Liu et al. define how the CRL2ZYG11B ubiquitin ligase assembles and recognizes Gly/N-degron substrates by cryo-EM. Structures with an NLRP1 Gly/N-degron and SARS-CoV-2 ORF10 reveal extended substrate-...

Targeted protein degradation is a powerful tool, but difficult to achieve in vivo with high specificity and control. Here, the authors develop two in vivo targeted protein degradation systems in mice,...

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

Abstract. Recent discoveries have fundamentally transformed the paradigm of plant oxygen sensing. Hypoxia is no longer viewed solely because of environment

Deubiquitylases are key proteolytic regulators of ubiquitin-dependent cellular processes, catalyzing the removal or remodelling of ubiquitin modifications on substrate proteins, including those target...

Selected proteins containing an N-terminal cysteine (Nt-Cys) are subjected to rapid, O2-dependent proteolysis via the Cys/Arg-branch of the N-degro...

Immunomodulatory imide drugs (IMiDs), including thalidomide, lenalidomide, and pomalidomide, can be used to induce degradation of a protein of interest that is fused to a short degron motif, which often comprises a zinc finger (ZF). These IMiDs, however, also induce the degradation of endogenous ZF-containing neosubstrates, including IKZF1, IKZF3, and SALL4. To improve degradation selectivity, we took a bump-and-hole approach to design and screen bumped IMiD analogues against 8380 ZF mutants. This yielded a bumped IMiD analogue that induces efficient degradation of a mutant ZF degron, while not affecting other cellular proteins, including IKZF1, IKZF3, and SALL4. In proof-of-concept studies, this system was applied to induce degradation of the optimum degron fused to CDK9, HPRT1, NanoLuc, or TRIM28. We anticipate that this system will be a valuable addition to the current arsenal of degron systems for use in target validation.

The N-degron pathway is essential for protein quality control and cellular homeostasis. GID4, a subunit of the GID ubiquitin ligase, is the main recog…

Abstract. Recent discoveries have fundamentally transformed the paradigm of plant oxygen sensing. Hypoxia is no longer viewed solely because of environment

The Arg/N-degron pathway of Saccharomyces cerevisiae is mediated by two interacting E3 ubiquitin ligases, Ubr1 and Ufd4. We show here that the mito...

Different types of SETBP1 variants cause variable developmental syndromes with only partial clinical and functional overlaps. Here, the authors report that SETBP1 variants outside the degron region impair DNA-binding, transcription, and neuronal differentiation capacity and morphologies.

Deubiquitylases are key proteolytic regulators of ubiquitin-dependent cellular processes, catalyzing the removal or remodelling of ubiquitin modifications on substrate proteins, including those target...