Poly(dA-dT) Promoter Elements Increase the Equilibrium Accessibility of Nucleosomal DNA Target Sites

ABSTRACT Polypurine tracts are important elements of eukaryotic promoters. They are believed to somehow destabilize chromatin, but the mechanism of their action is not known. We show that incorporating an A16 element at an end of the nucleosomal DNA and further inward destabilizes histone-DNA interactions by 0.1 ± 0.03 and 0.35 ± 0.04 kcal mol−1, respectively, and is accompanied by 1.5- ± 0.1-fold and 1.7- ± 0.1-fold increases in position-averaged equilibrium accessibility of nucleosomal DNA target sites. These effects are comparable in magnitude to effects of A16 elements that correlate with transcription in vivo, suggesting that our system may capture most of their physiological role. These results point to two distinct but interrelated models for the mechanism of action of polypurine tract promoter elements in vivo. Given a nucleosome positioned over a promoter region, the presence of a polypurine tract in that nucleosome's DNA decreases the stability of the DNA wrapping, increasing the equilibrium accessibility of other DNA target sites buried inside that nucleosome. Alternatively (if nucleosomes are freely mobile), the presence of a polypurine tract provides a free energy bias for the nucleosome to move to alternative locations, thereby changing the equilibrium accessibilities of other nearby DNA target sites.

[1]  R. Simpson,et al.  Structural features of a phased nucleosome core particle. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[2]  K. Struhl.  Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[3]  K. Struhl,et al.  Distinguishing between mechanisms of eukaryotic transcriptional activation with bacteriophage T7 RNA polymerase , 1987, Cell.

[4]  A. Klug,et al.  The structure of an oligo(dA)·oligo(dT) tract and its biological implications , 1987, Nature.

[5]  A. Travers,et al.  Asymmetry and polarity of nucleosomes in chicken erythrocyte chromatin. , 1989, The EMBO journal.

[6]  F. Thoma,et al.  Poly(dA).poly(dT) rich sequences are not sufficient to exclude nucleosome formation in a constitutive yeast promoter. , 1990, Nucleic acids research.

[7]  A. Wolffe,et al.  The structure of DNA in a nucleosome. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[8]  A. Wolffe,et al.  The histone core exerts a dominant constraint on the structure of DNA in a nucleosome. , 1991, Biochemistry.

[9]  M. Behe,et al.  Isolated oligopurine tracts do not significantly affect the binding of DNA to nucleosomes. , 1992, Biochemistry.

[10]  T. Steitz,et al.  A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend. , 1993, Journal of molecular biology.

[11]  J. Widom,et al.  Lifetime of the histone octamer studied by continuous-flow quasielastic light scattering: test of a model for nucleosome transcription. , 1993, Biochemistry.

[12]  J. Widom,et al.  Twist constraints on linker DNA in the 30-nm chromatin fiber: implications for nucleosome phasing. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[13]  S Karlin,et al.  Assessments of DNA inhomogeneities in yeast chromosome III. , 1993, Nucleic acids research.

[14]  M. Behe.  An overabundance of long oligopurine tracts occurs in the genome of simple and complex eukaryotes. , 1995, Nucleic acids research.

[15]  V. Iyer,et al.  Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. , 1995, The EMBO journal.

[16]  J. Widom,et al.  Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. , 1995, Journal of molecular biology.

[17]  J. Hansen,et al.  Reversible oligonucleosome self-association: dependence on divalent cations and core histone tail domains. , 1996, Biochemistry.

[18]  T. Richmond,et al.  Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Zhiwu Zhu,et al.  A Specialized Nucleosome Modulates Transcription Factor Access to a C. glabrata Metal Responsive Promoter , 1996, Cell.

[20]  M. Waye,et al.  Characterization of nucleosome core particles containing histone proteins made in bacteria. , 1997, Journal of molecular biology.

[21]  J. Widom,et al.  Nucleosome packaging and nucleosome positioning of genomic DNA. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[22]  E. Geiduschek,et al.  Nucleosome mobility and the maintenance of nucleosome positioning. , 1997, Science.

[23]  M. Behe,et al.  Oligoadenosine tracts favor nucleosome formation. , 1997, Biochemical and biophysical research communications.

[24]  J. Widom,et al.  Coupled-enzymatic assays for the rate and mechanism of DNA site exposure in a nucleosome. , 1997, Journal of molecular biology.

[25]  H. Widlund,et al.  TGGA repeats impair nucleosome formation. , 1998, Journal of molecular biology.

[26]  J. Widom,et al.  New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. , 1998, Journal of molecular biology.

[27]  M. Kuroda,et al.  Guilt by association: non-coding RNAs, chromosome-specific proteins and dosage compensation in Drosophila. , 1999, Trends in genetics : TIG.

[28]  Ali Hamiche,et al.  ATP-Dependent Histone Octamer Sliding Mediated by the Chromatin Remodeling Complex NURF , 1999, Cell.

[29]  K. Nasmyth,et al.  Ordered Recruitment of Transcription and Chromatin Remodeling Factors to a Cell Cycle– and Developmentally Regulated Promoter , 2016, Cell.

[30]  R. Kingston,et al.  ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. , 1999, Genes & development.

[31]  J. Widom,et al.  Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. , 1999, Journal of molecular biology.

[32]  G. Längst,et al.  Nucleosome Movement by CHRAC and ISWI without Disruption or trans-Displacement of the Histone Octamer , 1999, Cell.

[33]  K. Nasmyth,et al.  Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. , 1999, Cell.

[34]  J. Widom,et al.  Restriction enzymes as probes of nucleosome stability and dynamics. , 1999, Methods in enzymology.

[35]  Andrew Flaus,et al.  Nucleosome mobilization catalysed by the yeast SWI/SNF complex , 1999, Nature.

[36]  Kevin Struhl,et al.  Preferential Accessibility of the Yeast his3 Promoter Is Determined by a General Property of the DNA Sequence, Not by Specific Elements , 2000, Molecular and Cellular Biology.

[37]  J. Widom,et al.  Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. , 2000, Journal of molecular biology.

[38]  T. Mori,et al.  Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA)·poly(dT) tracts in vivo , 2000 .

[39]  J. Workman,et al.  Promoter targeting and chromatin remodeling by the SWI/SNF complex. , 2000, Current opinion in genetics & development.

[40]  C. Hunter,et al.  Sequence-dependent DNA structure: tetranucleotide conformational maps. , 2000, Journal of molecular biology.

[41]  J. Widom,et al.  Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes. , 2000, Journal of molecular biology.

[42]  J. Widom,et al.  Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites. , 2001, Journal of molecular biology.