Nucleotide sequence analysis of the long terminal repeat (LTR) of avian retroviruses: structural similarities with transposable elements.

The nucleotide sequences of the long terminal repeat (LTR) from six independently derived avian retrovirus recombinant DNA clones have been determined. The LTRs from three clones are approximately 350 bp in length and differ only in minor base insertions or substitutions. Three other clones have smaller LTRs, each with a large deletion which ranged from 89 to 161 bp. Sequence comparisons of the six LTRs indicate that there is conservation of sequences derived from the 5' terminus of viral RNA and extensive divergence of the 3'-specific sequences. The LTR sequences were obtained from clones of unintegrated viral DNA. Comparison of these LTRs with the sequence of an integrated Schmidt-Ruppin D provirus deduced previously reveals that two nucleotides present at the terminus of the LTR of the unintegrated DNA are absent in the integrated provirus. Analysis of the nucleotide sequence of the LTR from one clone, lambda RAV2-2, reveals several putative regulatory sites for the initiation and termination of transcription. There are also several structural features of the LTR which are analogous to procaryotic and eucaryotic transposable elements. These structural analogies include the presence of inverted complementary repeats at the termini of the LTR, deletions adjacent to LTR termini, and sequence homologies with transposable and other genetic elements. These observations suggest that the LTR of retroviruses function in the control of gene expression and integration.