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Updated: Oct 21, 2025
Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
Published on: March 9, 2022
Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome
Luka Bacic1, Guillaume Gaullier1, Anton Sabantsev1
1Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Abstract:
The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and suggest that ALC1 preferentially slides nucleosomes away from DNA breaks.
Insights
The chromatin remodeler ALC1 binds to DNA damage sites via poly(ADP-ribose) chains. This study reveals ALC1
Area of Science:
- Molecular Biology
- Structural Biology
- Cancer Therapeutics
Background:
- The chromatin remodeler ALC1 is activated by poly(ADP-ribose) (PAR) chains at DNA damage sites.
- ALC1 is a potential cancer drug target due to synthetic lethality in homologous recombination-deficient cells.
- Previous structural studies of ALC1 were limited by PARylation heterogeneity and requirements.
Purpose of the Study:
- To determine the structure of ALC1 bound to a PARylated nucleosome.
- To visualize intermediate states of ALC1 during nucleosome recognition and activation.
- To understand the functional role of nucleosomal epitopes in ALC1 remodeling activity.
Main Methods:
- Reconstitution of an ALC1 and PARylated nucleosome complex in vitro using PARP2 and HPF1.
- Cryo-electron microscopy (cryo-EM) structure determination without cross-linking.
- Functional biochemical assays using PARylated nucleosomes.
Main Results:
- Successfully determined the cryo-EM structure of the ALC1-PARylated nucleosome complex.
- Visualized multiple intermediate states of ALC1, from initial recognition to tight binding and activation.
- Demonstrated the importance of nucleosomal epitopes for productive remodeling by ALC1.
- Showed that ALC1 preferentially slides nucleosomes away from DNA breaks.
Conclusions:
- The study provides the first structural insights into ALC1's mechanism of action on PARylated nucleosomes.
- Nucleosomal epitopes are crucial for ALC1's recruitment and activation at DNA damage sites.
- ALC1's nucleosome sliding activity may contribute to DNA repair processes by repositioning DNA breaks.
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