GE44CH06-Heyer ARI 3 October 2010 11:50 Regulation of Homologous Recombination in Eukaryotes Wolf-Dietrich Heyer,1,2 Kirk T. Ehmsen,1 and Jie Liu1 1Department of Microbiology, University of California, Davis, Davis, California 95616-8665; email: [email protected] 2Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665 Annu. Rev. Genet. 2010. 44:113–39 Key Words First published online as a Review in Advance on cyclin-dependent kinase, DNA damage response (DDR), DNA repair, August 6, 2010 phosphorylation, sumoylation, ubiquitylation The Annual Review of Genetics is online at genet.annualreviews.org Abstract This article’s doi: Homologous recombination (HR) is required for accurate chromosome by CNRS-Multi-Site on 08/22/12. For personal use only. 10.1146/annurev-genet-051710-150955 segregation during the first meiotic division and constitutes a key re- Copyright c 2010 by Annual Reviews. pair and tolerance pathway for complex DNA damage, including DNA All rights reserved double-strand breaks, interstrand crosslinks, and DNA gaps. In addi- Annu. Rev. Genet. 2010.44:113-139. Downloaded from www.annualreviews.org 0066-4197/10/1201-0113$20.00 tion, recombination and replication are inextricably linked, as recombi- nation recovers stalled and broken replication forks, enabling the evo- lution of larger genomes/replicons. Defects in recombination lead to genomic instability and elevated cancer predisposition, demonstrating a clear cellular need for recombination. However, recombination can also lead to genome rearrangements. Unrestrained recombination causes undesired endpoints (translocation, deletion, inversion) and the accu- mulation of toxic recombination intermediates. Evidently, HR must be carefully regulated to match specific cellular needs. Here, we review the factors and mechanistic stages of recombination that are subject to regulation and suggest that recombination achieves flexibility and ro- bustness by proceeding through metastable, reversible intermediates. 113 GE44CH06-Heyer ARI 3 October 2010 11:50 INTRODUCTION genome instability (see sidebar, DNA Repair Proteins and Human Genetic Disease). How Homologous recombination (HR) is a key path- does the cell achieve the balance between too Homologous way to maintain genomic integrity between little and too much recombination? There must recombination (HR): generations (meiosis) and during ontogenic de- be regulation and the answer will depend on recombination velopment in a single organism (DNA repair). between identical or the organism, cell type, cell-cycle stage, chro- A typical diploid human cell needs to maintain nearly identical mosomal region, as well as the type and level of about 6×109 base pairs in the correct sequence sequences genotoxic stress. and chromosomal organization, a formidable HR in meiosis is subject to specific regula- task that is usually performed nearly perfectly tion that targets recombination events to ho- from one somatic cell generation to the next mologs, establishing crossover outcomes to as- (44). Recombination is required for the repair sist in meiotic chromosome segregation (46, or tolerance of DNA damage and the recovery 76). In addition, this volume contains a dedi- of stalled or broken replication forks (95). How- cated review on the RecQ helicases, which pro- ever, recombination is also potentially danger- vides a much more comprehensive discussion ous as it can lead to gross chromosomal rear- of this important class of proteins than can be rangements and potentially lethal intermediates achieved here (15). Due to space limitations (89). Not surprisingly, defects in HR and asso- we refer the reader to recent reviews on how ciated processes define a number of human can- modulation of the DNA substrate affects HR cer predisposition syndromes associated with (118, 157), including at specific nuclear terri- tories such as telomeres (34) and the nucleolus (99). DNA REPAIR PROTEINS AND HUMAN Here, we review how recombinational DNA GENETIC DISEASE repair is regulated in mammalian somatic and yeast vegetative cells. We only include exam- Defects in DNA repair proteins lead to various inherited hu- ples of meiotic regulation of HR factors that man diseases sharing common features such as genome instabil- may also be applicable to somatic cells. The ity and cancer predisposition (71). Mutations of several RecQ focus is on the mechanistic phases of recom- helicases, BLM, WRN, and RecQ4, cause Bloom, Werner, bination (Figure 1) and the factors that exe- and Rothmund-Thomson syndromes, respectively. The other cute them (Table 1), identifying key regulatory two RecQ helicases, RECQ1 and RECQ5, have not yet been transitions and mechanisms. We elaborate on implicated in human disease, but cellular studies demonstrate how HR is modulated by multiple levels of pos- by CNRS-Multi-Site on 08/22/12. For personal use only. that they function in genome maintenance. Fanconi anemia itive and, primarily, negative regulation. Mech- (FA) is an autosomal recessive disorder characterized by pro- anisms of antirecombination appear to be inte- gressive bone marrow failure. Mutations in FANC genes affect gral to the HR pathway. We suggest that HR Annu. Rev. Genet. 