Searching journal content for articles similar to Grimaldi et al. 24 (1): 117.

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  1. Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
    • Elisa Oberbeckmann,
    • Michael Wolff,
    • Nils Krietenstein,
    • Mark Heron,
    • Jessica L. Ellins,
    • Andrea Schmid,
    • Stefan Krebs,
    • Helmut Blum,
    • Ulrich Gerland,
    • and Philipp Korber
    Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
    ...with transcription levels (Fennessy and Owen-Hughes 2016; Vasseur et al. 2016). Many factors are involved in redepositing nucleosomes in the wake of RNA polymerase (Hennig and Fischer 2013; Smolle et al. 2013). Our finding that highly transcribed genes rarely exhibit low, but mostly exhibit high absolute nucleosome...
  2. Research: RNA synthesis precision is regulated by preinitiation complex turnover
    • Kunal Poorey,
    • Rebekka O. Sprouse,
    • Melissa N. Wells,
    • Ramya Viswanathan,
    • Stefan Bekiranov,
    • and David T. Auble
    Genome Res. December 2010 20: 1679-1688; Published in Advance September 20, 2010, doi:10.1101/gr.109504.110
    ...RNA synthesis precision is regulated by preinitiation complex turnover Kunal Poorey , Rebekka O. Sprouse 1 , Melissa N. Wells 1 , Ramya Viswanathan , Stefan Bekiranov 2 and David T. Auble 2 Department of Biochemistry...
  3. Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
    • Kristina Krassovsky,
    • Rajarshi P. Ghosh,
    • and Barbara J. Meyer
    Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
    ...structures -wide in embryos and starved L1 larvae of the nematode Caenorhabditis elegans.Studies before ours showed that actively transcribing RNA polymerase II (Pol II) is the primary source of DNA supercoils in eukaryotes (Teves and Henikoff 2014). To transcribe DNA, Pol II and its nascent RNA must rotate...
  4. Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
    • Hamish W. King,
    • Nadezda A. Fursova,
    • Neil P. Blackledge,
    • and Robert J. Klose
    Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
    ...and after TAM treatment.Remodeling of the PRC1-dependent nucleosome landscape is linked to RNA polymerase II activityPcG complexes are required to maintain a transcriptionally repressive chromatin environment at developmentally regulated gene promoters. Our characterization of the nucleosome landscape...
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  5. Research: Promoter-specific dynamics of TATA-binding protein association with the human genome
    • Yuko Hasegawa and
    • Kevin Struhl
    Genome Res. December 2019 29: 1939-1950; Published in Advance November 15, 2019, doi:10.1101/gr.254466.119
    ...-binding domain of the estrogen receptor. We apply this method to analyze the dynamics of the TATA-binding protein. In vivo, TBP is required for transcription from promoters mediated by all three nuclear RNA polymerases (Pol) (Cormack and Struhl 1992). These three classes of promoters are responsible...
  6. Methods: High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
    • Assaf Weiner,
    • Amanda Hughes,
    • Moran Yassour,
    • Oliver J. Rando,
    • and Nir Friedman
    Genome Res. January 2010 20: 90-100; Published in Advance October 21, 2009, doi:10.1101/gr.098509.109
    ...NFRs (Sekinger et al. 2005; Kaplan et al. 2008; Zhang et al. 2009). After 2 h of polymerase inactivation, the distribution of correlations shifted to a higher value of;0.5, indicating that RNA polymerase does help maintain nucleosomes in thermodynamically unfavored locations in vivo. Of course, much...
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  7. Letter: Nucleosome landscape and control of transcription in the human malaria parasite
    • Nadia Ponts,
    • Elena Y. Harris,
    • Jacques Prudhomme,
    • Ivan Wick,
    • Colleen Eckhardt-Ludka,
    • Glenn R. Hicks,
    • Gary Hardiman,
    • Stefano Lonardi,
    • and Karine G. Le Roch
    Genome Res. February 2010 20: 228-238; Published in Advance January 6, 2010, doi:10.1101/gr.101063.109
    ...eukaryotic model of transcription initiation after precise removal of nucleosomes. Genes in which mRNA products were detected at the schizont stage (and involved in invasion) in previousmicroarray expression analyses belong to this group (Le Roch et al. 2003). The apparent paradox of a closed state...
  8. 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
    ...with identifying the TSS, the RNA polymerase recruitment point. TF binding sites near the TSS form the promoter, whereas more distant ones are typically called enhancers (Bateman and Johnson 2022). Some genes have multiple functional TSSs, which complicates regulatory analysis, so alternative promoters must...
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  9. Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
    • Deepani W. Poramba-Liyanage,
    • Tessy Korthout,
    • Christine E. Cucinotta,
    • Ila van Kruijsbergen,
    • Tibor van Welsem,
    • Dris El Atmioui,
    • Huib Ovaa,
    • Toshio Tsukiyama,
    • and Fred van Leeuwen
    Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
    ...following chemical inhibition of RNA polymerase. Rapid reduction of RNA polymerase II binding was accompanied by reduced binding of many other core transcription proteins and gain of chromatin remodelers. In quiescent cells, where strong transcriptional repression is induced by physiological signals...
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  10. Research: Genome-wide uniformity of human ‘open’ pre-initiation complexes
    • William K.M. Lai and
    • B. Franklin Pugh
    Genome Res. January 2017 27: 15-26; Published in Advance November 10, 2016, doi:10.1101/gr.210955.116
    ...of general transcription factors such as TFIIB and RNA polymerase II (Pol II) and strand-separated or open DNA (Kostrewa et al. 2009; He et al. 2013; Sainsbury et al. 2015; Bernecky et al. 2016; Louder et al. 2016). Once Pol II initiates transcription, it then forms a paused complex (PC) 20–60 bp downstream...
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