INSERTION OF A SHORT ALU SEQUENCE INTO THE HMSH2 GENE FOLLOWING A DOUBLE CROSS-OVER NEXT TO SEQUENCES WITH CHI-HOMOLOGY

Alu repeat sequences and other multiple copy repetitive elements are p resent throughout the human genome and are active in promoting recombi nation. It is believed that reverse transcription of transcribed Alu r epeats followed by chromosomal integration has been responsible for th e wide dispersion and high copy number of these sequences. During stud ies on the hMSH2 gene we have used RT-PCR to amplify from peripheral b lood lymphocytes a cDNA species in which 553 base pairs of hMSH2 cDNA have been deleted to be replaced by a short 36 base pair Alu sequence as a result of a genomic insertion/deletion event. The 36 base pair Al u insert is homologous to a 26 base pair Alu sequence previously impli cated in the promotion of recombination and contains the GCTGG motif w hich is part of the prokaryotic chi sequence. A second chi-like sequen ce is also located within the deleted hMSH2 region. Both chi-like sequ ences are located within 4 bp of the two 4-bp regions of cross over co ntaining the insertion/deletion breakpoints. This suggests that a doub le recombination event has occurred, providing direct evidence for the recombinogenic activity of this Alu element. Furthermore, it suggests that chi-like sequences may define recombination hotspots as in proka ryotes.