Searching journal content for articles similar to Hughes et al. 28 (10): 1520.

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  1. Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
    • Yiqiao Zheng,
    • Gary D. Stormo,
    • and Shiming Chen
    Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
    ...of nonchromatin templates, we selected and tested a representative set of CRX-bound cis-regulatory elements (CREs) in episomal plasmids with massively parallel reporter assays (MPRAs) in explant WT and mutant mouse retinas (Methods; Fig. 7A; Supplemental Fig. S7A,B). We measured the regulatory activities...
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  2. Research: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
    • James L. Shepherdson,
    • Ryan Z. Friedman,
    • Yiqiao Zheng,
    • Chi Sun,
    • Inez Y. Oh,
    • David M. Granas,
    • Barak A. Cohen,
    • Shiming Chen,
    • and Michael A. White
    Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
    ...-regulatory function by deploying massively parallel reporter assays (MPRAs) in mouse retina explants carrying knock-ins of two variants, one in the DNA-binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation in these mutant Crx retinas...
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  3. Research: Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
    • Metewo Selase Enuameh,
    • Yuna Asriyan,
    • Adam Richards,
    • Ryan G. Christensen,
    • Victoria L. Hall,
    • Majid Kazemian,
    • Cong Zhu,
    • Hannah Pham,
    • Qiong Cheng,
    • Charles Blatti,
    • Jessie A. Brasefield,
    • Matthew D. Basciotta,
    • Jianhong Ou,
    • Joseph C. McNulty,
    • Lihua J. Zhu,
    • Susan E. Celniker,
    • Saurabh Sinha,
    • Gary D. Stormo,
    • Michael H. Brodsky,
    • and Scot A. Wolfe
    Genome Res. June 2013 23: 928-940; Published in Advance March 7, 2013, doi:10.1101/gr.151472.112
    ...Global analysis of Drosophila Cys 2 -His 2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants Metewo Selase Enuameh 1 , Yuna Asriyan 1 , Adam Richards 1 , Ryan G. Christensen 2 , Victoria L. Hall 1...
  4. Research: Systematic interrogation of human promoters
    • Shira Weingarten-Gabbay,
    • Ronit Nir,
    • Shai Lubliner,
    • Eilon Sharon,
    • Yael Kalma,
    • Adina Weinberger,
    • and Eran Segal
    Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
    ...expression, we and others have developed massively parallel reporter assays (MPRAs) probing the expression of various regulatory regions (Kwasnieski et al. 2012; Melnikov et al. 2012; Patwardhan et al. 2012; Sharon et al. 2012; Shalem et al. 2015). However, since these measurements are performed using...
  5. RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
    • Joshua L. Wetzel,
    • Kaiqian Zhang,
    • and Mona Singh
    Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
    ...–PWM pairs using previously determined known protein–DNA interfaces. Specifically, in the first large-scale assay of homeodomains in the fruit fly, DNA-binding specificities were characterized in a specialized experimental system that specifically allowed for a global alignment (with known orientation...
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  6. Resource: PRISM offers a comprehensive genomic approach to transcription factor function prediction
    • Aaron M. Wenger,
    • Shoa L. Clarke,
    • Harendra Guturu,
    • Jenny Chen,
    • Bruce T. Schaar,
    • Cory Y. McLean,
    • and Gill Bejerano
    Genome Res. May 2013 23: 889-904; Published in Advance February 4, 2013, doi:10.1101/gr.139071.112
    ..., which we call GREAT (for genomic regions enrichment of annotations tool) (McLean et al. 2010). GREATand similar analyses reveal yet another key property of ChIP-seq experiments—their context dependence. While TFs are often pleiotropic, playing key roles in multiple independent cellular contexts, a Ch...
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