Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome.

A canonical nucleosome architecture around promoters establishes the context in which proteins regulate gene expression. Whether gene regulatory proteins that interact with nucleosomes are selective for individual nucleosome positions across the genome is not known. Here, we examine on a genomic scale several protein-nucleosome interactions, including those that (1) bind histones (Bdf1/SWR1 and Srm1), (2) bind specific DNA sequences (Rap1 and Reb1), and (3) potentially collide with nucleosomes during transcription (RNA polymerase II). We find that the Bdf1/SWR1 complex forms a dinucleosome complex that is selective for the +1 and +2 nucleosomes of active genes. Rap1 selectively binds to its cognate site on the rotationally exposed first and second helical turn of nucleosomal DNA. We find that a transcribing RNA polymerase creates a delocalized state of resident nucleosomes. These findings suggest that nucleosomes around promoter regions have position-specific functions and that some gene regulators have position-specific nucleosomal interactions.

[1]  P. Grant,et al.  NuA4, an essential transcription adaptor/histone H4 acetyltransferase complex containing Esa1p and the ATM‐related cofactor Tra1p , 1999, The EMBO journal.

[2]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[3]  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.

[4]  L. Chapman,et al.  Specific interactions of the telomeric protein Rap1p with nucleosomal binding sites. , 2001, Journal of molecular biology.

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

[6]  J. Majors,et al.  The chromatin structure of the GAL1 promoter forms independently of Reb1p in Saccharomyces cerevisiae , 1998, Molecular and General Genetics MGG.

[7]  Dinshaw J. Patel,et al.  Multivalent engagement of chromatin modifications by linked binding modules , 2007, Nature Reviews Molecular Cell Biology.

[8]  J. Workman,et al.  RSC exploits histone acetylation to abrogate the nucleosomal block to RNA polymerase II elongation. , 2006, Molecular cell.

[9]  S. Holmberg,et al.  Neither Reb1p nor Poly(dA·dT) Elements Are Responsible for the Highly Specific Chromatin Organization at the ILV1Promoter* , 2002, The Journal of Biological Chemistry.

[10]  B. Cairns,et al.  The Interactions of Yeast SWI/SNF and RSC with the Nucleosome before and after Chromatin Remodeling* , 2001, The Journal of Biological Chemistry.

[11]  S. Buratowski,et al.  Bromodomain factor 1 corresponds to a missing piece of yeast TFIID. , 2000, Genes & development.

[12]  J. L. Rosa,et al.  The RCC1 superfamily: from genes, to function, to disease. , 2008, Biochimica et biophysica acta.

[13]  R. Tjian,et al.  Structure and function of a human TAFII250 double bromodomain module. , 2000, Science.

[14]  Nir Friedman,et al.  Dynamics of Replication-Independent Histone Turnover in Budding Yeast , 2007, Science.

[15]  M. Gartenberg.  The Sir proteins of Saccharomyces cerevisiae: mediators of transcriptional silencing and much more. , 2000, Current opinion in microbiology.

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

[17]  Karl Mechtler,et al.  Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins , 2001, Nature.

[18]  S. Buratowski,et al.  Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. , 2003, Molecular cell.

[19]  Clifford A. Meyer,et al.  Model-based analysis of tiling-arrays for ChIP-chip , 2006, Proceedings of the National Academy of Sciences.

[20]  Andrew J. Bannister,et al.  Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain , 2001, Nature.

[21]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[22]  B. Bartholomew,et al.  Domain Architecture of the Catalytic Subunit in the ISW2-Nucleosome Complex , 2007, Molecular and Cellular Biology.

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

[24]  Manolis Kellis,et al.  RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo , 2007, Nature Genetics.

[25]  Andrew J. Link,et al.  Proteomics of the Eukaryotic Transcription Machinery: Identification of Proteins Associated with Components of Yeast TFIID by Multidimensional Mass Spectrometry , 2002, Molecular and Cellular Biology.

[26]  J. Workman,et al.  Histone Acetyltransferase Complexes Stabilize SWI/SNF Binding to Promoter Nucleosomes , 2001, Cell.

[27]  S. Schreiber,et al.  Histone Variant H2A.Z Marks the 5′ Ends of Both Active and Inactive Genes in Euchromatin , 2006, Cell.

