Searching journal content for articles similar to Enuameh et al. 23 (6): 928.

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  1. 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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  2. Research: Exploring the DNA-recognition potential of homeodomains
    • Stephanie W. Chu,
    • Marcus B. Noyes,
    • Ryan G. Christensen,
    • Brian G. Pierce,
    • Lihua J. Zhu,
    • Zhiping Weng,
    • Gary D. Stormo,
    • and Scot A. Wolfe
    Genome Res. October 2012 22: 1889-1898; Published in Advance April 26, 2012, doi:10.1101/gr.139014.112
    ...the five key residues, residues 43, 46, 47, 50, and 54, from each of the seven HD variants within the sample set into three otherDrosophila melanogasterHD backbones: DFD, SCR, andUBX. These HDs share 53%, 51%, and 46% identity with Engrailed, respectively. We then determined the DNA-binding specificity...
  3. Perspective: Enabling functional genomics with genome engineering
    • Isaac B. Hilton and
    • Charles A. Gersbach
    Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
    ...occur with dCas9-based transcriptional/epigenetic modifiers, assessments of global gene expression suggest that changes are largely restricted to the intended target sites (Gilbert et al. 2013; PerezPinera et al. 2013a; Hilton et al. 2015; Polstein et al. 2015). Cas9 nucleases have also been found...
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  4. Research: A widespread role of the motif environment in transcription factor binding across diverse protein families
    • Iris Dror,
    • Tamar Golan,
    • Carmit Levy,
    • Remo Rohs,
    • and Yael Mandel-Gutfreund
    Genome Res. September 2015 25: 1268-1280; Published in Advance July 9, 2015, doi:10.1101/gr.184671.114
    ...regions around the binding motifs. Moreover, we show that the preferred nucleotide content has an overall high similarity to the core motif and exhibits unique DNA structural features. These results emphasize the intrinsic role of the sequence environment in protein–DNA recognition. We propose...
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