Searching journal content for articles similar to Liu and Gregersen 35 (11): 2550.

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  1. 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
    ...techniques have been developed that monitor transcription as it occurs. Pioneering work introduced methods such as global run-on sequencing (GRO-seq) (Core and Lis 2008) and precision nuclear run-on sequencing (PRO-seq) (Kwak et al. 2013), which measure the location and activity of engaged RNA polymerase II...
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  2. Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
    • Karine Choquet,
    • Louis-Philippe Chaumont,
    • Simon Bache,
    • Autum R. Baxter-Koenigs,
    • and L. Stirling Churchman
    Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
    ...) undergo several maturation steps before their release from chromatin. Most human pre-mRNAs have many introns that are removed through splicing, which takes place either cotranscriptionally or soon after transcription (Pandya-Jones and Black 2009; Tilgner et al. 2012; Yeom et al. 2021). Cleavage of the 3...
  3. Research: Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate
    • Gilad Fuchs,
    • Dror Hollander,
    • Yoav Voichek,
    • Gil Ast,
    • and Moshe Oren
    Genome Res. October 2014 24: 1572-1583; Published in Advance July 21, 2014, doi:10.1101/gr.176487.114
    ...with accumulation of RNA polymerase II (Pol II), suggesting that H2Bub1 levels within gene bodies reflect changes in Pol II elongation rates that are probably associated with cotranscriptional splicing. In support of this notion, we find a significant correlation between H2Bub1 levels and experimentally measured...
  4. 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
    ...-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites -wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation...
  5. Research: Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation
    • Stefano de Pretis,
    • Theresia R. Kress,
    • Marco J. Morelli,
    • Arianna Sabò,
    • Chiara Locarno,
    • Alessandro Verrecchia,
    • Mirko Doni,
    • Stefano Campaner,
    • Bruno Amati,
    • and Mattia Pelizzola
    Genome Res. October 2017 27: 1658-1664; Published in Advance September 13, 2017, doi:10.1101/gr.226035.117
    ...implications. Indeed, numerous studies focused on the analysis of MYC-induced transcriptional responses, typically measuring its binding through ChIP-seq and profiling transcriptional maps by RNA-seq (Kress et al. 2015). A series of papers proposed that, rather than acting as a gene-specific regulator,MYC acts...
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  6. Research: Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation
    • Joanna Y. Ip,
    • Dominic Schmidt,
    • Qun Pan,
    • Arun K. Ramani,
    • Andrew G. Fraser,
    • Duncan T. Odom,
    • and Benjamin J. Blencowe
    Genome Res. March 2011 21: 390-401; Published in Advance December 16, 2010, doi:10.1101/gr.111070.110
    ...in nascent transcripts, yet the extent and physiological relevance of this kinetic coupling between transcription and alternative splicing (AS) is not well understood. We performed experiments to perturb Pol II elongation and then globally compared AS patterns with genome-wide Pol II occupancy. RNA binding...
  7. 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
    ...DTA (Sun et al. 2012), GRAND-SLAM (Jürges et al. 2018), pulseR (Uvarovskii and Dieterich 2017), and DRiLL (Rabani et al. 2014). Eventually, these approaches have started to unveil how the modulation of RNA dynamics can determine gene-specific regulatory modes and elicit complex transcriptional responses...
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  8. Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
    • Walter Muskovic,
    • Eve Slavich,
    • Ben Maslen,
    • Dominik C. Kaczorowski,
    • Joseph Cursons,
    • Edmund Crampin,
    • and Maria Kavallaris
    Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
    ...provided a close fit to observed expression dynamics (Fig. 2A–G), enabling estimation of transcript-specific half-lives (Fig. 2H).View larger version: In this window In a new window Figure 2. Gene-specific degradation rates shape mRNA dynamics. (A–G) Pre-mRNA (top panels) and mRNA expression profiles...
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  9. Research: An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation
    • Andrew M. Lerner,
    • Austin J. Hepperla,
    • Gregory R. Keele,
    • Hashem A. Meriesh,
    • Hayretin Yumerefendi,
    • David Restrepo,
    • Seth Zimmerman,
    • James E. Bear,
    • Brian Kuhlman,
    • Ian J. Davis,
    • and Brian D. Strahl
    Genome Res. November 2020 30: 1605-1617; Published in Advance October 5, 2020, doi:10.1101/gr.264283.120
    ...uniform across all transcribed genes and mostly independent of RNA abundance, suggesting that H3K36me removal is largely uncoupled from transcription elongation.DiscussionIn this study we sought to quantitatively explore the dynamics of H3K36me addition and removal in response to Set2 modulation. We...
  10. Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
    • Lydia Herzel,
    • Korinna Straube,
    • and Karla M. Neugebauer
    Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
    ...-intron transcripts. The subcategory of partially spliced transcripts recapitulates the splicing differences seen by nRNA-seq and carries signatures of gene-specific intron retention.‘All or none’ splicing of single transcripts predominatesThe number of partially spliced transcripts (697) for the above analysis...
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