Nucleotide sequence and transcription of a rat tRNA(Phe) gene and a neighboring Alu-like element

A bacteriophage gamma Ch4A clone containing a 22-kb rat DNA insert was isolated and found to contain a solitary tRNA(Phe)GAA gene and, 436 bp downstream of it, an Alu-like element. The nucleotide sequence of a 1141-bp DNA fragment containing these genes was determined. The rat tRNA(Phe)GAA gene, with the exception of an additional A in the extra arm, has a sequence identical to that of a rabbit liver tRNA(Phe). The Alu-like element belongs to the rodent B2 family of short interspersed repetitive nucleotide sequences. This repetitive element, B2Phe, is flanked by 12-bp direct repeats, contains an internal split promoter (block A and block B) for RNA polymerase III and is devoid of an A-rich segment at the 3' end. Like other members of the B2 family, the B2Phe element presents 64% sequence homology with rat serine tRNA and contains a serine (GCT) anticodon. Both tRNA(Phe)GAA gene and B2Phe element were found to be transcriptionally active in HeLa cell and Xenopus oocyte nuclear extracts. The tRNA(Phe) gene transcripts were processed during the course of transcription to form mature-size tRNA(Phe). The transcription efficiency of the B2Phe element was found to be an order of magnitude higher than that of the tRNA(Phe) gene. Competition experiments demonstrate that the B2Phe DNA can form a more stable transcription complex than the tRNA(Phe) gene and compete with it for binding of transcription factors.