Our results reveal an unexpected interplay between Chd1 and the DNA repair-associated factors Atm, Kap1, and γH2A.X during the resolution of transcription-associated DSBs in ES cells. Chd1 promotes the chromatin recruitment/retention of these factors and the repair of DSBs at the promoters of active RNA Pol II-transcribed genes and rDNA in ES cells. In this study, we report that Chd1 interacts with DNA repair factors in undamaged ES cells. 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. Interestingly, 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. DNA breaks may relieve torsional stress and facilitate DNA unwinding and access of RNA Polymerases 16. Similar induction of target gene transcription mediated by DNA breaks occurs upon exposure to serum or heat shock 12, 13, during zygotic genome activation and in neurogenesis 14, 15. In hormone-responsive cells, target genes are induced via a mechanism that involves the generation of transient endogenous DNA breaks by Topoisomerase II at promoters 11. Hypertranscription is a dynamic phenomenon that is responsive to extrinsic cues 2, 4, 5, and may therefore share features with ligand-triggered target gene induction. Despite these recent insights, the molecular function of Chd1 in hypertranscribing cells remains unclear. Loss of Chd1 does not affect transcription per se, but it blunts the ability of stem cells to enter hypertranscription in vitro and in vivo 3. Chd1 removes nucleosomal barriers to transcriptional elongation 10 and is required for the optimal activity of RNA Pol I and II 3. Chd1 is an ATP-dependent chromatin remodeler that binds specifically to H3K4me3 and is found at sites of active transcription 8, 9. Some of the players implicated in promoting hypertranscription are the transcription factors Myc and Yap/Taz, the RNA Polymerase regulator pTEFb and the chromatin remodeler Chd1 (reviewed in Percharde et al. It is expected that hypertranscription involves a coordinated interplay between activating transcription factors, chromatin remodelers, and RNA Polymerases. The molecular regulation of hypertranscription, or even how it differs from general transcriptional regulation, remains poorly understood.

Hypertranscription has been documented to occur and play critical roles in embryonic stem (ES) cells 2, the post-implantation epiblast 3, emergence of definitive hematopoietic stem cells 4, primordial germ cells 5, and neurogenesis 6, and may take place in other settings during development, regeneration, and disease 1, 7. Hypertranscription is masked by most transcriptional profiling approaches, but has attracted renewed interest recently.

One way that stem/progenitor cells cope with this demand is to enter a state of hypertranscription, which involves a global elevation of nascent transcriptional output 1. Proliferating stem and progenitor cells are net generators of new cellular biomass and therefore have high biosynthetic demand. These results reveal a vulnerability of hypertranscribing stem cells to accumulation of endogenous DNA breaks, with important implications for developmental and cancer biology. 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. 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.

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. The chromatin remodeler Chd1 mediates hypertranscription in pluripotent cells but its mechanism of action remains poorly understood.

Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation.

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