Absence of a simple code: How transcription factors read the genome

Matthew Slattery, Tianyin Zhou, Lin Yang, Ana Carolina Dantas Machado, Raluca Gordân, Remo Rohs

Research output: Contribution to journalReview articlepeer-review

227 Scopus citations


Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs based on 3D structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.

Original languageEnglish (US)
Pages (from-to)381-399
Number of pages19
JournalTrends in Biochemical Sciences
Issue number9
StatePublished - Sep 2014


  • Chromatin
  • Cofactor
  • Cooperativity
  • DNA binding specificity models
  • High-throughput binding assays
  • Protein-DNA recognition

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