Retrotransposon profiling of RNA polymerase III initiation sites
- Xiaojie Qi1,4,
- Kenneth Daily2,4,5,
- Kim Nguyen1,4,6,
- Haoyi Wang3,7,
- David Mayhew3,
- Paul Rigor2,
- Sholeh Forouzan2,
- Mark Johnston3,8,
- Robi David Mitra3,
- Pierre Baldi1,2 and
- Suzanne Sandmeyer1,9
- 1Department of Biological Chemistry, School of Medicine,
- 2Department of Computer Science, School of Information and Computer Sciences, University of California, Irvine, California 92697, USA;
- 3Department of Genetics, School of Medicine, Washington University, St. Louis, Missouri 63108, USA
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↵4 These authors contributed equally to this work.
Abstract
Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked integration specificity. In yeast and slime mold, some retrotransposons are associated with tRNA genes (tDNAs). In the Saccharomyces cerevisiae genome, the long terminal repeat retrotransposon Ty3 is found at RNA polymerase III (Pol III) transcription start sites of tDNAs. Ty1, 2, and 4 elements also cluster in the upstream regions of these genes. To determine the extent to which other Pol III–transcribed genes serve as genomic targets for Ty3, a set of 10,000 Ty3 genomic retrotranspositions were mapped using high-throughput DNA sequencing. Integrations occurred at all known tDNAs, two tDNA relics (iYGR033c and ZOD1), and six non-tDNA, Pol III–transcribed types of genes (RDN5, SNR6, SNR52, RPR1, RNA170, and SCR1). Previous work in vitro demonstrated that the Pol III transcription factor (TF) IIIB is important for Ty3 targeting. However, seven loci that bind the TFIIIB loader, TFIIIC, were not targeted, underscoring the unexplained absence of TFIIIB at those sites. Ty3 integrations also occurred in two open reading frames not previously associated with Pol III transcription, suggesting the existence of a small number of additional sites in the yeast genome that interact with Pol III transcription complexes.
Footnotes
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↵9 Corresponding author.
E-mail sbsandme{at}uci.edu.
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.131219.111.
- Received August 27, 2011.
- Accepted January 25, 2012.
- Copyright © 2012 by Cold Spring Harbor Laboratory Press
