Copyright 0 1992 by the Genetics Societyof America The Evolution of Tandemly Repetitive DNA: Recombination Rules Rosalind M. Harding,* A. J. Boyce? andJ. B. Clegg* *MRC MolecularHaematology Unit, Institute of Molecular Medicine, University of Oxford, JohnRadcliffe Hospital, Headington, Oxford OX3 SOU, England, and ?Department of Biological Anthropology, University of Oxford, Oxford OX2 64S, England Manuscript received April 3, 1992 Accepted for publication August 3, 1992 ABSTRACT Variable numbers of tandem repeats (VNTRs), which include hypervariable regions, minisatellites and microsatellites, can be assigned together with satellite DNAs to define a class of noncoding tandemly repetitive DNA (TR-DNA). The evolution of TR-DNA is assumed to be driven by an unbiased recombinational process.A simulation modelof unequal exchange is presented and used to investigate the evolutionary persistence of single TR-DNA lineages. Three different recombination rules are specified to govern the expansion and contraction of a TR-DNA lineage from an initial array of two repeats to, finally, a single repeat allele, which cannot participate in a misalignment and exchange process. In the absence of amplification or selection acting to bias array evolution toward expansion, the probability of attaining a target array size is a function only of the initial number of repeats. Weshow that the proportions oflineages attaining a targeted array size are the same irrespective of recombination rule and rate, demonstrating that our simulation modelis well behaved. The time takento attain a target array size, the persistence of the target array, and the total persistence time of repetitive array structure,are functions of the initial number of repeats, the rate of recombination, and the rules of misalignment preceding recombinational exchange. These relation- ships are investigated usingour simulation model. While misalignmentcontraint is probably greatest for satellite DNA it also seems important in accounting for the evolution of VNTR loci including minisatellites. This conclusion is consistent with the observed nonrandom distributions of VNTRs and other TR-DNAs in the human genome. ONCODINGDNA sequenceswith “variable VNTRs to be examined within a context of TR-DNA N numbers of tandem repeats,” termed VNTRs, evolution. includethose loci called hypervariableregions The evolution of TR-DNA can be viewed within (HVRs), minisatellites and microsatellites. Grouping the even broader contextof the evolution of repetitive VNTRs together with satellite DNA creates a class of DNA, for which there area large numberof analytical noncoding tandemly repetitive DNA, hereafter de- and simulation models. Much attention has beengiven noted as TR-DNA. Satellite TR-DNA regions may to the evolutionary forces acting on multigenefamilies also have variable numbers of tandem repeats, but (HARDISON199 1 ; HUGHES199 1 ; LOOMISand GILPIN this is difficult todetermine. Because VNTRs are 1986; MAEDA and SMITHIES1986) andon inter- extensively polymorphic they can be used to address spersed repeats such as transposable elements(CHAR- a wide range of problems in forensicscience (JEFFREYS LESWORTH and LANGLEY1991; MARUYAMAand et al. 199 l), the determination of family relationships HARTL1991), SINES and LINES (BUCHETON1990; (JEFFREYS, TURNERand DEBENHAM1991), human SINGER 1982; ZUCKERKANDL, LATTER and JURKA gene mapping (NAKAMURAet al. 1987), and popula- 1989). Questionsabout the evolution of repetitive tion genetics (BAIRDet al. 1986; BALAZSet al. 1989; DNA haveaddressed two broad issues. First, how CHAKRABORTYet al. 1991 ; DEKA,CHAKRABORTY and does recombinational exchange resolving as genecon- FERRELL199 1; FLINTet al. 1989). The many appli- version,promote the evolutionary persistence and cations of VNTR loci rest on assumptions about their spreading of particular repeat lineages across the ge- evolutionary dynamics.Interestingly, a minisatellite nome of a species (NAGYLAKIand PETES1982; NA- VNTR modelpresented by GRAY and JEFFREYS GYLAKI 1984a,b, 1990; OHTA 1978, 1989; OHTA and (199 1) seems to sit at odds with general models for DOVER 1983)? Second,what processesof unequal TR-DNA, developed before the explosion of interest exchange promoteor control the variationin numbers in VNTRs. Are VNTRs, minisatellites in particular, of repeats within lineages (KRUGERand VOGEL1975; qualitatively different from otherTR-DNAs? The aim PERELSONand BELL 1977; SMITH1976; TAKAHATA of the study reported here is to review the biology of 1981)? The studies addressing the second question TR-DNA, in particular the VNTR loci, and on this are pertinent to the developmenta TR-DNA of model foundation, build a simulation model which enables which can account for VNTR dynamics. Genetics 132: 847-859 (November, 1992) 848 R. M. Harding, A. J. Boyce and J. B. Clegg A major aim of these earlier theoretical studies was This model is shown to be compatible with the expan- to determine the balance of evolutionary forces per- sion times of two minisatellite VNTRs in humans from mitting the accumulation and stabilization of large homologous TR-DNA loci in a primate ancestor.The arrays ofrepeats. The dual parametersof genetic drift justification for this model is that, while the probabil- and unequal exchange, unbiased toward array expan- ity of generating a large and hypervariable tandem sion by amplification or selection, cannot account for array at any particular locus is small, given the vast equilibrium distributions of large numbers of repeats number of potential TR-DNA lociin the genome, (WALSH1987). Amplification is ageneralized term many arrays should be large. for any mutational process that expands DNA length. We mean by unequal exchange a mutational process BIOLOGICALBACKGROUND TO ATR-DNA of recombination either between homologous chro- MODEL mosomes or within chromosomes between sister chro- matids. To counteract the loss of repeats by drift and Structure: Minisatellite DNA, HVRs andother unequal exchange it is necessary to posit a balancing VNTRs, including simple-sequence or microsatellite rate of amplification or positive selection. Unless these DNA (TAUTZ1989; WEBERand MAY 1989)share evolutionary forces are ongoing, the probability of commonstructural features with highly repeated finding a large tandem array at a potential TR-DNA DNA such as telomeric (BLACKBURN 1990; 199 1) and locus is low. Selection is important in studies applica- satellite (WILLARDand WAYE 1987)sequences. Their ble to multigene families (TAKAHATA1981), as is similarities suggest that these DNAs are subject to the amplification in those of transposable elements and same generalevolutionary processes of recombina- retroposons(CHARLESWORTH and LANGLEY 199 1). tional mutation. Within this class of polymorphic non- Either selection or amplification, or both, have also coding TR-DNA loci, however, there is a range of been incorporated into evolutionary models of TR- repeatunit size andnumber. The oligonucleotide repeat unit sequences of several to tens of base pairs DNA lineages to account forthe accumulation of large UEFFREYS, WILSONand THEIN1985; WoNG et al. stable tandem arraysof satellite DNA (STEPHAN1986, 1987) in minisatellite loci are shorter than thetypical 1987, 1989; WALSH1987). An important conclusion motifs of satellite DNA (SINGER 1982), but larger than of these analyses is that the evolutionary persistence the di- and trinucleotide repeats of microsatellite loci, of large arrays critically depends on balancea between such as CA repeats (TAUTZ1989). Also, the average a moderate, or at least equivalent, rate of amplifica- copy numbers per minisatellite allele in the tens to tion relative to a low rate of unequal exchange. hundreds are intermediatebetween the thousandfold GRAY andJEFFREYS (1991) have alternatively em- copies of satellite sequences and the few copies com- phasized that sufficient rates of amplification may be prizing amicrosatellite allele. This structuralvariation low, even when rates of unequal exchange are high. among TR-DNAs points to differences in the recom- In their model for the evolutionary dynamics of a binational rules acting on them. minisatellite, MS32, amplification is simulated as a Rules and rates of recombination: Recombination duplication of uniquesequence creating an initial of minisatellite alleles probably occurs during, or after array of two tandem repeats. The dynamics subse- replication, as DNA slippage or unequal sister chro- quent to the single amplification event are modeled matid exchange (USCE). The evidence against a role as a random walk via a path of unbiased array expan- for homologous recombination within minisatellite sion and contraction to a single repeat evolutionary arraysderives from the nonrandom association of dead end.Rates of unequal exchangeare proportional minisatellite alleles on different haplotypes. This has to allele size and ordersof magnitude higher than the been observed for the insulin 5’HVR (ROTWEINet al. low rates determined for stable, persistent TR-DNA 1986), the VNTRlocus, YNZ22 (WOLFF,NAKAMURA by analytical modeling (WALSH1987). Since there is and WHITE 1988), theminisatellite (MS 1) locus, D S71 a moderate probability (in the range of 0.001-0.05) (WOLFFet al. 1989), the HRAS1 3’VNTR (KASPER- that a long sequence of unequal exchange events is CZYK, DIMARTINOand KRONTIRIS1990) anda-globin initiated by a single duplication, it seems that a low 3‘HVR alleles (MARTINSON1991). On the other hand, rate of amplification is sufficient. In this model, short