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Research: Retrotransposon profiling of RNA polymerase III initiation sites
- Xiaojie Qi,
- Kenneth Daily,
- Kim Nguyen,
- Haoyi Wang,
- David Mayhew,
- Paul Rigor,
- Sholeh Forouzan,
- Mark Johnston,
- Robi David Mitra,
- Pierre Baldi,
- and Suzanne Sandmeyer
Genome Res. April 2012 22: 681-692; Published in Advance January 27, 2012, doi:10.1101/gr.131219.111
...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 ( i...
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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
...sequence motif centered on but extending beyond the target site duplication. A strong sequence-independent preference for nucleosomal integration sites was observed, in distinction to the preferences of the Hermes DNA transposon engineered to jump in yeast and the Tf1 retrotransposon of Schizosaccharomyces...
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Research: A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon
- Joshua A. Baller,
- Jiquan Gao,
- Radostina Stamenova,
- M. Joan Curcio,
- and Daniel F. Voytas
Genome Res. April 2012 22: 704-713; Published in Advance January 4, 2012, doi:10.1101/gr.129585.111
..., and this tethers the integration complex to specific genomic sites, resulting in target-site biases (Bushman 2003). Examples of retrotransposons that recognize chromatin during integration include the Schizosaccharomyces pombe Tf1 retrotransposon and the S. cerevisiae Ty3 retrotransposon, which integrate upstream...
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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...evidence for this “genomic shock hypothesis” in the fission yeast Schizosaccharomyces pombe. In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human-induced, hybridization. We used long-read sequencing data to assemble s of 37 samples derived from 31 S. pombe strains...
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Research: Transposable element insertions in fission yeast drive adaptation to environmental stress
- Caroline Esnault,
- Michael Lee,
- Chloe Ham,
- and Henry L. Levin
Genome Res. January 2019 29: 85-95; Published in Advance December 12, 2018, doi:10.1101/gr.239699.118
...and Levin 2015; Majumdar and Rio 2015; Sandmeyer et al. 2015; Sultana et al. 2017). Integration of the LTR retrotransposon Tf1 of Schizosaccharomyces pombe has been studied by determining as many as 1 million integration events with high-throughput sequencing (Guo and Levin 2010; Chatterjee et al. 2014...
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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
...Ty study in which a barcoding strategy rigorously distinguished independent events, previous studies of both Ty1 and Ty3 (Ji et al. 1993; Bachman et al. 2004; Qi et al. 2012) inferred preferential use of targets by relying on data sets from individual loci or high-throughput sequencing lacking...
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LETTER: The Mouse Clock Locus: Sequence and Comparative Analysis of 204 Kb from Mouse Chromosome 5
- Lisa D. Wilsbacher,
- Ashvin M. Sangoram,
- Marina P. Antoch,
- and Joseph S. Takahashi
Genome Res. December 1, 2000 10: 1928-1940; doi:10.1101/gr.155400
...the shotgun sequencing approach ( Sulston et al. 1992 ; Ansari-Lari et al. 1998 ) to obtain genomic sequence near the Clock locus. Specifically, we adapted the high-throughput shotgun sequencing protocols available at the Washington University Genome Sequencing Center ( http...
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ARTICLE: Retroviruses and yeast retrotransposons use overlapping sets of host genes
- Becky Irwin,
- Michael Aye,
- Pierre Baldi,
- Nadejda Beliakova-Bethell,
- Henry Cheng,
- Yimeng Dou,
- Willy Liou,
- and Suzanne Sandmeyer
Genome Res. May 2005 15: 641-654; Published in Advance April 18, 2005, doi:10.1101/gr.3739005
...of Schizosaccharomyces pombe ( Levin 2002 ) have been studied in order to identify host functions that affect the retrotransposon lifecycle and, potentially, the retrovirus lifecycle. Host genes that activate or suppress viral replication represent a source of novel antiviral targets and therapeutics. Ty elements...
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