with cohesin to anchor chromatin loops. How CTCF facilitates proper embryonic development remains unclear, necessitating temporal control to resolve its stage-specific functions. By combining gastruloids, an in vitro model of embryonic development, with a degron system to rapidly deplete CTCF at defined timepoints, we show that early CTCF depletion impairs early gastruloid morphogenesis. Surprisingly, ATAC-seq and time-resolved RNA-seq revealed that differentiation was unaffected. CTCF binding is strongly enriched at promoters of downregulated genes. Re-expression of a CTCF variant with an N-terminal truncation, incapable of looping, was sufficient to rescue the expression of CTCF-promoter bound genes and the defects in morphogenesis. However, extended culture (up to 168 hours) of gastruloids reconstituted with N-terminal truncated CTCF led to their collapse. Our work shows that CTCF has a dual function in early mammalian development: at early stages CTCF regulates developmentally important genes through promoter binding, while at later stages its looping function is required for correct development. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 637587, 865459 Dutch Research Council, https://ror.org/04jsz6e67, 016.161.316, VI.C.222.049 Dutch Cancer Society, https://ror.org/0368jnd28, N/A

Acute depletion of NIPBL reveals a class of chromatin loops that are independent of NIPBL for their maintenance but not their establishment and that NIPBL is necessary for the expression of lineage-de...

Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in ...

Classifying chromatin loops from 3D genomics data according to their epigenetic and structural attributes is important for inferring their functional roles. Currently, such classification typically relies on the manual intersection of epigenomic signal peaks and loop anchor locations. To automate this, remove peak-calling biases and include information inherent to 3D genomics signal structure, we developed LoopBin, a framework based on a variational deep embedding (VaDE) neural network. We applied LoopBin to kilobase-resolution Micro-C data and segmented tens of thousands of loops into clusters with distinct features using minimal histone modification and transcription factor-binding data. These features were indicative of apparently distinct biological function by each subgroup of loops. Therefore, LoopBin can provide insights into the dynamic shifts in loop classification that can occur upon perturbation of cell homeostasis or signaling. ### Competing Interest Statement The authors have declared no competing interest.

Three-dimensional (3D) genome organization plays a central role in gene regulation, chromatin folding, and genome stability. Although chromosome-conformation capture (3C)-derived methods have revoluti...