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SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced genes

ABSTRACT: Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, to reveal the function of S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases, polyubiquitinated proteins by SKP1A were prepared by pull-down assays and characterized by LC-MS/MS

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Haruhiko Koseki

PROVIDER: PXD047556 | JPOST Repository | Wed Aug 27 00:00:00 BST 2025

REPOSITORIES: jPOST

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			Action	DRS
	PK20047-01_SKP1_WT_GST_pull_down.raw	Raw
	PK20047-02_SKP1_KOd2_GST_pull_down.raw	Raw
	PK20047-05_SKP1_WT_GST-TUBE_pull_down.raw	Raw
	PK20047-06_SKP1_KOd2_GST-TUBE_pull_down.raw	Raw
	PK20047-09_SKP1_WT_GST_pull_down.raw	Raw

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Publications

SKP1A bound to Polycomb-silenced genes mediates degradation of PRC2 and preconditions their activation.

Kondo Takashi T Ito Shinsuke S Takano Junichiro J Han Yong-Woon YW Endo Takaho T Kondo Kaori K Shibata Marika M Kawashima Yusuke Y Sugishita Hiroki H Harachi Mio M Sharif Jafar J Seita Jun J Ohara Osamu O Nakayama Manabu M Koseki Haruhiko H

Molecular cell 20250820

Polycomb group (PcG) proteins are repressors of developmental genes. Paradoxically, the same PcG proteins also function in gene activation via mechanisms that are not yet fully understood. Here, we found that SKP1A, an essential factor of SKP1A/CUL1/F-box (SCF) ubiquitin ligases and Polycomb-repressive complex 1 (PRC1) containing PCGF1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin proteasomal degradation. By using differentiating mouse embryonic stem cells a ...[more]

PMID: 40858113

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SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced genes

2025-08-27 | PXD047552 | JPOST Repository

SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [CUT&Tag]

Project description:Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, we found that S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases and a subunit of the PCGF1 (Polycomb group RING finger protein 1) component of Polycomb repressive complex 1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin-dependent proteasomal degradation. By using differentiating mouse embryonic stem cells, we found that SKP1A removes EED, a core component of Polycomb repressive complex 2 (PRC2) that is bound to PcG target gene promoters, via proteasomal degradation, and it thereby sensitises these genes for subsequent activation. Furthermore, we show that SKP1A removes EED from the Meis2 promoter in the midbrain of developing mouse embryos, leading to Meis2 gene expression. In summary, we reveal here a previously unknown role of SKP1A in activating PcG-target genes via the proteasomal degradation of PRC2. This implies that SKP1A-containing PCGF1-PRC1 may confer reversibility on PcG-mediated gene silencing for robust spatiotemporal regulation of target genes.

2025-08-25 | GSE297309 | GEO

SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [4C-seq]

2025-08-25 | GSE297093 | GEO

SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [RNA-seq]

2025-08-25 | GSE293160 | GEO

SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [ChIP-seq]

2025-08-31 | GSE293161 | GEO

SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [ChIP-seq 2]

2025-08-25 | GSE297094 | GEO

The U-box family genes in Medicago truncatula: key elements in response to salt, cold, and drought stresses

Project description:The ubiquitination pathway regulates growth, development, and stress responses in plants, and the U-box protein family of ubiquitin ligases has important roles in this pathway. Here, 64 putative U-box proteins were identified in the Medicago truncatula genome. In addition to the conserved U-box motif, other functional domains, such as the ARM, kinase, KAP, and WD40 domains, were also detected. Phylogenetic analysis of the M. truncatula U-box proteins grouped them into six subfamilies, and chromosomal mapping and synteny analyses indicated that tandem and segmental duplications may have contributed to the expansion and evolution of the U-box gene family in this species. Using RNA-seq data from M. truncatula seedlings subjected to three different abiotic stresses, we identified 33 stress-inducible plant U-box genes (MtPUBs). Specifically, 25 salinity-, 15 drought-, and 16 cold-regulated MtPUBs were detected. Among them, MtPUB10, MtPUB17, MtPUB18, MtPUB35, MtPUB42, and MtPUB44 responded to all three stress conditions. Expression profiling by real-time PCR was consistent with the RNA-seq data, and stress-related elements were identified in the promoter regions. The present findings strongly indicate that U-box proteins play critical roles in abiotic stress response in M. truncatula.

2019-09-04 | GSE136739 | GEO

Gene expression in RAW264.7 cells infected with VSV and HSV-1

Project description:The purpose of this study was to determine which genes are differentially regulated virus infection in RAW264.7 cells. Cells were infected with Vesicular Stomatitis Virus (VSV) or herpes simplex virus 1 (HSV-1) for 6h. Then the differentially regulated genes were analyzed, focusing on F-box proteins and E3 ubiquitin ligases.

2016-04-05 | GSE72077 | GEO

N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity

Project description:Most eukaryotic proteins are N-terminally acetylated, but the functional impact on a global scale has remained obscure. Using genome-wide CRISPR knockout screens in human cells, we reveal a strong genetic dependency between a major N-terminal acetyltransferase and specific ubiquitin ligases. Biochemical analyses uncover that both the ubiquitin ligase complex UBR4-KCMF1 and the acetyltransferase NatC recognize proteins bearing an unacetylated N-terminal methionine followed by a hydrophobic residue. NatC KO-induced protein degradation and phenotypes are reversed by UBR knockdown, demonstrating the central cellular role of this interplay. We reveal that loss of Drosophila NatC is associated with male sterility, reduced longevity, and age-dependent loss of motility due to developmental muscle defects. Remarkably, muscle-specific overexpression of UbcE2M, one of the proteins targeted for NatC KO mediated degradation, suppresses defects of NatC deletion. In conclusion, NatC-mediated N-terminal acetylation acts as a protective mechanism against protein degradation, which is relevant for increased longevity and motility.

2023-09-18 | GSE221447 | GEO

Piperlongumine (PL) conjugates induce targeted protein degradation

Project description:PROteolysis Targeting Chimeras (PROTACs) are bifunctional molecules that degrade target proteins through recruiting E3 ligases. However, their application is limited in part because few E3 ligases can be recruited by known E3 ligase ligands. In this study, we identified piperlongumine (PL), a natural product, as a covalent E3 ligase recruiter, which induces CDK9 degradation when it is conjugated with SNS032, a CDK9 inhibitor. The lead conjugate 955 can potently degrade CDK9 in a ubiquitin-proteasome-dependent manner and is much more potent than SNS-032 against various tumor cells in vitro. Mechanistically, we identified KEAP1 as the E3 ligase recruited by 955 to degrade CDK9 through a TurboID-based proteomics study, which was further confirmed by KEAP1 knockout and the nanoBRET ternary complex formation assay. In addition, PL-Ceritinib conjugate can degrade EML4-ALK fusion oncoprotein, suggesting that PL may have a broader application as a covalent E3 ligase ligand in targeted protein degradation.

2022-06-26 | GSE206612 | GEO

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