2. Academic Validation
  3. An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation

An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation

  • Mol Cell. 2026 Apr 2;86(7):1397-1416.e11. doi: 10.1016/j.molcel.2026.03.004.
Satoshi Yamanaka 1,  Koya Nagaoka 2,  Yuki Shoya 2,  Kohei Nishino 3,  Yumi Mikura 2,  Kenshi Tanaka 2,  Keisuke Konishi 2,  Yoshinori Hasegawa 4,  Atsushi Hijikata 5,  Hidetaka Kosako 6,  Tatsuya Sawasaki 7
Affiliations

Affiliations

  • 1 Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan; Division of Proteo-Interactome, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan. Electronic address: [email protected].
  • 2 Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan; Division of Proteo-Interactome, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
  • 3 Division of Cell Signaling, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan.
  • 4 Department of Applied Genomics, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
  • 5 Laboratory of Computational Genomics, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
  • 6 Division of Cell Signaling, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan; Laboratory of Proteomics, Institute of Photonics and Human Health Frontier, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan. Electronic address: [email protected].
  • 7 Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan. Electronic address: [email protected].
PMID: 41932313 DOI: 10.1016/j.molcel.2026.03.004
Abstract

The DDB1- and CUL4-associated factor (DCAF) family functions as substrate receptors within Cullin4-really interesting new gene (RING) ubiquitin ligases (CRL4s), facilitating proteasomal degradation of targeted substrates. Although CRL4-based targeted protein degradation (TPD) has emerged as a promising strategy to modulate undruggable proteins, the complex formation, substrates, and functional properties of many DCAFs remain poorly defined. In this study, using proximity biotinylation-based interactome analysis in human HEK293T cells, we systematically annotated interactors and functional associations of individual DCAFs. Furthermore, we identified substrates of the model DCAFs COP1 and DCAF3 using proximity biotinylation coupled with multi-omics approaches. By combining biochemical and cell-based analyses, we establish CRL4 complex formation and DCAF autodegradation as experimentally tractable proxy indicators to evaluate DCAF degradation activity and propose a set of high-activity DCAFs. These datasets establish a resource for functional characterization of DCAFs and provide a framework for their prioritization in TPD.

Keywords

AirID; BioID; CRL4; DCAF; E3 ligase; interactome; proteomics; proximity labeling; targeted protein degradation; ubiquitination.

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