Promoters and heterogeneous 5′ termini of the messenger RNAs of adenovirus serotype 2

Abstract

Adenovirus serotype 2 messenger RNAs are transcribed from nine separate transcription units, which function during early, intermediate and late stages of infection. We have sequenced capped 5′ termini of messenger RNAs from each of these transcription units, and located the templates for each capped terminus in the sequence of the Ad2† genome. These results define the putative initiation sites and promoters for all major Ad2 transcripts. By comparing the termini and promoter DNA sequences, we conclude that seven of nine initiation sites including EIa, EIb, PIX, major late, EIII, EIV and the late form of region IIa mRNA have clearly defined “TATA” box homologies. With early region IIa and IVa2, this homology is absent. For most messengers, the mRNA terminus is microheterogeneous, and encoded within a two to seven-base cap region located ~30 nucleotides downstream from the TATA box. However, the two transcription units that lack TATA boxes display equivalent microheterogeneity. Purine termini are greatly favored over pyrimidine termini. We propose a model for Ad2 cap site recognition in which RNA polymerase scans short DNA segments for purine starts, and discuss the model in the context of EIV mRNAs of Ad2 and Ad5, which differ in their promoter region DNA sequence.