Mammalian embryos see a substantial increase in available oxygen once the placenta forms. This increase in oxygen exposure serves as a trigger for initiating the development of the hindlimb, thus cont...

This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...

Development depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...

Journal club: Judd et al 2026 -- a surprising result about natural selection in recessive genes

Using 4C technology, higher-order topological features of the pluripotent genome are identified; in pluripotent stem cells, Nanog clusters specifically with other pluripotency genes and this clustering is centred around Nanog-binding sites, suggesting that Nanog helps to shape the three-dimensional structure of the pluripotent genome and thereby contributes to the robustness of the pluripotent state.

Super-enhancers have been proposed to cluster in the nucleus when compared to other genomic elements. Le et al. found that super-enhancer clustering was rare and driven by non-specific interactions. P...

Housekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di...

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

Using an in situ genome-rewriting platform, Zhou et al. demonstrate that precise transcriptional regulation of the NMU promoter is governed by a 3D regulatory hub comprising a core retroviral LTR enhancer, a decoy LTR promoter, and activity-boosting “facilitator” elements.

This study contributes a resource of predicted effects of noncoding variants on chromatin accessibility and a method to identify noncoding variants with extreme regulatory effects, with application to...

The 2027 Gordon Research Conference on Developmental Biology will be held in Lucca (Barga), Lucca Italy. Apply today to reserve your spot.

Zhuoxin Chen, a postdoctoral fellow in the lab of Assistant Professor Evgeny Kvon at the Department of Developmental & Cell Biology at the Charlie Dunlop School of Biological Sciences, has been awarde...

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...

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The authors deplete the cohesin activator NIPBL during the mitosis-to-G1-phase transition. They observe that structural loop formation is impaired proportionally to loop length, while gene activation ...

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

Identification of ZAD-ZnF genes as key regulators of genome organization during Drosophila embryogenesis.