CHARACTERIZATION OF RAT PSEUDOGENES FOR ENHANCER FACTOR-I SUBUNIT-A - RIPPING PROVIDES CLUES TO THE EVOLUTION OF THE EFI(A)/DBPB/YB-1 MULTIGENE FAMILY

Genomic Southern blot analysis of rat EFI(A) (gene encoding enhancer factor I subunit A) reveals a complex band pattern when cDNA subfragment probes are used. Screening a rat genomic library with a rat EFI(A) cDNA probe yields two different processed EFI(A) pseudogenes, designated rat PSIEFIA#(213) and #(417), in addition to two other different, but less extensively characterized clones. PSIEFIA#(417) has no open reading frame (ORF) sequences. PSIEFIA#(213) contains two ORFs (83 and 178 codons), the products of which (if expressed) might be negative-acting EFI, transcription factors. Located nearly 0.6 kb upstream from PSIEFI(A)#(2/3) is a perfect 69-bp dinucleotide (CT) tandem repeat, a sequence element associated with other isolated pseudogenes. Additionally, the 3' end of this processed gene is interrupted by an unusual retroposon, an inverted dimeric B1-like short interspersed repetitive element (SINE). The isolation of several independent clones of the same EFI(A) processed pseudogenes indicates that they comprise a significant component of the rat EFI(A) copy multiplicity. The phenomenon of repeat induced point mutagenesis (ripping) at rat EFI(A) pseudogene CpG doublets occurs at a frequency at least 6.5 times higher than predicted from random mutagenesis. This is consonant with the proposal that ripping may be the mechanism which inactivates the ectopic recombination potential of the rat EFI(A) pseudogenes.