Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations

Abstract

How spatial chromosome organization influences genome integrity is still poorly understood.Here we show that DNA double-strand breaks (DSBs) mediated by topoisomerase 2 (TOP2) activities, are enriched at chromatin loop anchors with high transcriptional activity. Recurrent DSBs occur at CTCF/cohesin bound sites at the bases of chromatin loops and their frequency positively correlates with transcriptional output and directionality. The physiological relevance of this preferential positioning is indicated by the finding that genes recurrently translocating to drive leukemias, are highly transcribed and are enriched at loop anchors. These genes accumulate DSBs at recurrent hot spots that give rise to chromosomal fusions relying on the activity of both TOP2 isoforms and on transcriptional elongation. We propose that transcription and 3D chromosome folding jointly pose a threat to genomic stability, and are key contributors to the occurrence of genome rearrangements that drive cancer. Reimand et al., 2016) and topological constraints during loop extrusion dynamics (Canela et al., 2017).Although physiologically important, TOP2 functions are also inherently risky for a cell, as they involve the formation of a transient DSB to allow the passage of duplex DNA through the break. During this controlled process, the two-TOP2 subunits are covalently linked through their active sites to each 5′-terminus of a DSB via a phosphodiester bond (Pommier et al., 2016).These key intermediates of TOP2 activity, called TOP2 cleavage complexes (TOP2ccs) are normally short-lived, as topoisomerases quickly ligate the DNA ends upon the passage of the duplex DNA. In the presence of nearby DNA lesions or upon treatment with topoisomerase poisons, however, these cleavage complexes can be stabilized on DNA and may contribute to genomic instability by acting as road blocks to DNA-tracking systems that attempt to traverse them (Ashour et al., 2015).The mechanism by which TOP2ccs are converted to DSBs underlies the action of widely used class of anticancer agents that trap TOP2 at the intermediate cleavage complex step (Nitiss, 2009). The TOP2 poison etoposide (ETO), is among the most effective and widely used anticancer agents in the clinic, but treatment with etoposide is associated with the occurrence of therapy-related acute myeloid leukemias (t-AMLs) (Allan and Travis, 2005; Wright and Vaughan, 2014). Approximately one third of t-AML cases are associated with recurrent chromosome translocations between the mixed lineage leukemia gene (MLL) and various potential translocation partners, and amongst them, AF9, AF4, AF6, and ENL, account for approximately 80% of the cases. Sequencing of MLL fusions from patients with t-AML has shown that MLL breakpoints occur in breakpoint cluster regions (BCRs) at restricted genomic positions near exon 12 of the MLL gene, while BCRs within potential translocation partners are ENL fusions two times more frequently than MLL-AF4, MLL-AF6, MLL-AF9 ( Figure 2D), although the frequency of ENL breakage was not signi...

Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation

“…Recent works support a key function of genome architecture, TADs borders and loop extrusion in genome stability, including immunoglobulin loci rearrangements 36,37 and in DSB occurrence through topoisomerase reactions 38,39 . Our study shows that genome architecture is also instrumental for the correct establishment of H2AX and DDR foci formation, expanding the function of genome organization within TADs to the response to DNA damage.…”

Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51

“…More recently, signal-induced DSBs, occur-ring upon transcription of early-response genes (following neuronal activation [Madabhushi et al, 2015], estrogen treatment [Ju et al, 2006], androgen induction [Haffner et al, 2010], serum induction [Bunch et al, 2015], and heat shock [Bunch et al, 2015]), have been revealed, adding to the complexity of mapping DSBs. Physiological DSBs are required for releasing the torsional tension that develops during transcription and replication, and at loop anchors involved in three-dimensional (3D) genome folding (Barlow et al, 2013;Canela et al, 2017Canela et al, , 2019Gothe et al, 2019;Ju et al, 2006;Madabhushi et al, 2015;Wei et al, 2016). In particular, DSBs and subsequent DDR signaling were shown to promote effective RNA polymerase II (Pol II) pause release and transcriptional elongation for induction of early-response genes (Bunch et al, 2015).…”

“…Yan et al (2017) were able to assess the genome-wide off-target activity of two CRISPR-associated RNA-guided endonucleases, Cas9 and Cpf1, demonstrating that Cpf1 has higher specificity than Cas9. More recently, BLISS was used to map DSBs at sites involved in recurrent genome rearrangements and chromosomal translocations in cancer cells (Dellino et al, 2019;Gothe et al, 2019). Nevertheless, the landscape of DSBs across the genome and their repair in cancer cells is poorly characterized.…”

Transposable elements strongly contribute to cell-specific and species-specific looping diversity in mammalian genomes

“…Alternatively, they may utilize the association between CTCF and double strand breaks (52) to facilitate integration into the host genome. Regardless of the mechanism, these elements appear to exist in a symbiotic relationship with their hosts, harnessing host transcriptional machinery to proliferate while contributing substrates for regulatory innovation.…”