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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
...discussions. This work was supported in part by NIH grant GM36481 to J.D.B. References Bachman N, Eby Y, Boeke JD. 2004. Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes. Genome Res 14: 1232–1247. Bachman N, Gelbart ME, Tsukiyama T, Boeke JD. 2005. TFIIIB subunit Bdp...
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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
...showed that tRNA genes (tDNAs) are targeted at widely different frequencies even within isoacceptor families. Ectopic expression of Ty3 integrase (IN) showed that it localized to targets independent of other Ty3 proteins and cDNA. IN, RNAP3, and transcription factor Brf1 were enriched at tDNA targets...
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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
...the periodic pattern of Ty1 insertion upstream of class III gene targets (Bachman et al. 2005). However, this is likely due to changes in nucleosome positioning, as catalytically inactive ISW2 does not change overall targeting to tRNA genes (Gelbart et al. 2005). Nucleosomes are also preferred targets...
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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
...novo Ty3 integration sites identified in HTS Target sites Genome alignment Number Proximal genes (cluster ID #) Notes tRNA Single 262 Multiple 2 tL(CAA)G2 tL(CAA)M Not in original data set 11 tD(GUC)B Part of tD-tR tandem pairs, originally assigned to tR tD(GUC)D tD(GUC)J2 tD(GUC)J3 tM(CAU)J3 Sequence...
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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
...to 400 nucleotides. The association of Tf insertions with pol II promoters was very similar to the preference previously observed for Tf1 integration. We found that the recently active Tf elements were absent from centromeres and pericentromeric regions of the genome containing tandem tRNA gene...
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Article: Comparative genomics of protoploid Saccharomycetaceae
- The Génolevures Consortium,
- Jean-Luc Souciet,
- Bernard Dujon,
- Claude Gaillardin,
- Mark Johnston,
- Philippe V. Baret,
- Paul Cliften,
- David J. Sherman,
- Jean Weissenbach,
- Eric Westhof,
- Patrick Wincker,
- Claire Jubin,
- Julie Poulain,
- Valérie Barbe,
- Béatrice Ségurens,
- François Artiguenave,
- Véronique Anthouard,
- Benoit Vacherie,
- Marie-Eve Val,
- Robert S. Fulton,
- Patrick Minx,
- Richard Wilson,
- Pascal Durrens,
- Géraldine Jean,
- Christian Marck,
- Tiphaine Martin,
- Macha Nikolski,
- Thomas Rolland,
- Marie-Line Seret,
- Serge Casarégola,
- Laurence Despons,
- Cécile Fairhead,
- Gilles Fischer,
- Ingrid Lafontaine,
- Véronique Leh,
- Marc Lemaire,
- Jacky de Montigny,
- Cécile Neuvéglise,
- Agnès Thierry,
- Isabelle Blanc-Lenfle,
- Claudine Bleykasten,
- Julie Diffels,
- Emilie Fritsch,
- Lionel Frangeul,
- Adrien Goëffon,
- Nicolas Jauniaux,
- Rym Kachouri-Lafond,
- Célia Payen,
- Serge Potier,
- Lenka Pribylova,
- Christophe Ozanne,
- Guy-Franck Richard,
- Christine Sacerdot,
- Marie-Laure Straub,
- and Emmanuel Talla
Genome Res. October 2009 19: 1696-1709; Published in Advance June 12, 2009, doi:10.1101/gr.091546.109
...protein-coding genes andmore introns than other yeasts andhas a larger variety of transposable elements. It also has several peculiarities, such as multiple subtelomeric rDNA loci and dispersed 5S RNA coding genes, half of which are transcriptionally fused to tRNA genes (Acker et al. 2008). A second...
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LETTER: Recombination Rate and the Distribution of Transposable Elements in the Drosophila melanogaster Genome
- Carène Rizzon,
- Gabriel Marais,
- Manolo Gouy,
- and Christian Biémont
Genome Res. March 1, 2002 12: 400-407; Published in Advance February 15, 2002, doi:10.1101/gr.210802
...are not randomly distributed in yeast, but are mainly located in genes transcribed by RNA polymerase III, such as tRNA genes ( Kim et al. 1998 ). It is, however, difficult to explain why the non-uniform homolog pairing in Saccharomyes cerevisiae ( Kleckner and Weiner 1993 ), as opposed to the close homolog...

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