Searching journal content for articles similar to Guo et al. 19 (7): 1301.

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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
    ...).Predicted regulatory sites can be validated experimentally using reporter gene assays. In this assay, the transcriptional activity of a predicted promoter, or an enhancer, of a specific GOI can be investigated using plasmids that include the predicted regulatory sequence upstream of a reporter gene (for...
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  2. Research: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha
    • James M. Davison,
    • Colin R. Lickwar,
    • Lingyun Song,
    • Ghislain Breton,
    • Gregory E. Crawford,
    • and John F. Rawls
    Genome Res. July 2017 27: 1195-1206; Published in Advance April 6, 2017, doi:10.1101/gr.220111.116
    ...possiblemode ofHNF4A regulation bywhich themicrobiota could suppress HNF4A activitywithout impacting the gene transcription of all HNF4A-associated genes. Methods Yeast one-hybrid ORFeome screen The yeast one-hybrid ORFeome screen was performed using the Clontech Matchmaker Gold Yeast One-hybrid Library...
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  3. REVIEW: Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
    • Albertha J.M. Walhout
    Genome Res. December 2006 16: 1445-1454; Published in Advance October 19, 2006, doi:10.1101/gr.5321506
    ...-throughput methods for protein–DNA interaction mapping. ( A ) protein–DNA interactions can be mapped using either TF- or gene-centered methods, as indicated by the arrows. Y1H, yeast one-hybrid assays; ChIP, chromatin-immunoprecipitations; PBM, protein binding microarray; B1H, bacterial one-hybrid system; Dam...
  4. Perspective: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
    • Lesley T. MacNeil and
    • Albertha J.M. Walhout
    Genome Res. May 2011 21: 645-657; Published in Advance February 4, 2011, doi:10.1101/gr.097378.109
    .... At the level of mRNA synthesis, transcription factors (TFs) control gene expression by directly interacting with cis-regulatory genomicDNA sequences that are usually located in or around their target genes. Changes in the abundance or activity of TFs can result in an increase or decrease in the expression...
  5. Research: Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions
    • Marina Naval-Sánchez,
    • Delphine Potier,
    • Lotte Haagen,
    • Máximo Sánchez,
    • Sebastian Munck,
    • Bram Van de Sande,
    • Fernando Casares,
    • Valerie Christiaens,
    • and Stein Aerts
    Genome Res. January 2013 23: 74-88; Published in Advance October 15, 2012, doi:10.1101/gr.140426.112
    ...The identification of transcription factor binding sites, enhancers, and transcriptional target genes often relies on the integration of gene expression profiling and computational cis-regulatory sequence analysis. Methods for the prediction of cis-regulatory elements can take advantage of comparative genomics...
  6. Method: SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
    • Liyang Zhang,
    • Gabriella D. Martini,
    • H. Tomas Rube,
    • Judith F. Kribelbauer,
    • Chaitanya Rastogi,
    • Vincent D. FitzPatrick,
    • Jon C. Houtman,
    • Harmen J. Bussemaker,
    • and Miles A. Pufall
    Genome Res. January 2018 28: 111-121; Published in Advance December 1, 2017, doi:10.1101/gr.222844.117
    ...) protein binding microarrays (PBMs) (Berger and Bulyk 2009), bacterial one-hybrid (B1H) (Meng et al. 2005), and (solution-based) high-throughput SELEX (HT-SELEX) (Zhao et al. 2009; Jolma et al. 2010, 2013). These methods have generated rich data sets that have been exploited to define DNA-binding ‘motifs...
  7. Erratum: Erratum Genome Res. September 2009 19: 1691
    ...genome;19/9/1691 1088-9051 Erratum Erratum Genome Research 19: 1301–1308 (2009) Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system Manman Guo, Hui Feng, Jun Zhang, Wenqin Wang, Yi Wang, Yuqing Li, Chunhui Gao, Huanchun Chen, Ying Feng, and Zheng-Guo He...
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