2010.44:113-139. Downloaded from www.annualreviews.org DNA interstrand crosslink repair; among them, FANCJ ( = BRIP, gains flexibility and robustness by proceeding BACH1), FANCM, FANCD1 ( = BRCA2), FANCN ( = PALB2), through reversible, metastable intermediates. and RAD51C are involved in HR. BRCA1 and BRCA2 are major breast and ovarian tumor suppressor genes and both function in HR. Defective ATM, a key sensor kinase in the DDR pathway, MECHANISM OF HOMOLOGOUS leads to ataxia telangiectasia (A-T), a neurodegenerative disease RECOMBINATION with severe physical disabilities. Mutations of MRE11 and NBS1 Significant strides have been made in identify- in the MRN complex cause similar diseases, A-T–like disorder ing the proteins that catalyze HR in eukary- and Nijmegen breakage syndrome, respectively. Mutations im- otes and defining their mechanisms of action pairing DNA mismatch repair result in hereditary nonpolyposis (69, 91, 129, 161). HR can be conceptually di- colorectal cancer (HNPCC), an autosomal dominant disease with vided into three stages—presynapsis, synapsis, highly elevated risk for colon cancer. postsynapsis—and we briefly discuss the princi- pal proteins and structures involved (Figure 1). 114 Heyer · Ehmsen · Liu GE44CH06-Heyer ARI 3 October 2010 11:50 Ku70-Ku80 Rad52, Saw1- DNA-PKcs Rad1-Rad10 Pol4, ARTEMIS Rad50-Mre11-Xrs2 [NBS1] [ERCC1-XPF] Ligase 4 Sae2 [CtIP], Exo1, Dna2 Msh2-Msh3 Sgs1-Top3-Rmi1, [BLM] RPA Rad51, Rad52, Rad55-Rad57 [RAD51B, RAD51C, RAD51D, XRCC2, XRCC3] BRCA2-DSS1 Rad51, Rad54, Rdh54 D-loop RAD54B NHEJ SSA Sgs1-Top3-Rmi1 [BLM] Sgs1-Top3-Rmi1 [BLM] Mph1, Fml1 [FANCM] Mph1, Fml1 [FANCM] Srs2 Slx1-Slx4, Yen1 [GEN1] Mus81-Mms4 [EME1] dHJ Half-crossover Noncrossover CrossoverNoncrossover Noncrossover (LOH) BIR SDSA dHJ subpathway Homologous recombination (HR) Damaged dsDNA Generic protein Presynaptic phase Abc with broken ends designation HR Synaptic phase Homologous dsDNA Human-specific protein as repair template ABCD designation Postsynaptic phase by CNRS-Multi-Site on 08/22/12. For personal use only. Figure 1 Pathways of double-strand break repair. Protein names refer to the budding yeast Saccharomyces cerevisiae (blue). Where different in human, names (brown) are given in brackets. For proteins without a yeast homolog, brackets for human proteins are omitted. Broken Annu. Rev. Genet. 2010.44:113-139. Downloaded from www.annualreviews.org lines indicate new DNA synthesis and stretches of heteroduplex DNA that upon mismatch repair (MMR) can lead to gene conversion. Abbreviations: BIR, break-induced replication; dHJ, double Holliday junction; NHEJ, non-homologous end joining; LOH, loss of heterozygosity; SDSA, synthesis-dependent strand annealing; SSA, single-strand annealing. In presynapsis, the DNA damage is pro- Sgs1 (human BLM; see sidebar) (104). Bind- DSB: double-strand cessed to form an extended region of single- ing of RPA eliminates secondary structures break stranded DNA (ssDNA), which is bound by the in ssDNA, which is needed for competent MRX, MRN: ssDNA-binding protein RPA (replication pro- Rad51 filaments to assemble. However, RPA Saccharomyces cerevisiae tein A). For DNA double-strand breaks (DSBs) bound to ssDNA also forms a kinetic barrier Mre11-Rad50-Xrs2 in the budding yeast Saccharomyces cerevisiae, against Rad51 filament assembly, necessitating complex or human MRE11-RAD50- this step involves a surprising complexity of four so-called mediator proteins to allow timely NBS1 complex nuclease [Mre11-Rad50-Xrs2 (MRX) (human Rad51 filament formation on RPA-covered RPA: replication MRE11-RAD50-NBS1[MRN]), Exo1, Dna2, ssDNA. Three different classes of mediators protein A Sae2 (human CtIP)] and a helicase activity have been described, but their mechanisms www.annualreviews.org • Regulation of Homologous Recombination 115 GE44CH06-Heyer ARI 3 October 2010 11:50 Table 1 Posttranslational modifications and their effects on proteins involved in homologous recombination Protein Organism PTM Function and PTM effect Reference BLM Homo sapiens Multiple roles in DNA damage signaling and HR SUMO BLM-K317/331-SUMO required for full activity and Rad51 focus (47, 120) formation after HU treatment BRCA1 H. sapiens E3 ligase involved in HR and NHEJ SUMO PIAS1/4-dependent SUMO of BRCA1-K119 enhances BRCA1 UBI (107) ligase activity