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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
...(Fig. 4A), followed by TE-terminated transcripts with 10.63% and 9.45% and in TE-initiated transcripts with 1.79% and 1.51%. All species have a similar number of expressed genes (heads: x¯ = 9508, σ = 300; larvae: x¯ = 11,375, σ = 117), but we observed on average 11-fold fewer chimeric transcripts in D...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...on potentially misleading predictions.Prediction of potential regulatory sitesThis review focuses on gene-specific transcriptional regulation via direct TF binding to regulatory DNA sites. The initial task is thus to locate candidate DNA regions potentially involved in TF binding, and this starts...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several time points...
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Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...in the sequence conservation of pleiotropic CREs.One of the initial perplexing revelations of the human project was the seemingly limited number of genes, which did not align with the increase in complexity compared with organisms such as yeast, worms, and flies. It became evident that this complexity must stem...
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Resource: Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. July 2019 29: 1198-1210; Published in Advance May 10, 2019, doi:10.1101/gr.245456.118
...using no-amplification nontagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. We mapped ∼1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact of the budding yeast. The comprehensive TSS maps allowed us to identify core promoters for ∼96...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...change of centromere sequences observed across species, including the potential roles of recombination. We outline putative modes of selection that could act within the centromeres, as well as the role of repeats in driving cycles of centromere evolution. Although our primary focus is on plant s, we draw...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
...and are consistent with previous literature (Zajac et al. 2013; Cumbie et al. 2015; Wulf et al. 2019). Taken together, these observations indicate that STRIPE-seq effectively and comprehensively profiles the yeast initiation landscape.Quantification of transcript levels with STRIPE-seqAs the primary focus of STRIPE...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...collection of wild and naturally evolving high-quality Eucalyptus s covering 1 million to 50 million years of divergent evolution. Using these s, we find a pattern of evolution led by an initial rapid accumulation of rearrangements and subsequently a slow loss of both rearranged and syntenic sequences...
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Research: A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes
- Stefanie Mühlhausen,
- Peggy Findeisen,
- Uwe Plessmann,
- Henning Urlaub,
- and Martin Kollmar
Genome Res. July 2016 26: 945-955; Published in Advance May 6, 2016, doi:10.1101/gr.200931.115
...A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes Stefanie Mühlhausen 1 , Peggy Findeisen 1 , Uwe Plessmann 2 , Henning Urlaub 2 , 3 and Martin Kollmar 1 1Group Systems...
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Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
- Alexander Morin,
- Eric Ching-Pan Chu,
- Aman Sharma,
- Alex Adrian-Hamazaki,
- and Paul Pavlidis
Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
...Columbia V6T 1Z4, Canada; 3Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Corresponding author: paul@msl.ubc.caAbstractMapping the gene targets of chromatin-associated transcription regulators (TRs) is a major goal of genomics research. Ch...

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