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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...by cactophilic Drosophila species differs in its composition in terms of yeasts and alkaloids (Fogleman et al. 1982; Fogleman and Danielson 2001). Therefore, species have adapted to feed and breed on different hosts, as demonstrated by behavioral and physiological response when species feed and breed...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...endothelial cells. Bov-tA elements originated through recombination between tRNA-Glu-derived SINEs and a fragment of BovB element before the radiation of Pecoran ruminants (∼25–30 MYA) (Nijman et al. 2002; Nilsson et al. 2012). Collectively, Bov-tA1/2/3 gave rise to more than 750,000 copies in the modern cow...
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Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
- Alexandra Dallaire,
- Bethan F. Manley,
- Maya Wilkens,
- Iliana Bista,
- Clement Quan,
- Edouard Evangelisti,
- Charles R. Bradshaw,
- Navin B. Ramakrishna,
- Sebastian Schornack,
- Falk Butter,
- Uta Paszkowski,
- and Eric A. Miska
Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
...AGO-binding proteins (ARB1 and ARB2 in fission yeast) (Buker et al. 2007), and two genes involved in RNAi-mediated heterochromatin assembly (HRR1 and STC1 in fission yeast) (Motamedi et al. 2004; Bayne et al. 2010) but found no RDRP (Supplemental Fig. S4D; Supplemental Table S4). Most RNAi pathway...
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Research: Sir3 mediates long-range chromosome interactions in budding yeast
- Myriam Ruault,
- Vittore F. Scolari,
- Luciana Lazar-Stefanita,
- Antoine Hocher,
- Isabelle Loïodice,
- Romain Koszul,
- and Angela Taddei
Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
..., the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here, we investigate the well-conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3–5 foci in exponentially growing cells. This clustering is functionally...
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Research: Common genomic elements promote transcriptional and DNA replication roadblocks
- Kevin Roy,
- Jason Gabunilas,
- Abigail Gillespie,
- Duy Ngo,
- and Guillaume F. Chanfreau
Genome Res. October 2016 26: 1363-1375; Published in Advance August 18, 2016, doi:10.1101/gr.204776.116
...of Nrd1p or Nab3p also resulted in low levels of SNR53 readthrough (Fig. 6C). These results suggested that NNS is dependent on tRNA transcription for efficient SNR53 termination. The results obtained by nuclear depletion of Bdp1p were confirmed by deleting tG(GCC)E in WT and rrp6Δ backgrounds (Fig. 6C...
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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
...) for 10 min. Slides were then subjected to three washes in cold PBS and blocked in a buffer consisting of 1× SSC, 20 μg/μL yeast tRNA (Thermo Fisher Scientific), 20 μg/μL salmon sperm DNA (Thermo Fisher Scientific), 0.5% Triton X-100, 2% BSA, and 1 U/μL RNasin plus (Promega) for 1 h at 37°C.The probe...
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Research: Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts
- Tomasz W. Turowski,
- Ewa Leśniewska,
- Clementine Delan-Forino,
- Camille Sayou,
- Magdalena Boguta,
- and David Tollervey
Genome Res. July 2016 26: 933-944; Published in Advance May 20, 2016, doi:10.1101/gr.205492.116
...Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts Tomasz W. Turowski 1 , 2 , Ewa Leśniewska 3 , Clementine Delan-Forino 1 , Camille Sayou 1 , Magdalena Boguta 3 and David Tollervey...
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Research: Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis
- Mihaela Ola,
- Caoimhe E. O'Brien,
- Aisling Y. Coughlan,
- Qinxi Ma,
- Paul D. Donovan,
- Kenneth H. Wolfe,
- and Geraldine Butler
Genome Res. May 2020 30: 684-696; Published in Advance May 18, 2020, doi:10.1101/gr.257816.119
...of genes (4409) was chosen (Supplemental Fig. S4). Inter-chromosomal breaks were identified using pairwise comparison of synteny maps.Tagging Cse4C. parapsilosis strains CLIB214 and 90-137 were edited using a tRNA plasmid based CRISPR-Cas9 gene editing system as described by Lombardi et al. (2017, 2019a...
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Research: High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface
- Bianca M. Schmitt,
- Konrad L.M. Rudolph,
- Panagiota Karagianni,
- Nuno A. Fonseca,
- Robert J. White,
- Iannis Talianidis,
- Duncan T. Odom,
- John C. Marioni,
- and Claudia Kutter
Genome Res. November 2014 24: 1797-1807; Published in Advance August 13, 2014, doi:10.1101/gr.176784.114
...enhancer mark of H3K27ac and, to a lesser extent, H3K4me3. Further, the expression of the anticodon isoacceptor families, relative to each other, was stable across mammalian development. In yeast, tRNA genes can compensate for changing levels of expression of another member of their isoacceptor family...
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Research: Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
- Éléonore Durand,
- Isabelle Gagnon-Arsenault,
- Johan Hallin,
- Isabelle Hatin,
- Alexandre K. Dubé,
- Lou Nielly-Thibault,
- Olivier Namy,
- and Christian R. Landry
Genome Res. June 2019 29: 932-943; Published in Advance May 31, 2019, doi:10.1101/gr.239822.118
...; Supplemental Fig. S1). iORF alignment coordinates were converted to genomic coordinates on the respective s and were removed if there was any overlap with a known feature annotation (rRNA, tRNA, ncRNA, snoRNA, nonconserved genes, pseudogenes) on the reference S288C. Additional masking was performed by removing...
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