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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
.... Whereas much research has focused on the initiation of transcription, regulation of elongation plays an important role not only in transcription dynamics but also in cotranscriptional RNA processing and stability. Despite advances in high-throughput approaches for global quantification of RNA polymerase...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...that influence both enhancer and RNA polymerase activity (Bell et al. 2024). These effects may involve alterations in chromatin accessibility or post-translational modifications of chromatin-associated proteins. Additionally, the changes initiated by one TF at an enhancer, such as increasing chromatin...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...is required to maintain pluripotency by regulating the PSN enhancer network via the recruitment of RNA polymerase II.Acetylation of lysine residues in histone tails is an essential post-translational modification (PTM), dynamically regulated by the opposing actions of histone acetyltransferases (HATs...
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Research: MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites
- Yi Xiang See,
- Kaijing Chen,
- and Melissa J. Fullwood
Genome Res. April 2022 32: 629-642; Published in Advance February 3, 2022, doi:10.1101/gr.276313.121
.... Coverslips were mounted onto slides and imaged on the Nikon A1R confocal microscope at 100× magnification.Reverse transcription and quantitative polymerase chain reaction (RT-qPCR)RNA was extracted from U2OS cells with or without MYC induction in triplicate, using the RNeasy Mini kit (QIAGEN). RNA...
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Research: Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II
- Diyavarshini Gopaul,
- Cyril Denby Wilkes,
- Arach Goldar,
- Nathalie Giordanengo Aiach,
- Marie-Bénédicte Barrault,
- Elizaveta Novikova,
- and Julie Soutourina
Genome Res. August 2022 32: 1516-1528; Published in Advance June 23, 2022, doi:10.1101/gr.276371.121
...equally to this work. Corresponding author: julie.soutourina@cea.frAbstractMediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/ERCC5(XPG) endonuclease...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...form during transcription as the nascent RNA anneals with the template DNA strand behind RNA polymerase II (RNA pol II). Many lncRNAs are transcribed by RNA pol II and may be more likely to form RLs owing to the lack of cotranscriptional processing, which actively resolves these structures; however...
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Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
- Mattia Furlan,
- Eugenia Galeota,
- Nunzio Del Gaudio,
- Erik Dassi,
- Michele Caselle,
- Stefano de Pretis,
- and Mattia Pelizzola
Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
...both total and nascent RNA (de Pretis et al. 2017). In that study, the integrative analysis of both data types with the INSPEcT+ approach revealed that MYC acts predominantly by modulating the rate of synthesis of its target genes, with an important, albeit less prevalent, impact on processing...
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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
...cotranscriptionally. Thus, we studied A-to-I editing regulation in the context of transcription and pre-mRNA processing. We show that stimulation of transcription impacts editing levels. Activation of the transcription factor MYC leads to an up-regulation of A-to-I editing, particularly in transcripts...
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Research: Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest
- Andrea Orioli,
- Viviane Praz,
- Philippe Lhôte,
- and Nouria Hernandez
Genome Res. May 2016 26: 624-635; Published in Advance March 3, 2016, doi:10.1101/gr.201400.115
...Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest Andrea Orioli 1 , Viviane Praz 1 , 2 , Philippe Lhôte 1 and Nouria Hernandez 1 1Center...
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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...-mediated degradation (Wyers et al. 2005; Preker et al. 2008; De Santa et al. 2010). Global Run-On (GRO)-seq (Core et al. 2008) facilitates a sensitive and quantitative evaluation of transcriptionally engaged RNA polymerase molecules and thus serves as an indirect measure of nascent transcription at promoters...

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