Abstract: We show that overexpression of Sub2p, a multifunctional Saccharomyces cerevisiae helicase family member that is involved in mRNA elongation and transport, also suppresses heterochromatic silencing at telomeres. Genetic assays show cells that overexpress SUB2 from a high copy plasmid exhibit increased survival rates when selecting for a telomere-silenced URA3 reporter. Two temperature-sensitive sub2 mutations that affect different helicase domains were also examined at the permissive temperature; these mutants also overcome silencing of the URA3 reporter. The degree to which silencing is suppressed correlates with SUB2 RNA and protein levels. Additionally, we find that Sub2p localizes to the telomeres, as determined by chromatin immunoprecipitation assays, suggesting that Sub2p has a direct effect at telomeres. Genome-wide analysis of transcripts was used to assess whether Sub2p overproduction affects only the silenced URA3 reporter gene, or whether other subtelomeric genes are also affected. Of the 70 RNA transcripts elevated in the Sub2p overexpressing cells, 28% are encoded by subtelomeric genes that are located within 5 Kbp of a core X or Y' repeat. The remainder of the transcripts clustered into several functional groups, including the iron homeostasis pathway, purine nucleotide metabolism, and miscellaneous transport genes, among others. These results suggest a targeted effect of Sub2p on transcription. Our results also confirm that Sub2p affects heterochromatic gene expression, similar to that observed with the Drosophila Hel25E homologue. The above observations imply that Sub2p affects chromatin structure in addition to, or in parallel with, its functions in transcription elongation, splicing and mRNA transport. Copyright (c) 2005 John Wiley & Sons, Ltd.