title: Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping.
abstract: Large-scale DNA deformation is ubiquitous in transcriptional regulation in prokaryotes and eukaryotes alike. Though much is known about how transcription factors and constellations of binding sites dictate where and how gene regulation will occur, less is known about the role played by the intervening DNA. In this work we explore the effect of sequence flexibility on transcription factor-mediated DNA looping, by drawing on sequences identified in nucleosome formation and ligase-mediated cyclization assays as being especially favorable for or resistant to large deformations. We examine a poly(dA:dT)-rich, nucleosome-repelling sequence that is often thought to belong to a class of highly inflexible DNAs; two strong nucleosome positioning sequences that share a set of particular sequence features common to nucleosome-preferring DNAs; and a CG-rich sequence representative of high G+C-content genomic regions that correlate with high nucleosome occupancy in vivo. To measure the flexibility of these sequences in the context of DNA looping, we combine the in vitro single-molecule tethered particle motion assay, a canonical looping protein, and a statistical mechanical model that allows us to quantitatively relate the looping probability to the looping free energy. We show that, in contrast to the case of nucleosome occupancy, G+C content does not positively correlate with looping probability, and that despite sharing sequence features that are thought to determine nucleosome affinity, the two strong nucleosome positioning sequences behave markedly dissimilarly in the context of looping. Most surprisingly, the poly(dA:dT)-rich DNA that is often characterized as highly inflexible in fact exhibits one of the highest propensities for looping that we have measured. These results argue for a need to revisit our understanding of the mechanical properties of DNA in a way that will provide a basis for understanding DNA deformation over the entire range of biologically relevant scenarios that are impacted by DNA deformability.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America ; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Johnson
authors.forename: Yi-Ju
authors.initials: YJ
authors.lastname: Chen
authors.forename: Rob
authors.initials: R
authors.lastname: Phillips
mesh_terms: D020856:AT Rich Sequence / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001482:Base Composition; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D017930:Genes, Reporter; D006801:Humans; D055029:Inverted Repeat Sequences / Q000235:genetics*; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D011067:Poly dA-dT / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D008164:Luminescent Proteins; D009707:Nucleosomes; C054562:yellow fluorescent protein, Bacteria; D011067:Poly dA-dT; D004247:DNA