Structural basis for histone H2B deubiquitination by the SAGA DUB module

Area of Science:

• Epigenetics
• Molecular Biology
• Structural Biology

Background:

• Monoubiquitinated histone H2B is crucial for transcription activation.
• The Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator complex includes a deubiquitinating (DUB) module responsible for H2B removal.
• Understanding the DUB module's interaction with histones is key to deciphering transcription regulation.

Purpose of the Study:

• To elucidate the structural basis of the SAGA DUB module's interaction with ubiquitinated histones.
• To investigate the mechanism by which the DUB module deubiquitinates histone H2B.
• To determine the implications of these interactions for transcription processes.

Main Methods:

• X-ray crystallography to determine the structure of the DUB module bound to a ubiquitinated nucleosome.
• Biochemical assays to assess deubiquitination activity in different contexts.
• Analysis of protein-protein interactions between the DUB module, histones, and histone chaperones.

Main Results:

• The crystal structure reveals specific contacts between the DUB module and the H2A/H2B acidic patch, mediated by an arginine cluster on Sgf11.
• The Ubp8 catalytic domain interacts with both H2B and the attached ubiquitin.
• The DUB module efficiently deubiquitinates H2B in both nucleosomal and H2A/H2B dimer forms, including those associated with the FACT chaperone.

Conclusions:

• The SAGA DUB module utilizes a precise structural mechanism to recognize and bind ubiquitinated H2B on the nucleosome.
• Deubiquitination activity is maintained across different histone contexts, suggesting a role in dynamic nucleosome remodeling.
• SAGA's DUB module likely targets H2B during multiple stages of nucleosome turnover, impacting transcription regulation.