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Retrotransposon profiling of RNA polymerase III initiation sites
Xiaojie Qi1, Kenneth Daily, Kim Nguyen
1Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697, USA.
Genome Research
|January 31, 2012
Summary
Retrotransposons like Ty3 show specific integration near RNA polymerase III (Pol III) transcribed genes in yeast. This study maps 10,000 Ty3 retrotranspositions, revealing new target sites beyond tRNA genes.
Area of Science:
- Molecular Biology
- Genetics
- Genomics
Background:
- Retroviruses integrate promiscuously, but retrotransposons can exhibit specific integration.
- In yeast, some retrotransposons, including Ty3, are known to target tRNA genes (tDNAs).
Purpose of the Study:
- To investigate the genomic targets of the Ty3 retrotransposon beyond tDNAs.
- To determine the extent of Ty3 integration at other RNA polymerase III (Pol III)-transcribed genes.
Main Methods:
- Mapping of 10,000 Ty3 genomic retrotranspositions using high-throughput DNA sequencing.
- Analysis of integration sites in the Saccharomyces cerevisiae genome.
Main Results:
- Ty3 integrations were found at all known tDNAs, tDNA relics, and six non-tDNA Pol III-transcribed genes (RDN5, SNR6, SNR52, RPR1, RNA170, SCR1).
- Seven loci binding TFIIIC but lacking TFIIIB were not targeted, indicating TFIIIB's crucial role.
- Integrations also occurred in two open reading frames not previously linked to Pol III transcription.
Conclusions:
- Ty3 retrotransposon integration is not limited to tDNAs and targets a broader range of Pol III-transcribed genes in yeast.
- The study highlights the importance of transcription factor IIIB (TFIIIB) in directing Ty3 integration.
- New potential sites interacting with Pol III transcription complexes were identified.
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