TY  - JOUR
A1  - Qi, Xiaojie
A1  - Daily, Kenneth
A1  - Nguyen, Kim
A1  - Wang, Haoyi
A1  - Mayhew, David
A1  - Rigor, Paul
A1  - Forouzan, Sholeh
A1  - Johnston, Mark
A1  - Mitra, Robi David
A1  - Baldi, Pierre
A1  - Sandmeyer, Suzanne
T1  - Retrotransposon profiling of RNA polymerase III initiation sites
Y1  - 2012/04/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 681 
EP  - 692 
DO  - 10.1101/gr.131219.111 
VL  - 22 
IS  - 4 
UR  - http://genome.cshlp.org/content/22/4/681.abstract 
N2  - 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. 
ER  -