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Research: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
- Gregory T. Booth,
- Isabel X. Wang,
- Vivian G. Cheung,
- and John T. Lis
Genome Res. June 2016 26: 799-811; Published in Advance May 12, 2016, doi:10.1101/gr.204578.116
..., however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.Budding...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...the structure of the most recent bilaterian common ancestor. These highly conserved bilaterian blocks of orthologous genes are retained in species from phyla as divergent as chordates, echinoderms, molluscs, and annelids (Wang et al. 2017; Simakov et al. 2022; Marlétaz et al. 2023; Martín-Zamora et al. 2023...
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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
...Haiyue Liu and Lea H. Gregersen Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark Corresponding author: leag@sund.ku.dkAbstractTranscription is regulated at multiple levels, including initiation, elongation, and termination...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...fusions or fissions. Also, the comparison of T. panzhihuanense with the long-read-based high-quality Morchella sextelata M. Kuo assembly revealed relatively high levels of mesosynteny conservation between the two species (Fig. 5B; Supplemental Fig. S14B). Indeed, 61% of the T. panzhihuanense and 70...
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Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
- Yang Li and
- Jianzhi Zhang
Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
...function, we compare the transcriptomic and proteomic effects of systematic gene deletions in budding yeast (Saccharomyces cerevisiae) with those effects in fission yeast (Schizosaccharomyces pombe). Despite evidence for functional conservation of orthologous genes, their deletions result in no more...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...learning model to reveal the distinct motif configuration of S. pombe poly(A) sites, which show more precise cleavage than S. cerevisiae. Altogether, our deep learning models provide unprecedented insights into poly(A) site formation of yeast species, and our results highlight divergent poly(A) signals...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...RNA to the fission yeast S. pombe, an intron-rich unicellular eukaryote that has become a very useful model to study splicing (Yan et al. 2015; Fair and Pleiss 2017). Our strategy was based on obtaining a very high coverage of the transcriptome to uncover alternative splice forms and lowly expressed transcripts. We...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...).ResultsMNase-seq profiling reveals -wide chromatin changes in genetic perturbation experimentsTo investigate chromatin changes in response to the deletion of individual transcriptional regulators, we profiled -wide chromatin occupancy in 201 yeast knockout strains (Supplemental Fig. S1; Giaever et al. 2002; Giaever...
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Research: Mediator dynamics during heat shock in budding yeast
- Debasish Sarkar,
- Z. Iris Zhu,
- Elizabeth R. Knoll,
- Emily Paul,
- David Landsman,
- and Randall H. Morse
Genome Res. January 2022 32: 111-123; Published in Advance November 16, 2021, doi:10.1101/gr.275750.121
...to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates preinitiation complex (PIC) assembly, only transiently before Pol II escape. Interruption...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
..., presumably via accelerated recombination during fbxn gene duplication, thereby reinforcing genetic divergence among populations and between species.An unusually conserved genomic region is identified surrounding Cni-neib-1Given the highly dynamic nature of fbxn genes across C. nigoni populations...

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