The structural basis of modified nucleosome recognition by 53BP1

Area of Science:

• Molecular Biology
• Structural Biology
• Epigenetics

Background:

• DNA double-strand breaks (DSBs) trigger histone modification cascades for DNA repair.
• RNF8 and RNF168 enzymes sequentially ubiquitinate histones H1 and H2A.
• RNF168-mediated H2AK13ub and H2AK15ub recruit 53BP1 to DSB sites.

Purpose of the Study:

• To elucidate the structural mechanism of 53BP1 interaction with ubiquitinated nucleosomes.
• To understand how 53BP1 recognizes H2AK15ub and H4K20me2 marks.
• To determine the basis for 53BP1 selectivity in recruiting to DSB sites.

Main Methods:

• Electron cryomicroscopy (cryo-EM) to determine the structure of 53BP1 bound to a modified nucleosome.
• High-resolution structural analysis (4.5 Å) of the nucleosome core particle with H4K20me2 and H2AK15ub (NCP-ubme) complexed with a 53BP1 fragment.

Main Results:

• The cryo-EM structure reveals intimate contacts between 53BP1 and multiple nucleosomal elements, including the acidic patch, for H4K20me2 and H2AK15ub recognition.
• 53BP1 recognition of ubiquitin is unusual, with its UDR segment sandwiched between ubiquitin and the nucleosome.
• Selectivity for H2AK15ub is mediated by arginine fingers in the H2A N-terminal tail, positioning ubiquitin over the UDR segment.

Conclusions:

• The structure explains 53BP1 recruitment to DSB sites by detailing its interaction with specific histone marks and nucleosomal context.
• This work highlights how combined histone modifications and nucleosomal features orchestrate precise chromatin responses to DNA damage.
• The findings provide insights into the molecular mechanisms underlying DNA repair pathway activation.