DNA Repair: Rad51, friend or foe?
- University of Oxford, United Kingdom
Imagine your frustration if, in the event of a breakdown, the emergency mechanic not only failed to repair your vehicle but actually damaged it even further. A similar situation can arise with our own DNA which, when damaged, is subjected to a system of rigorous checks and balances by the DNA repair machinery. However, DNA can also be damaged through the actions of structures called R-loops. These are RNA-DNA hybrids formed when an RNA transcript invades the DNA double helix, and they are a natural byproduct of the transcription process (Aguilera and Garcia-Muse, 2012). Now, in eLife, Douglas Koshland at the University of California, Berkeley, and co-workers reveal that proteins normally involved in DNA repair can also facilitate the formation of R-loops, thus increasing DNA damage (Wahba et al., 2013).
Initial work in bacteria showed that the repair protein RecA (Kasahara et al., 2000) can potentiate the formation of R-loops in the absence of active transcription. Building on this study, Koshland and colleagues—including Lamia Wahba, who is also at Johns Hopkins University, and Steven Gore—report three sets of experiments on the yeast counterpart of RecA, which is known as Rad51. Firstly, they provide evidence that Rad51 is also involved in R-loop formation. Secondly, they show that Rad51 is already present at R-loops before DNA damage occurs, suggesting that it may be oncogenic (i.e., have the potential to cause cancer). Thirdly, through elegant experimentation, they challenge the dogma that R-loop formation must invariably occur at the site of transcription (cis-acting) by revealing that R-loops can also be formed by RNA invading the DNA duplex at a remote genomic location (trans-acting).
Figure 1
Rad51 can contribute to DNA repair or DNA assault.
Left: DNA repair through homologous recombination, where one strand is used as a template to repair the other. DNA damage (red bolt) leads to double-strand breaks. At the break point, one strand of the DNA is slightly longer than the other and Rad52 (not shown) promotes the loading of Rad51 (orange) onto these single-strand overhangs. This initiates the process of DNA repair via homologous recombination. Rad51 is removed from the single-strand overhangs by the negative regulator Srs2 (not shown) before the final stages of DNA repair. Right: Rad51 can promote the formation of DNA-RNA hybrids (R-loops), which can damage DNA. R-loops form when Rad51 binds repeatedly to RNA (red lines). Srs2 (not shown) inhibits R-loop formation by removing Rad51.
Wahba et al. show that the accumulation of R-loops is dependent on Rad51 activity: in the absence of Rad51, aberrant transcription does not result in the formation of R-loops and the genome remains intact. To measure the destabilizing effects of R-loops on DNA, Wahba et al. used a yeast artificial chromosome (or YAC), which they introduced into the yeast nucleus. They found that Rad51 does not work alone but is regulated by other factors: removing a positive protein regulator of Rad51, called Rad52, blocks the formation of R-loops, whereas removing a negative protein regulator, Srs2, increases their formation.
Koshland and colleagues reveal, in addition, that Rad51 localizes to R-loops. Previous work has shown that Rad51 binds at break points in DNA to initiate DNA repair (Sugawara et al., 2003). Moreover, mammalian Rad51 is known to help cells resist the damaging effects of ionizing radiation, chemotherapeutic agents, and the spontaneous breaks and aberrations that occur during DNA replication. A natural assumption therefore is that the high levels of Rad51 expression seen in tumour cells (Klein, 2008) reflect the protein’s role in DNA repair; in other words, that Rad51 may act as a tumour suppressor.
So what is Rad51 doing at R-loop sites? To address this question, Wahba et al. studied the deposition of a histone called H2AX—a well-defined marker for the formation of double-strand DNA breaks—and compared the timing of this event with the accumulation of Rad51 at an R-loop site. They confirmed that Rad51 was present prior to DNA damage, suggesting that rather than contributing to repair, Rad51 could be driving R-loop-mediated genome instability in cancer cells, and promoting tumour biogenesis.
Having established that Rad51 induces the formation of R-loops, and drawing encouragement from bacterial work, Koshland and colleagues went on to show that R-loop formation is not directly dependent on the act of transcription. To do this, they created yeast cells that contained two copies of a particular DNA sequence—one in a YAC and the other in one of the yeast’s own chromosomes—and placed the latter under the control of a transcriptional switch. When the switch was triggered, the induced chromosomal transcript—with the help of Rad51—invaded the homologous DNA in the YAC. This resulted in the formation of an R-loop, distinct and distant from the original site of transcription. And sure enough, this trans induced R-loop destabilized the YAC DNA.
