Searching journal content for articles similar to Baquero Pérez et al. 35 (10): 2226.

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  1. 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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  2. Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
    • Kamal Ajit,
    • Adele Alagia,
    • Kaspar Burger,
    • and Monika Gullerova
    Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
    ...Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage Kamal Ajit1, Adele Alagia1, Kaspar Burger2,3 and Monika Gullerova1 1Sir William Dunn School of Pathology, Oxford, OX1 3RE...
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  3. 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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  4. 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...
  5. Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
    • Shruthi Rengarajan,
    • Jason Derks,
    • Daniel W. Bellott,
    • Nikolai Slavov,
    • and David C. Page
    Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
    ...cells and by negative auto-regulation of DDX3X in 46,XX cells. DDX3X–DDX3Y cross-regulation is mediated through mRNA destabilization—as shown by metabolic labeling of newly transcribed RNA—and buffers total levels of DDX3X and DDX3Y protein in human cells. We infer that post-transcriptional auto...
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  6. 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
    ...RNA (eRNA) production at intergenic C1 and C2 sites. These results were concordant with ATAC-seq results indicating that C1 sites produce very little eRNA without AR activation, whereas C2 sites were already transcriptional active (Fig. 3A; Supplemental Fig. S5A). AR activation substantially increased...
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  7. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
    • Yuange Duan,
    • Min Huang,
    • Lin Ye,
    • Ling Ma,
    • Yashuai Wu,
    • Yating Du,
    • Jiyao Liu,
    • Fan Song,
    • Li Tian,
    • Wanzhi Cai,
    • Hu Li,
    • Xin Zhou,
    • and Shiqi Luo
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...(Supplemental Fig. S1). The full-length cloned Adar transcript is 2545 bp, encoding a predicted protein of 663 amino acids (AAs). The N terminus contains two dsRNA-binding domains (AA positions 78–140 and 197–241), and the C terminus contains one deaminase domain (AA positions 294–659). A-to-I RNA editomes...
  8. 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
    ...also considered that the direction of regulation may not be the same across a regulatory cascade or pathway. For example, although activators typically promote gene expression by facilitating the recruitment of RNA polymerase and transcriptional machinery, their effects on downstream targets can...
  9. Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...), and similar results were reported for the mouse(Kiyosawa et al. 2003), Drosophila(Misra et al. 2002), Arabidopsis(Meyers et al. 2004; Wang et al. 2014), and rice s(Osato et al. 2003). In addition, many long intergenic non-coding RNAs (lincRNAs) have been identified as antisense transcripts, further...
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  10. 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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