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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
...that are incorporated into completed transcripts and allow for their identification, for example, by hybridization-based techniques with radiolabeling (Smale 2009). This approach was recently improved by including modified nucleotides that allow for enrichment of the emergent transcripts by affinity isolation. Some...
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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
...et al. 2019, 2020) for estimating average RNAPII elongation rates. Like the other methods mentioned, DRB/TTchem-seq tracks nascent transcripts at different time points after synchronized release from promoter-proximal pausing. RNAPII is first restricted to the area close to the transcription start...
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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
...Chromosome-level sub-aware de novo assembly provides insight into Saccharomyces bayanus divergence after hybridization Cory Gardner1,2,5, Junhao Chen3,5, Christina Hadfield2, Zhaolian Lu3, David Debruin2, Yu Zhan3, Maureen J. Donlin2,4, Tae-Hyuk Ahn1,2 and Zhenguo Lin2,3 1Department of Computer...
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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
...in response to various environmental stimuli in a classic model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start sites (TSSs) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...to the nucleosome core in the following. The close interactions between DNA and histones in nucleosomes inhibit DNA access for many factors and thereby constitute an important level of regulation for all DNA-dependent processes, like transcription or DNA repair (Venkatesh and Workman 2015; Seeber et al. 2018...
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Resource: Global analysis of protein homomerization in Saccharomyces cerevisiae
- Yeonsoo Kim,
- Jong Pil Jung,
- Chan-Gi Pack,
- and Won-Ki Huh
Genome Res. January 2019 29: 135-145; Published in Advance December 19, 2018, doi:10.1101/gr.231860.117
...in lipid metabolism. Eur J Biochem 266: 1–16. doi:10.1046/j.1432-1327.1999.00822.x ↵Athenstaedt K, Zweytick D, Jandrositz A, Kohlwein SD, Daum G. 1999. Identification and characterization of major lipid particle proteins of the yeast Saccharomyces cerevisiae. J Bacteriol 181: 6441–6448. ↵Babu M, Vlasblom J...
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Research: Evolution of transcription factor binding through sequence variations and turnover of binding sites
- Gat Krieger,
- Offir Lupo,
- Patricia Wittkopp,
- and Naama Barkai
Genome Res. June 2022 32: 1099-1111; Published in Advance May 26, 2022, doi:10.1101/gr.276715.122
...closely related yeast species.ResultsMapping allele-specific binding of 27 transcription factors within an interspecies hybridTo examine systematically the effect of cis variation on TF binding, we generated F1 hybrids by mating two closely related budding yeast species: Saccharomyces cerevisiae...
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Method: Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
- Xiangxiu Wang,
- Wen Wang,
- Yiman Wang,
- Jia Chen,
- Guifen Liu,
- and Yong Zhang
Genome Res. February 2022 32: 378-388; Published in Advance December 29, 2021, doi:10.1101/gr.275837.121
...Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN Xiangxiu Wang1, Wen Wang1, Yiman Wang, Jia Chen, Guifen Liu1 and Yong Zhang Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research...
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Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
...transcription start sites (TSSs) has been identified in a budding yeast Saccharomyces cerevisiae (“scanning model”). Herein, we applied genomic approaches to elucidate the origin of the scanning model and its underlying genetic mechanisms. We first identified TSSs at single-nucleotide resolution for 12 yeast...
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Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
- Jennifer Hammelman,
- Konstantin Krismer,
- Budhaditya Banerjee,
- David K. Gifford,
- and Richard I. Sherwood
Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
...of chromatin. Because many transcription factors are incapable of binding in inaccessible or “closed” chromatin, the regulation of chromatin accessibility ensures such transcription factors do not bind to extraneous or deleterious locations in the .Transcription factors that interact with closed chromatin...
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