Cis-acting requirements in flanking DNA for the programmed elimination of mse2.9: a common mechanism for deletion of internal eliminated sequences from the developing macronucleus of Tetrahymena thermophila

During macronuclear development in the ciliated protozoan Tetrahymena therm ophila, extensive DNA deletions occur, eliminating thousands of internal el iminated sequences (IESs), Using an rDNA-based transformation assay we have analyzed the role during DNA deletion of DNA flanking mse2.9, an IES withi n the second intron of a gene encoding an as yet incompletely characterized protein, We establish that a cis-acting sequence for mse2.9 deletion acts at a distance to specify deletion boundaries. A complex sequence element ne cessary for efficient and accurate mse2.9 deletion is located in the region 47-81 bp from the right side of mse2.9. The ability of a variety of IES fl anking sequences to rescue a processing deficient mse2.9 construct indicate s that some cis-acting signal is shared among different IESs, In addition, the short intronic sequence that flanks mse2.9 is able to direct efficient and accurate processing. Despite no obvious sequence similarity between mse 2.9 and other IESs, we suggest that a common mechanism is used to delete di fferent families of IESs in Tetrahymena.