Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome

Abstract

A prominent feature of transcription in Giardia lamblia is the abundant production of sterile antisense transcripts (Elmendorf et al. The abundance of sterile transcripts in Giardia lamblia. Nucleic Acids., 29, 4674-4683). Here, we use a computational biology analysis of SAGE data to assess the abundance and distribution of sense and antisense messages in the parasite genome. Sterile antisense transcripts are produced at approximately 50% of loci with detectable transcription, yet their abundance at a given locus does not correlate to the abundance of the complementary sense transcripts at that locus or to transcription levels at neighboring loci. These data suggest that sterile antisense transcripts are not simply a local effect of open chromatin structure. Using 5'RACE, we demonstrate that Giardia promoters are a source of antisense transcripts through bidirectional transcription, producing both downstream coding sense and upstream sterile antisense transcripts. We use a dual reporter system to explore roles of specific promoter elements in this bidirectional initiation of transcription and suggest that the degenerate AT-rich nature of TATA and Inr elements in Giardia permits them to function interchangeably. The phenomenon of bidirectional transcription in G. lamblia gives us insight into the interaction between transcriptional machinery and promoter elements, and may be the prominent source of the abundant antisense transcription in this parasite.