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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...and differences in the molecular mechanisms governing TL regulation. Genome-wide association studies (GWAS) or linkage analyses could leverage the genetic diversity to identify new genes or variants contributing to TL regulation, an approach that has yielded important insight into TL regulators (Gatbonton et al...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...aberrations in cell-cycle control. In non-small-cell lung cancer (NSCLC), instability occurs early in tumor growth, resulting in pronounced intratumor heterogeneity, including changes in gene copy number, and whole- doubling (WGD) in ∼75% of tumors. Gene duplication, genetic drift, and selection mediate...
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Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
...of HXT genes in each lineage. (D) Synteny of HXT and adjacent genes on Chr IV 5′ subtelomere. One representative S. cerevisiae isolate in each lineage was chosen. Numbers denote coordinates. Numbers in brackets were annotated genes until chromosome end.Gene duplication played an important role...
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Research: LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
- Shengjun Tan,
- Margarida Cardoso-Moreira,
- Wenwen Shi,
- Dan Zhang,
- Jiawei Huang,
- Yanan Mao,
- Hangxing Jia,
- Yaqiong Zhang,
- Chunyan Chen,
- Yi Shao,
- Liang Leng,
- Zhonghua Liu,
- Xun Huang,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. December 2016 26: 1663-1675; Published in Advance October 20, 2016, doi:10.1101/gr.204925.116
...structures, each containing the partial sequences of two unlinked genes. In total, 17 parental genes were involved in the formation of 15 polymorphic retrocopies (Table 1). LTR retrotransposons mediate retroposition in Drosophila populations The 15 retrocopies tend to be partial with a median length of 26...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...the introgression of Saccharomyces cerevisiae, such as those involved in the maltose metabolism. Finally, the patterns of recombination and LOH suggest an allotetraploid origin of S. bayanus. The gene acquisition and rapid LOH in the hybrid probably facilitated its adaptation to maltose brewing environments...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...(Saponaro et al. 2014). Factors involved in cotranscriptional RNA processing have also been shown to impact elongation rate. The splicing regulator SRSF2 (also known as SC35) promotes transcription elongation in a gene-specific manner (Lin et al. 2008), and U1 small nuclear ribonucleoprotein (U1 sn...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
..., Wang W. 2008. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179: 487–496. doi:10.1534/genetics.107.084491 ↵Canchaya C, Proux C, Fournous G, Bruttin A, Brüssow H. 2003. Prophage genomics. Microbiol Mol Biol Rev 67: 238–276. doi:10.1128/MMBR.67...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...-associated bubble upstream of the KIT gene. (A) Bandage plots showing the paths traversed for the three observed alleles (two for white-headed breeds and one for color-headed) through the pan. Unless stated otherwise, n = 1 for the breed. The gray arrow paths indicate the segmental duplication regions, whereas...
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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
...cotranscriptional processes, RDD produces transcripts with different functions and affects cellular phenotypes. Deaminases do not play a key role in yeast RDD formation After characterizing the RDDs, next we took advantage of yeast mutants to search for genes that are involved in RDD formation. The two known RNA...
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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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