DNA Footprinting

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  Subject Areas on Research

  • A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. 
  • A developmental switch from TCR delta enhancer to TCR alpha enhancer function during thymocyte maturation. 
  • A hot spot for hydrogen peroxide-induced damage in the human hypoxia-inducible factor 1 binding site of the PGK 1 gene. 
  • An integrated encyclopedia of DNA elements in the human genome. 
  • Analyses of promoter-proximal pausing by RNA polymerase II on the hsp70 heat shock gene promoter in a Drosophila nuclear extract. 
  • Base-pairing potential identified by in vitro selection predicts the kinked RNA backbone observed in the crystal structure of the alfalfa mosaic virus RNA-coat protein complex. 
  • Characterization of the SarA virulence gene regulator of Staphylococcus aureus. 
  • Characterization of the rat type III hexokinase gene promoter. A functional octamer 1 motif is critical for basal promoter activity. 
  • Cloning and characterization of a novel endothelial promoter of the human CYP19 (aromatase P450) gene that is up-regulated in breast cancer tissue. 
  • Cooperation among multiple transcription factors is required for access to minimal T-cell receptor alpha-enhancer chromatin in vivo. 
  • DNase I sensitivity QTLs are a major determinant of human expression variation. 
  • Distinct roles for c-Myb and core binding factor/polyoma enhancer-binding protein 2 in the assembly and function of a multiprotein complex on the TCR delta enhancer in vivo. 
  • Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. 
  • Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. 
  • GABP and PU.1 compete for binding, yet cooperate to increase CD18 (beta 2 leukocyte integrin) transcription. 
  • Identification of an enhancer element in the estrogen receptor upstream region: implications for regulation of ER transcription in breast cancer. 
  • Mapping of peroxyl radical induced damage on genomic DNA. 
  • Phylogenetic footprint analysis of IGF2 in extant mammals. 
  • Predicting cell-type-specific gene expression from regions of open chromatin. 
  • The CovR response regulator of group A streptococcus (GAS) acts directly to repress its own promoter. 
  • The accessible chromatin landscape of the human genome. 
  • The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding. 
  • The human T-cell leukemia virus-1 transcriptional activator Tax enhances cAMP-responsive element-binding protein (CREB) binding activity through interactions with the DNA minor groove. 
  • Yin Yang 1 contains G-quadruplex structures in its promoter and 5'-UTR and its expression is modulated by G4 resolvase 1. 
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  Keywords of People

  • Krangel, Michael S., George Barth Geller Distinguished Professor of Immunology, Immunology