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Research: Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast
- Vahid Aslanzadeh,
- Yuanhua Huang,
- Guido Sanguinetti,
- and Jean D. Beggs
Genome Res. February 2018 28: 203-213; Published in Advance December 18, 2017, doi:10.1101/gr.225615.117
...for the first time how transcription elongation mutants affect splicing fidelity and alternative splicing in budding yeast.ResultsAltering transcription elongation rate changes the amount of nascent RNA that is spliced cotranscriptionallyTo gain further insight into the coupling between splicing...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...displayed a different regulatory pattern (Fig. 4C,D). Both genes showed significantly increased expression in OLs compared with OPCs, accompanied by substantial demethylation at their promoter regions, particularly for CNP. These findings suggest that CNP and FA2H are transcriptionally activated during OL...
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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
...first approach the question of what regulates your GOI transcriptionally, you should start by compiling available information on chromatin landscape (especially regulatory region hallmarks) and TF binding from browsers (e.g., UCSC Genome Browser) and user-friendly databases (e.g., Harmonizome). For most...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...splicing has been linked to neurodegenerative, neurodevelopmental, and neuropsychiatric diseases (Dredge et al. 2001; Lopez Soto et al. 2019). Neuronal alternative splicing is downstream from calcium-calmodulin-dependent protein kinase (CaMK) signaling, which regulates RNA-binding proteins both post-transcriptionally...
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Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
- Boning Chen,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
...understand how CAF-1 affects chromatin maturation dynamics, we also generated NCOPs in cells lacking Cac1, the largest subunit of CAF-1. In budding yeast, the deletion of CAC1 (cac1Δ) is sufficient to abrogate the histone chaperone activity of CAF-1 without affecting the viability of the cells (Liu et al...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...exhibit significant changes in XIST expression, but the direction of change depends on the disease (lower in PNP and higher in cardiomyopathy), suggesting that XIST (specifically sXIST because it is the only apparent transcript in male hearts) could potentially affect the expression of some genes...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...whole- sequencing of 140 cutaneous melanomas (Hayward et al. 2017). Unlike in budding yeast, CG dinucleotides in the human are frequently methylated, which is known to affect CPD formation when exposed to UVB wavelengths present in sunlight (e.g., Pfeifer et al. 2005; Lindberg et al. 2019; Wilson...
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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: 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
...are limited when the rDNA is transcriptionally active, possibly owing to a stronger anchoring at the nuclear periphery when the rDNA is active. Alternatively, the high density of ongoing transcripts could prevent telomeres from contacting the rDNA through steric hindrance. Finally, long-range contacts may...
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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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