Searching journal content for articles similar to Frith et al. 16 (6): 713.

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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
    ...sitesA eukaryotic gene typically consists of regulatory elements such as distal enhancers, which can act over long distances; a proximal promoter containing key TF binding sites; a core promoter surrounding the transcription start site (TSS) where the preinitiation complex assembles, followed...
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  2. 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
    ...(lower). ChEC-seq signal is the 5′ end of reads, presented in purple. Nucleosome occupancy data of the hybrid (Tirosh et al. 2010) are presented as gray lines. Transcription start sites are presented in gray dashed lines (Pelechano et al. 2013; Park et al. 2014). For Swi5, CCAGC motif sequences...
  3. Method: Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq
    • Bo Yan,
    • George Tzertzinis,
    • Ira Schildkraut,
    • and Laurence Ettwiller
    Genome Res. January 2022 32: 162-174; Published in Advance November 23, 2021, doi:10.1101/gr.275784.121
    ...: ettwiller@neb.comAbstractDetermination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5′ end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the other RNA polymerases that also play...
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  4. 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
    ...-mRNA expression (pre-mRNA), MYC signal at transcription start sites (MYC TSS Share), RNA Pol II signal at transcription start sites (RNAP_TSS), gene body regions (RNAP_GB), transcription end sites (RNAP_TES), mRNA expression (mature), synthesis rates (synthesis), degradation rates (degradation), and processing...
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  5. Research: Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
    • Cai Li,
    • Boris Lenhard,
    • and Nicholas M. Luscombe
    Genome Res. May 2018 28: 676-688; Published in Advance April 4, 2018, doi:10.1101/gr.231449.117
    ...in biology. Transcription start sites (TSSs) are especially interesting because they are central to initiating gene expression. Previous studies revealed widespread transcription initiation and fast turnover of TSSs in mammalian s. Yet, how new TSSs originate and how they evolve over time remain poorly...
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  6. Research: Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
    • Iris Zhu and
    • David Landsman
    Genome Res. October 2023 33: 1662-1672; Published in Advance October 26, 2023, doi:10.1101/gr.278130.123
    ...genes with NCBI RefSeq transcript ID that start with NM_ or NR_ are considered), which include 3297 out of 4781 (69%) housekeeping genes previously reported (Li et al. 2017). The number of strong enhancers associated with the 6107 genes are 8281 and 6756 in ESCs and MEF cells, respectively. The number...
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  7. Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
    • Kimberly N. Griffin,
    • Benjamin William Walters,
    • Haixin Li,
    • Huafeng Wang,
    • Giulia Biancon,
    • Toma Tebaldi,
    • Carolyn B. Kaya,
    • Jean Kanyo,
    • TuKiet T. Lam,
    • Andy L. Cox,
    • Stephanie Halene,
    • Jean-Ju Chung,
    • and Bluma J. Lesch
    Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
    ...poorly understood.Mammalian spermatogenic cells represent an exceptional system to discover the in vivo nuclear contributions of AGO2. As mature sperm develop in mammals, the undergoes extensive chromatin reorganization and uses distinct mechanisms of transcriptional regulation. During meiosis...
  8. Research: Global analyses of the dynamics of mammalian microRNA metabolism
    • Elena R. Kingston and
    • David P. Bartel
    Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
    ...of miR-7 by the Oip5os1 (also known as Cyrano) long noncoding RNA (lncRNA) in mammalian tissues (Kleaveland et al. 2018).Questions also remain regarding the rates of miRNA turnover and the extent to which degradation is regulated in a miRNA-specific manner. Most miRNAs that have been examined are highly...
  9. Resource: The transcription start site landscape of C. elegans
    • Taro Leo Saito,
    • Shin-ichi Hashimoto,
    • Sam Guoping Gu,
    • J. Jason Morton,
    • Michael Stadler,
    • Thomas Blumenthal,
    • Andrew Fire,
    • and Shinichi Morishita
    Genome Res. August 2013 23: 1348-1361; Published in Advance May 1, 2013, doi:10.1101/gr.151571.112
    ...The transcription start site landscape of C. elegans Taro Leo Saito 1 , Shin-ichi Hashimoto 2 , Sam Guoping Gu 3 , 6 , J. Jason Morton 4 , 7 , Michael Stadler 3 , Thomas Blumenthal 4 , Andrew Fire 5 , 8...
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  10. 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
    .... When compared with Conserved and Shifted core promoters, Turnover core promoters tended to show lower transcriptional activity (Fig. 5B) and usually were located at further upstream of the translation start codons (Fig. 5C).We examined the genomic sequences from −20 to +20 bp surrounding the dominant...
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