Common fragile sites (CFSs) are genomic regions frequently involved in cancer-associated rearrangements. Most CFSs lie within large genes, and their instability involves transcription- and replication-dependent mechanisms. Here, we uncover a role for the mitochondrial stress response pathway in the regulation of CFS stability in human cells. We show that FANCD2, a master regulator of CFS stability, dampens the activation of the mitochondrial stress response and prevents mitochondrial dysfunction. Genetic or pharmacological activation of mitochondrial stress signaling induces CFS gene expression and concomitant relocalization to CFSs of FANCD2. FANCD2 attenuates CFS gene transcription and promotes CFS gene stability. Mechanistically, we demonstrate that the mitochondrial stress-dependent induction of CFS genes is mediated by ubiquitin-like protein 5 (UBL5), and that a UBL5-FANCD2 dependent axis regulates the mitochondrial UPR in human cells. We propose that FANCD2 coordinates nuclear and mitochondrial activities to prevent genome instability.

38Common fragile sites (CFSs) are genomic regions frequently involved in cancer-associated 39 rearrangements. Most CFSs lie within large genes, and their instability relies on 40 transcription-and replication-dependent mechanisms. Here, we uncover a role for the 41 UBL5-dependent branch of the unfolded protein response pathway (UPR) in the 42 maintenance of CFS stability. We show that genetic or pharmacological UPR activation 43 induces CFS gene expression and concomitant relocalization of FANCD2, a master 44 regulator of CFS stability, to CFSs. Furthermore, a genomic analysis of FANCD2 binding 45 sites identified an enrichment for mitochondrial UPR transcriptional response elements in 46 FANCD2 bound regions. We demonstrated that depletion of FANCD2 increases CFS gene 47 transcription and their instability while also inducing mitochondrial dysfunction and triggering 48 the activation of the UPR pathway. Depletion of UBL5, a mediator of the UPR, but not ATF4, 49reduces CFS gene expression and breakage in FANCD2-depleted cells. We thus 50 demonstrate that FANCD2 recruitment and function at CFSs depends on transcription and 51 UPR signaling, and in absence of transcription or UBL5, FANCD2 is dispensable for CFS 52 stability. We propose that FANCD2 coordinates nuclear and mitochondrial activities by 53 tuning the UPR to prevent genome instability. 54 55 56 57 58 CFS gene transcription and rescues chromosome fragility. Conversely, genetic or 127 pharmacological activation of the UPR induces CFS gene transcription and FANCD2 128 relocalization to CFS genes, dampening the UPR and preventing CFS instability. FANCD2 129 binding to CFS is dependent on CFS gene transcription and increases in a dose-dependent 130 manner. In addition, we show that FANCD2 is dispensable for maintaining CFS stability in 131 the absence of transcription. Mechanistically, we demonstrate that the UPR-dependent 132 induction of CFS genes is mediated by Ubiquitin-Like Protein 5 (UBL5), which was 133 previously shown to be involved in mitochondrial UPR signaling in C. elegans, and that 134 breaking up this signaling partially restores chromosome stability. We propose that CFSs 135 are part of a metabolic checkpoint, and by tuning the UPR with CFS replication, FANCD2 136 promotes metabolic homeostasis and genome integrity. 137 138 Results 140mRNA expression ATF4