February 16, 2021

Extensive remodeling of chromatin after DNA damage

In eukaryotes, histones are often modified and evicted at site of DNA double-strand breaks in order to facilitate end-resection and break repair. Together with the protein analysis facility of the FMI, the Gasser group has quantified massive changes in the chromatin associated proteome in response to DNA damage. Triggered by ubiquitin ligases, these changes drive the degradation of core and linker histones genome-wide, evict the transcription machinery and increase the efficiency of homologous recombination.

Our genomes frequently encounter many types of DNA lesions. In order to repair DNA damage and safeguard the integrity of the genome, repair mechanisms are of primordial importance. An earlier study from the Gasser group showed that a fraction of nucleosomes are depleted across the genome in response to oxidizing damage and the activated DNA damage checkpoint. The reduction in nucleosome occupancy appeared to stem from a controlled degradation of the four core histones. However, the exact mechanism of histone eviction and degradation was not understood, nor was it clear how this affected overall chromatin structure and its associate activities.

In a major accomplishment now published in Molecular Cell, Kiran Challa, a postdoc in the Gasser lab, teamed up with the FMI Proteomics & Protein Analysis platform to produce a quantitative mass spectrometry profile of all chromatin-associated proteins, and to follow the changes in the proteome in response to DNA damage. The study confirmed that core histones and the linker histone H1 were partially lost from chromatin. It also showed that the enzymatic machineries that mediate replication, transcription and chromatin remodeling were depleted as well. In contrast, a host of ubiquitin ligases and the proteasome were recruited to chromatin following DNA damage, contributing to core and linker histone depletion and an efficient homology-directed repair.

This study is the first comprehensive analysis of changes in the chromatin landscape in response to an acute stress situation, that is, DNA damage. The response not only affects the nucleosomes at sites of damage, but genome-wide, coincident with the down-regulation of transcription and replication. The end-result is a decompaction of chromatin, which increases DNA accessibility for recombination-mediated repair without stimulation of promiscuous transcription.   

An interesting spin-off from this work may be the use of ubiquitin ligases to improve gene editing efficiency, like that mediated by CRISPR-Cas9. CRISPR-mediated gene editing uses recombination at a targeted DNA break to change or correct DNA sequence. Coupling CRISPR with the reversible degradation of histones mediated by ubiquitin ligation may lead to enhanced recombination-mediated gene repair.

Original publication:
Kiran Challa, Christoph D.Schmid, Saho Kitagawa, Anaïs Cheblal, Vytautas Iesmantavicius, Andrew Seeber, Assaf Amitai, Jan Seebacher, Michael H. Hauer, Kenji Shimada, Susan M. Gasser (2021) Damage-induced chromatome dynamics link ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair. Molecular Cell 81, 1–19

FMI Model of the role played by ubiquitine ligases and the remodeling of the chromatome in response to DNA damage. Click the image to see the text/details.

About the first author:
Kiran Challa was born in India, in the state of Telangana. After completing his master’s in India, he moved to Japan for a PhD at Osaka University, studying meiotic chromosome organization and chromatin modifications. He joined the FMI in 2017 as a postdoc in the group of Susan Gasser. Kiran is interested in DNA repair mechanisms and genome-wide changes in response to various DNA damaging agents. His main hobbies include table tennis, the gym and photography.