ESTIMATING ALLELIC DIVERSITY GENERATED BY EXCISION OF DIFFERENT TRANSPOSON TYPES

Methods are presented for calculating the number and type of different DNA sequences generated by base excision and insertion events at a gi ven site in a known DNA sequence. We calculate, for example, that exci sion of the Mu1 transposon from the bz1::Mu1 allele of maize should ge nerate more than 500,000 unique alleles given the extent of base delet ion (up to 34 bases removed) and base insertion (0-5 bases) observed t hus far in sequenced excision alleles. Analysis of this universe of po tential alleles can, for example, be used to predict the frequency of creation of stop codons or repair-generated duplications. In general, knowledge of the distribution of alleles can be used to evaluate model s of both excision and repair by determining whether particular events occur more frequently than expected. Such quantitative analysis compl ements the qualitative description provided by the DNA sequence of ind ividual events. Similar methods can be used to evaluate the outcome of other cases of DNA breakage and repair such as programmed V(D)J recom bination in immunoglobin genes.