3D genome organization contributes to genome instability at fragile sites

Abstract

Common fragile sites (CFSs) are regions susceptible to replication stress and are hotspots for chromosomal instability in cancer. Several features were suggested to underlie CFS instability, however, these features are prevalent across the genome. Therefore, the molecular mechanisms underlying CFS instability remain unclear. Here, we explore the transcriptional profile and DNA replication timing (RT) under mild replication stress in the context of the 3D genome organization. The results reveal a fragility signature, comprised of a TAD boundary overlapping a highly transcribed large gene with APH-induced RT-delay. This signature enables precise mapping of core fragility regions in known CFSs and identification of novel fragile sites. CFS stability may be compromised by incomplete DNA replication and repair in TAD boundaries core fragility regions leading to genomic instability. The identified fragility signature will allow for a more comprehensive mapping of CFSs and pave the way for investigating mechanisms promoting genomic instability in cancer.

Low replication stress leads to specific replication timing advances associated to chromatin remodelling in cancer cells

“…Analysis of the aphidicolin-RT-impacted loci (aRTIL) led to the identification of regions with significant RT delays (DEL aRTIL), as previously reported (30,32) (Figure 1c,d). In RPE-1 and HCT116, these DEL aRTIL represent the majority of impacted loci with 38/47 and 74/96 loci respectively.…”

“…The fragility of these chromosomal regions has been widely studied, revealing incomplete DNA replication before mitosis (21,23,28,29) mainly due to conflicts with large transcription units (30)(31)(32) or/and origin paucity (33,34).…”

“…Evidence of aberrant RT in many different genetic diseases and cancers suggests this cellular process is important for genomic stability (35)(36)(37). Interestingly, replication stress inducing CFS expression also affects the RT of these specific chromosomal domains (30,32).…”

Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis

“…In leukemias, the TOP2-induced DSBs are reported to accumulate at those genes which have high transcriptional activity and are enriched at chromatin loop anchors [ 19 ]. Common fragile sites refer to large genomic regions with active transcription and high rates of DNA breakage under replication stress [ 40 ]. A recent study demonstrated that common fragile sites span TAD boundaries and harbor highly transcribed large genes (> 300 kb) with sensitivity to replication stress caused by DNA polymerase inhibitor aphidicolin [ 40 ].…”

“…Common fragile sites refer to large genomic regions with active transcription and high rates of DNA breakage under replication stress [ 40 ]. A recent study demonstrated that common fragile sites span TAD boundaries and harbor highly transcribed large genes (> 300 kb) with sensitivity to replication stress caused by DNA polymerase inhibitor aphidicolin [ 40 ]. Mechanically, the selective pressure to maintain intact TADs and molecular property of the chromatin at TAD boundaries jointly result in this phenomenon [ 7 ].…”