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Research: Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots
- Loris Mularoni,
- Yulian Zhou,
- Tyson Bowen,
- Sunil Gangadharan,
- Sarah J. Wheelan,
- and Jef D. Boeke
Genome Res. April 2012 22: 693-703; Published in Advance January 4, 2012, doi:10.1101/gr.129460.111
...1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs. Genes Dev 19: 955–964. Baller JA, Gao J, Stamenova R, Curcio MJ, Voytas DF. 2012. A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1...
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LETTER: Local Definition of Ty1 Target Preference by Long Terminal Repeats and Clustered tRNA Genes
- Nurjana Bachman,
- Yolanda Eby,
- and Jef D. Boeke
Genome Res. July 2004 14: 1232-1247; Published in Advance June 14, 2004, doi:10.1101/gr.2052904
...DNAs and LTRs surrounding the target tDNA dramatically influenced the frequency of insertion events upstream of that target. Ty1 is an LTR retrotransposon in Saccharomyces cerevisiae that integrates specifically into the host and generates target-site duplications. Previous work has shown that the Ty1's...
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RESEARCH: Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence
- Jin M. Kim,
- Swathi Vanguri,
- Jef D. Boeke,
- Abram Gabriel,
- and Daniel F. Voytas
Genome Res. May 1, 1998 8: 464-478; doi:10.1101/gr.8.5.464
...of Medicine, Baltimore, Maryland 21205 USA Abstract We conducted a genome-wide survey of Saccharomyces cerevisiae retrotransposons and identified a total of 331 insertions, including 217 Ty1, 34 Ty2, 41 Ty3, 32 Ty4, and 7 Ty5 elements. Eighty-five percent of insertions were solo long terminal...
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Research: Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
- Kurt Patterson,
- Farbod Shavarebi,
- Christophe Magnan,
- Ivan Chang,
- Xiaojie Qi,
- Pierre Baldi,
- Virginia Bilanchone,
- and Suzanne B. Sandmeyer
Genome Res. August 2019 29: 1298-1309; Published in Advance June 27, 2019, doi:10.1101/gr.240861.118
...of the Ty3/Gypsy LTR retrotransposon class of Saccharomyces cerevisiae (Hansen et al. 1988; Sandmeyer et al. 2015; Sultana et al. 2017). Ty3 insertion occurs at the narrowly defined, nucleosome-free transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3), including 275 tDNAs, SNR6...
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ARTICLE: Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe
- Nathan J. Bowen,
- I. King Jordan,
- Jonathan A. Epstein,
- Valerie Wood,
- and Henry L. Levin
Genome Res. September 2003 13: 1984-1997; doi:10.1101/gr.1191603
...that an asparagine can function in place of the second aspartic acid ( Bowen and McDonald 1999 ). Additionally, it has been shown that the same aspartic acid to asparagine substitution in the active site of the S. cerevisiae LTR-retrotransposon, Ty1, retains near wild-type polymerase activity, indicating...
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Method: Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
- Dalibor Miklík,
- Jiří Grim,
- Daniel Elleder,
- and Jiří Hejnar
Genome Res. August 2023 33: 1395-1408; Published in Advance July 18, 2023, doi:10.1101/gr.277694.123
...models, we also identify HIV-1-favored palindromic sequences in Alu repeats serving as local hotspots for integration. The application of the novel statistical approach provides deeper insight into the selection of retroviral integration sites and may prove to be a valuable tool in the analysis of any...
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ARTICLE: Genomic Analysis of Caenorhabditis elegans Reveals Ancient Families of Retroviral-like Elements
- Nathan J. Bowen and
- John F. McDonald
Genome Res. October 1, 1999 9: 924-935; doi:10.1101/gr.9.10.924
...) Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae Mol. Biol. Evol. 16 : 419 – 422 , ibid . ↵ ( 1999b ) Tempo and mode of Ty element evolution in saccharomyces cerevisiae. Genetics 151 : 1341 – 1351 , ibid . ↵ Kazazian H.H. , Jr. ( 1998 ) Mobile elements...

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