It is noteworthy that R-loops are not always deleterious. As obligatory intermediates, they are essential for mitochondrial DNA replication (Pohjoismaki et al., 2010) and immunoglobulin gene class-switch recombination (Yu et al., 2003)—a complex process in which antibody genes genetically rearrange during the development of immune cells called B cells. They are also implicated in transcription termination (Skourti-Stathaki et al., 2011) and in transcription activation of CpG island promoters (Ginno et al., 2012). However, when R-loops occur out of their natural context and pose a threat to cell survival, all is not lost. Cells have the innate capacity to counteract such hazardous structures. One line of defense is Srs2, which can remove Rad51 from DNA. Other options include Sen1 helicase, an enzyme that can unwind R-loops formed in the wake of transcription (Mischo et al., 2011), and RNAse H, which can degrade RNA that is base-paired with DNA in R-loops (Cerritelli and Crouch, 2009). All of these proteins serve to protect the cellular genome from destruction.
Exploring and harnessing the potential applications of Rad51-dependent R-loop formation is an exciting prospect. The current findings have intriguing parallels with the CRISPR system (Horvath and Barrangou, 2013), which is a mechanism used by bacteria and archaea to defend themselves against invading phages. In brief, short DNA fragments from phage genomes are integrated into the bacterial or archael genome within the CRISPR locus, and transcripts from the CRISPR regions then form R-loops with the infecting phage DNA. These R-loops recruit enzymes to destroy the phage genome. Engineered CRISPR-derived constructs have been used to successfully target specific DNA sequences for replacement or modification in mammalian cells (Wang et al., 2013). Koshland and colleagues now potentially add Rad51 to the arsenal available for genetic search and destroy missions. Consequently, their work may have broad implications for synthetic biology, gene function studies and gene therapy.
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© 2013, Tan-Wong and Proudfoot
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DNA Repair: Rad51, friend or foe?
eLife 2:e00914.
https://doi.org/10.7554/eLife.00914
Further reading
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- Chromosomes and Gene Expression
Cells evoke the DNA damage checkpoint (DDC) to inhibit mitosis in the presence of DNA double-strand breaks (DSBs) to allow more time for DNA repair. In budding yeast, a single irreparable DSB is sufficient to activate the DDC and induce cell cycle arrest prior to anaphase for about 12–15 hr, after which cells ‘adapt’ to the damage by extinguishing the DDC and resuming the cell cycle. While activation of the DNA damage-dependent cell cycle arrest is well understood, how it is maintained remains unclear. To address this, we conditionally depleted key DDC proteins after the DDC was fully activated and monitored changes in the maintenance of cell cycle arrest. Degradation of Ddc2ATRIP, Rad9, Rad24, or Rad53CHK2 results in premature resumption of the cell cycle, indicating that these DDC factors are required both to establish and maintain the arrest. Dun1 is required for the establishment, but not the maintenance, of arrest, whereas Chk1 is required for prolonged maintenance but not for initial establishment of the mitotic arrest. When the cells are challenged with two persistent DSBs, they remain permanently arrested. This permanent arrest is initially dependent on the continuous presence of Ddc2, Rad9, and Rad53; however, after 15 hr these proteins become dispensable. Instead, the continued mitotic arrest is sustained by spindle assembly checkpoint (SAC) proteins Mad1, Mad2, and Bub2 but not by Bub2’s binding partner Bfa1. These data suggest that prolonged cell cycle arrest in response to 2 DSBs is achieved by a handoff from the DDC to specific components of the SAC. Furthermore, the establishment and maintenance of DNA damage-induced cell cycle arrest require overlapping but different sets of factors.
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- Chromosomes and Gene Expression
- Developmental Biology
About 70% of human cleavage stage embryos show chromosomal mosaicism, falling to 20% in blastocysts. Chromosomally mosaic human blastocysts can implant and lead to healthy new-borns with normal karyotypes. Studies in mouse embryos and human gastruloids showed that aneuploid cells are eliminated from the epiblast by p53-mediated apoptosis while being tolerated in the trophectoderm. These observations suggest a selective loss of aneuploid cells from human embryos, but the underlying mechanisms are not yet fully understood. Here, we investigated the cellular consequences of aneuploidy in a total of 125 human blastocysts. RNA-sequencing of trophectoderm cells showed activated p53 pathway and apoptosis proportionate to the level of chromosomal imbalance. Immunostaining corroborated that aneuploidy triggers proteotoxic stress, autophagy, p53-signaling, and apoptosis independent from DNA damage. Total cell numbers were lower in aneuploid embryos, due to a decline both in trophectoderm and in epiblast/primitive endoderm cell numbers. While lower cell numbers in trophectoderm may be attributed to apoptosis, aneuploidy impaired the second lineage segregation, particularly primitive endoderm formation. This might be reinforced by retention of NANOG. Our findings might explain why fully aneuploid embryos fail to further develop and we hypothesize that the same mechanisms lead to the removal of aneuploid cells from mosaic embryos.
