Searching journal content for articles similar to Verfaillie et al. 26 (7): 882.

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  1. Perspective: Challenges and considerations for reproducibility of STARR-seq assays
    • Maitreya Das,
    • Ayaan Hossain,
    • Deepro Banerjee,
    • Craig Alan Praul,
    • and Santhosh Girirajan
    Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
    ...reporter assays are high-throughput assays that quantify the activity of a test fragment, typically cloned downstream from a minimal promoter, via massively parallel sequencing of barcoded reporter transcripts.Multiplexing: A process in which multiple libraries are pooled and sequenced on the same lane...
  2. Research: Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity
    • Zdenek Andrysik,
    • Matthew D. Galbraith,
    • Anna L. Guarnieri,
    • Sara Zaccara,
    • Kelly D. Sullivan,
    • Ahwan Pandey,
    • Morgan MacBeth,
    • Alberto Inga,
    • and Joaquín M. Espinosa
    Genome Res. October 2017 27: 1645-1657; Published in Advance September 13, 2017, doi:10.1101/gr.220533.117
    ...-occupancy TP53 enhancers, high levels of paused RNA polymerases, and accessible chromatin. Interestingly, two different shRNA screens failed to identify a single TP53 target gene required for the anti-proliferative effects of TP53 during pharmacological activation in vitro. Furthermore, bioinformatics analysis...
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  3. Research: The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions
    • Julie Dubois-Chevalier,
    • Vanessa Dubois,
    • Hélène Dehondt,
    • Parisa Mazrooei,
    • Claire Mazuy,
    • Aurélien A. Sérandour,
    • Céline Gheeraert,
    • Penderia Guillaume,
    • Eric Baugé,
    • Bruno Derudas,
    • Nathalie Hennuyer,
    • Réjane Paumelle,
    • Guillemette Marot,
    • Jason S. Carroll,
    • Mathieu Lupien,
    • Bart Staels,
    • Philippe Lefebvre,
    • and Jérôme Eeckhoute
    Genome Res. June 2017 27: 985-996; Published in Advance April 11, 2017, doi:10.1101/gr.217075.116
    ...in higher eukaryotes as well as their ability to respond and adapt to changing environmental conditions. While active TP53-recruiting cis-regulatory modules (CRMs) were shown to harbor an unsophisticated organization and very low complexity (Verfaillie et al. 2016), other studies have demonstrated...
  4. Research: Enhancers display constrained sequence flexibility and context-specific modulation of motif function
    • Franziska Reiter,
    • Bernardo P. de Almeida,
    • and Alexander Stark
    Genome Res. March 2023 33: 346-358; Published in Advance March 20, 2023, doi:10.1101/gr.277246.122
    ...STARR trained on -wide enhancer activity data (de Almeida et al. 2022) and the BPNet model trained on endogenous TF binding and cooperativity (Avsec et al. 2021), suggesting that these rules are important in wild-type enhancer sequences. As an ectopic reporter assay STARR-seq measures the potential of sequences...
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