title: Absence of a simple code: how transcription factors read the genome.
abstract: 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.
authors.affiliation: Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: mslatter@umn.edu.
authors.forename: Matthew
authors.initials: M
authors.lastname: Slattery
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Tianyin
authors.initials: T
authors.lastname: Zhou
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Yang
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Ana Carolina
authors.initials: AC
authors.lastname: Dantas Machado
authors.affiliation: Center for Genomic and Computational Biology, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA. Electronic address: raluca.gordan@duke.edu.
authors.forename: Raluca
authors.initials: R
authors.lastname: Gordân
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: rohs@usc.edu.
authors.forename: Remo
authors.initials: R
authors.lastname: Rohs
mesh_terms: D000818:Animals; D001665:Binding Sites; D055592:Biophysical Phenomena / Q000235:genetics*; D019295:Computational Biology; D004247:DNA / Q000235:genetics* / Q000378:metabolism; D016678:Genome / Q000235:genetics*; D006801:Humans; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA
keywords: DNA binding specificity models; chromatin; cofactor; cooperativity; high-throughput binding assays; protein-DNA recognition