[28]  K. Struhl,et al.  Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo , 2009, Nature Structural &Molecular Biology.

[29]  H. Madhani,et al.  Mechanisms that Specify Promoter Nucleosome Location and Identity , 2009, Cell.

[30]  J. Lieb,et al.  A chromatin-mediated mechanism for specification of conditional transcription factor targets , 2006, Nature Genetics.

[31]  M. Aebi,et al.  A yeast mutant, PRP20, altered in mRNA metabolism and maintenance of the nuclear structure, is defective in a gene homologous to the human gene RCC1 which is involved in the control of chromosome condensation , 1990, Molecular and General Genetics MGG.

[32]  D. Shore,et al.  RAP1: a protean regulator in yeast. , 1994, Trends in genetics : TIG.

[33]  D. S. Gross,et al.  Heat shock factor gains access to the yeast HSC82 promoter independently of other sequence-specific factors and antagonizes nucleosomal repression of basal and induced transcription , 1996, Molecular and cellular biology.

[34]  Ruchir Shah,et al.  RNA polymerase is poised for activation across the genome , 2007, Nature Genetics.

[35]  Steven M. Johnson,et al.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.

[36]  K. Garbett,et al.  Yeast TFIID Serves as a Coactivator for Rap1p by Direct Protein-Protein Interaction , 2006, Molecular and Cellular Biology.

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

[38]  Timothy J. Richmond,et al.  Interactions of Isw2 Chromatin Remodeling Complex with Nucleosomal Arrays: Analyses Using Recombinant Yeast Histones and Immobilized Templates , 2001, Molecular and Cellular Biology.

[39]  F. Robert,et al.  Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. , 2007, Molecular cell.

[40]  Anjanabha Saha,et al.  Chromatin remodeling by RSC involves ATP-dependent DNA translocation. , 2002, Genes & development.

[41]  Istvan Albert,et al.  GeneTrack - a genomic data processing and visualization framework , 2008, Bioinform..

[42]  Wolfgang Huber,et al.  A high-resolution map of transcription in the yeast genome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Daria A. Gaykalova,et al.  Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II. , 2006, Molecular cell.

[44]  R. Morse,et al.  Chromatin Opening and Transactivator Potentiation by RAP1 in Saccharomyces cerevisiae , 1999, Molecular and Cellular Biology.

[45]  B. Pugh,et al.  NuA4-Directed Chromatin Transactions throughout the Saccharomyces cerevisiae Genome , 2007, Molecular and Cellular Biology.

[46]  C. Allis,et al.  Chromatin docking and exchange activity enhancement of RCC1 by histones H2A and H2B. , 2001, Science.

[47]  E. Serra,et al.  Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association , 2001, Nature Genetics.

[48]  Huiming Ding,et al.  A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. , 2003, Molecular cell.

[49]  Bryan J Venters,et al.  A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome , 2008, Genome research.

[50]  J. Workman,et al.  Function and Selectivity of Bromodomains in Anchoring Chromatin-Modifying Complexes to Promoter Nucleosomes , 2002, Cell.

[51]  Andrew J Link,et al.  A Protein Complex Containing the Conserved Swi2/Snf2-Related ATPase Swr1p Deposits Histone Variant H2A.Z into Euchromatin , 2004, PLoS biology.

[52]  J. Workman,et al.  Nucleosome binding by the constitutive transcription factor Sp1. , 1994, The Journal of biological chemistry.

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

[54]  E. Spencer.  From the Library , 1936, British Journal of Ophthalmology.

[55]  D. Shore,et al.  RAP1 protein activates and silences transcription of mating-type genes in yeast. , 1991, Genes & development.

[56]  Michael P Washburn,et al.  The HIR corepressor complex binds to nucleosomes generating a distinct protein/DNA complex resistant to remodeling by SWI/SNF. , 2005, Genes & development.

[57]  W. Bandlow,et al.  The general regulatory factor Reb1p controls basal, but not Gal4p-mediated, transcription of the GCY1 gene in yeast , 1997, Molecular and General Genetics MGG.

[58]  Christopher L. Warren,et al.  A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. , 2008, Molecular cell.