Mechanisms that Specify Promoter Nucleosome Location and Identity

[1]  S. Henikoff,et al.  Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks , 2008, Nature.

[2]  M. Segal Re-Cracking the Nucleosome Positioning Code , 2008, Statistical applications in genetics and molecular biology.

[3]  Bryan J Venters,et al.  A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. , 2008, Genome research.

[4]  M. Gerstein,et al.  The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.

[5]  Stephan C. Schuster,et al.  Nucleosome organization in the Drosophila genome , 2008, Nature.

[6]  E. O’Shea,et al.  Chromatin decouples promoter threshold from dynamic range , 2008, Nature.

[7]  Dustin E. Schones,et al.  Dynamic Regulation of Nucleosome Positioning in the Human Genome , 2008, Cell.

[8]  B. Cairns,et al.  RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes , 2008, The EMBO journal.

[9]  Guo-Cheng Yuan,et al.  Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion , 2007, PLoS Comput. Biol..

[10]  Oliver J. Rando,et al.  Chromatin remodelling at promoters suppresses antisense transcription , 2007, Nature.

[11]  Steven J. M. Jones,et al.  Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation , 2007, PLoS biology.

[12]  Ronald W. Davis,et al.  A high-resolution atlas of nucleosome occupancy in yeast , 2007, Nature Genetics.

[13]  William Stafford Noble,et al.  Nucleosome positioning signals in genomic DNA. , 2007, Genome research.

[14]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[15]  I. Albert,et al.  Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome , 2007, Nature.

[16]  Jun S. Song,et al.  High-throughput mapping of the chromatin structure of human promoters , 2007, Nature Biotechnology.

[17]  G. Narlikar,et al.  The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing , 2006, Nature Structural &Molecular Biology.

[18]  I. Albert,et al.  Nucleosome positions predicted through comparative genomics , 2006, Nature Genetics.

[19]  Irene K. Moore,et al.  A genomic code for nucleosome positioning , 2006, Nature.

[20]  B. Pugh,et al.  Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. , 2006, Genes & development.

[21]  Toshio Tsukiyama,et al.  Antagonistic forces that position nucleosomes in vivo , 2006, Nature Structural &Molecular Biology.

[22]  J. Workman,et al.  Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Mathieu Blanchette,et al.  Variant Histone H2A.Z Is Globally Localized to the Promoters of Inactive Yeast Genes and Regulates Nucleosome Positioning , 2005, PLoS biology.

[24]  S. Schreiber,et al.  Histone Variant H2A.Z Marks the 5′ Ends of Both Active and Inactive Genes in Euchromatin , 2005, Cell.

[25]  B. Cairns,et al.  Genome-Wide Dynamics of Htz1, a Histone H2A Variant that Poises Repressed/Basal Promoters for Activation through Histone Loss , 2005, Cell.

[26]  G. Krauss,et al.  In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae , 2005, FEBS letters.

[27]  Lani F. Wu,et al.  Genome-Scale Identification of Nucleosome Positions in S. cerevisiae , 2005, Science.

[28]  Nicola J. Rinaldi,et al.  Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.

[29]  S. Schreiber,et al.  Global nucleosome occupancy in yeast , 2004, Genome Biology.

[30]  David R. Liu,et al.  Directed evolution of ligand dependence: small-molecule-activated protein splicing. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[31]  D. Gordenin,et al.  Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  U. Oechsner,et al.  Reb1p-dependent DNA Bending Effects Nucleosome Positioning and Constitutive Transcription at the Yeast Profilin Promoter* , 2003, The Journal of Biological Chemistry.

[33]  Hiten D. Madhani,et al.  Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin , 2003, Cell.

[34]  Kevin Struhl,et al.  Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. , 2002, Genes & development.

[35]  S. Dudoit,et al.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. , 2002, Nucleic acids research.

[36]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[37]  B. Stillman,et al.  Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair. , 1999, Genes & development.

[38]  B. Cairns,et al.  Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. , 1999, Molecular cell.

[39]  Paul Tempst,et al.  RSC, an Essential, Abundant Chromatin-Remodeling Complex , 1996, Cell.

[40]  C. Brandl,et al.  Defining the sequence specificity of the Saccharomyces cerevisiae DNA binding protein REB1p by selecting binding sites from random‐sequence oligonucleotides , 1994, Yeast.

[41]  L. Grivell,et al.  The multifunctional regulatory proteins ABF1 and CPF1 are involved in the formation of a nuclease‐hypersensitive region in the promoter of the QCR8 gene , 1993, Yeast.

[42]  R. Young,et al.  Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis , 1987, Molecular and cellular biology.

[43]  Y. Aloni,et al.  A nucleosome-free region in SV40 minichromosomes , 1980, Nature.

[44]  M. Yaniv,et al.  Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA , 1980, Cell.

[45]  R. Dohmen,et al.  Heat-inducible degron and the making of conditional mutants. , 2005, Methods in enzymology.

[46]  R. Kornberg,et al.  RSC unravels the nucleosome. , 2001, Molecular cell.