The Fanconi Anemia Pathway Resolves R-Loops to Prevent Genomic Instability

Rapid repair of stalled replication forks during DNA replication is necessary to prevent replication fork collapse, which causes DNA damage and genomic instability. The Fanconi anemia (FA) pathway counteracts replication stress and ensures faithful DNA replication. However, the endogenous substrate that activates the FA pathway has not been determined. Using cells lacking the central FA component FANCD2, Schwab and colleagues showed that the FA pathway protects against replication stress–induced DNA damage and prevents replication fork collapse induced by transcription. Inhibition of transcription restored the normal replication program and reduced the DNA damage response in FANCD2-deficient cells. In addition, deficiency for FANCD2 or other FA proteins also resulted in an increase in transcription-associated DNA:RNA hybrids (R-loops), which contributed to the genomic instability in FA-deficient cells. Removal of DNA:RNA hybrids via overexpression of RNase H1 decreased FA pathway activation and rescued the impaired replication fork progression and DNA damage accumulation in FANCD2-deficient cells. Additionally, aldehydes, which arise as by-products of cellular metabolism and have been shown to promote DNA damage and leukemia in FA-deficient mice, induced DNA:RNA hybrids in FANCD2-depleted cells. Mechanistically, another component of the FA pathway, FANCM, directly removed DNA:RNA hybrids via its translocase activity, and depletion of FANCM increased the frequency of DNA:RNA hybrids. Taken together, these results indicate that the FA pathway is necessary to limit the accumulation of DNA:RNA hybrids and that absence of functional FA signaling leads to replicative stress, DNA breaks, and genome instability. The FA pathway may therefore suppress tumorigenesis by resolving transcription-dependent replication blockade and preventing replication fork collapse.

Schwab RA, Nieminuszczy J, Shah F, Langton J, Martinez DL, Liang CC, et al. The Fanconi anemia pathway maintains genome stability by coordinating replication and transcription. Mol Cell 2015 Oct 22 [Epub ahead of print].