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Updated: Jan 15, 2026

In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones
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In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones

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Mechanism of USP21 autoinhibition and histone H2AK119 deubiquitination

Sanim Rahman1, Chad W Hicks1, Alexander Gwizdala1

  • 1Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Science Advances
|October 10, 2025
PubMed

Insights

Ubiquitin-specific protease 21 (USP21) deubiquitinates histone H2AK119ub, a mark of gene silencing. Researchers discovered USP21

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Epigenetics

Background:

  • Histone H2A lysine 119 monoubiquitination (H2AK119ub) is a key epigenetic mark linked to gene silencing.
  • Ubiquitin-specific protease 21 (USP21) is a critical enzyme that removes H2AK119ub, impacting cellular processes.
  • The precise mechanisms of USP21 action and regulation remain largely unelucidated.

Purpose of the Study:

  • To elucidate the structural basis of USP21's recognition and deubiquitination of H2AK119ub.
  • To investigate the regulatory mechanisms governing USP21 activity.
  • To explore the potential for phosphorylation-dependent autoregulation in USP enzymes.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) to determine the structure of USP21 bound to H2AK119ub nucleosomes.
  • AlphaFold-Multimer for virtual screening of USP21 interacting partners.
  • AlphaFold3 modeling to investigate structural mechanisms of autoinhibition.

Main Results:

  • The cryo-EM structure revealed a novel recognition mode of H2AK119ub by USP21, distinct from other related enzymes.
  • USP21's N-terminal intrinsically disordered region (IDR) was found to inhibit its catalytic activity (autoinhibition).
  • Kinases that phosphorylate the USP21 IDR were identified, relieving autoinhibition and activating the enzyme.

Conclusions:

  • USP21 employs a unique mechanism to deubiquitinate H2AK119ub.
  • Phosphorylation of the USP21 IDR is a critical regulatory mechanism that relieves autoinhibition.
  • This study uncovers a novel mode of phosphorylation-dependent autoregulation in deubiquitinating enzymes, potentially applicable to other USP enzymes.

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