Chd1 protects genome integrity at promoters to sustain hypertranscription in embryonic stem cells

Aydan Bulut-Karslioglu,Miroslav Hejna,Maximilian Stötzel,Anthony D Whetton,Andrew J K Williamson,Miguel Ramalho-Santos,Marcela Guzman-Ayala,Hu Jin,Brandon Cho,Yun-Kyo Kim,Jun S Song

doi:10.1038/s41467-021-25088-3

Abstract

Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation. The chromatin remodeler Chd1 mediates hypertranscription in pluripotent cells but its mechanism of action remains poorly understood. Here we report a novel role for Chd1 in protecting genome integrity at promoter regions by preventing DNA double-stranded break (DSB) accumulation in ES cells. Chd1 interacts with several DNA repair factors including Atm, Parp1, Kap1 and Topoisomerase 2β and its absence leads to an accumulation of DSBs at Chd1-bound Pol II-transcribed genes and rDNA. Genes prone to DNA breaks in Chd1 KO ES cells are longer genes with GC-rich promoters, a more labile nucleosomal structure and roles in chromatin regulation, transcription and signaling. These results reveal a vulnerability of hypertranscribing stem cells to accumulation of endogenous DNA breaks, with important implications for developmental and cancer biology.

Highlights

Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation
In order to probe the function of Chd[1] in the regulation of hypertranscription, we identified its interacting proteins by immunoprecipitation followed by mass spectrometry (IP-MS) using a Chd1-Flag knock-in mouse embryonic stem (ES) cell line[3]
Our results point to a central role for rDNA at the nucleolus in the coordination between hypertranscription and DNA integrity in hypertranscribing ES cells. rRNA comprises ~80% of the RNA being synthesized in ES cells and represents both a major focal point of hypertranscription as well as a vulnerability to DNA breaks

Summary

Introduction

Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation. Genes prone to DNA breaks in Chd[1] KO ES cells are longer genes with GC-rich promoters, a more labile nucleosomal structure and roles in chromatin regulation, transcription and signaling These results reveal a vulnerability of hypertranscribing stem cells to accumulation of endogenous DNA breaks, with important implications for developmental and cancer biology. Endogenous DNA breaks have recently been shown to occur throughout the genome at the promoters of transcribed genes[17], suggesting that the link between DNA breaks and transcription may be more general It remains unknown how cells coordinate the occurrence of DNA breaks and their repair with transcription, a coordination that is anticipated to be of particular importance in hypertranscribing pluripotent cells. Our results reveal an unexpected interplay between Chd[1] and the DNA repair-associated factors Atm, Kap[1], and γH2A.X during the resolution of transcription-associated DSBs in ES cells

Methods

Results

Conclusion