Intergenic regions, ARS elements, and transcription: a role for molecular shielding.
Yves Sucaet (1), Christi Magrath (2)
(1) Troy State University, Biological and Environmental Science, Troy, AL 36082;
(2) Biological & Environmental, Troy State University, University Blvd., Troy, AL, 36082, United States of America
Autonomous Replication Sequences (ARSs) tend to localize to intergenic regions that are convergently or tandemly arrayed relative to the flanking genes; 88% of annotated ARSs are positioned adjacent to the 3'-end of a gene, increasing the potential for interference due to transcriptional readthrough. Thus, ARS elements may have an increased need for 'molecular shielding', and efficient transcription termination and reduced gene expression levels from ARS-flanking genes may shield ARS elements from transcriptional occlusion. An assessment of the distribution of transcription termination sequences (TTSs) in S.cerevisiae relative to the annotated location of ARSs on Chromosomes III, VI, and X indicates that an overrepresentation of TTSs in ARSs and in ARS-containing intergenic regions exists relative to intergenic regions devoid of ARS elements. Increased AT-richness cannot account for the differences in frequency and density of TTS elements. Also, an expression profile of ARS-adjacent genes relative to other genes in S.cerevisiae (utilizing SAGE data from various phases of the cell cycle) indicates ARSs are located in regions flanked by genes with low expression levels and that gene directionality may influence ARS positioning. In conclusion, the results suggest that ARSs are shielded from transcriptional interference by high TTS frequency and low expression levels of ARS-flanking genes. Project funding provided by the NSF (CAREER Grant 9985156).
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