The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism

ISWI family chromatin remodelers typically organize nucleosome arrays, while SWI/SNF family remodelers (RSC) typically disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism and reveal different mechanisms at two different promoter architectures. DOI: http://dx.doi.org/10.7554/eLife.06073.001

[1]  A. Johnsson,et al.  HAT–HDAC interplay modulates global histone H3K14 acetylation in gene‐coding regions during stress , 2009, EMBO reports.

[2]  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.

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

[4]  T. Borodina,et al.  Transcriptome analysis by strand-specific sequencing of complementary DNA , 2009, Nucleic acids research.

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

[6]  Bradley R Cairns,et al.  Histone trimethylation by Set1 is coordinated by the RRM, autoinhibitory, and catalytic domains , 2005, The EMBO journal.

[7]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[8]  T. Hughes,et al.  A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription , 2013, PLoS genetics.

[9]  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.

[10]  David A. Nix,et al.  Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks , 2008, BMC Bioinformatics.

[11]  B. Cairns,et al.  The RSC Chromatin Remodeling Complex Bears an Essential Fungal-Specific Protein Module With Broad Functional Roles , 2006, Genetics.

[12]  Anjanabha Saha,et al.  Chromatin remodeling through directional DNA translocation from an internal nucleosomal site , 2005, Nature Structural &Molecular Biology.

[13]  B. Pugh,et al.  Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers , 2012, Cell.

[14]  K. Nightingale,et al.  A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. , 2002, Nucleic acids research.

[15]  Nils Krietenstein,et al.  The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening , 2014, Nucleic acids research.

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

[17]  Vamsi K. Gangaraju,et al.  Dependency of ISW1a Chromatin Remodeling on Extranucleosomal DNA , 2007, Molecular and Cellular Biology.

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

[19]  G. Längst,et al.  Critical Role for the Histone H4 N Terminus in Nucleosome Remodeling by ISWI , 2001, Molecular and Cellular Biology.

[20]  E. Segal,et al.  Poly(da:dt) Tracts: Major Determinants of Nucleosome Organization This Review Comes from a Themed Issue on Protein-nucleic Acid Interactions Edited , 2022 .

[21]  L. Pillus,et al.  Functional Antagonism between Sas3 and Gcn5 Acetyltransferases and ISWI Chromatin Remodelers , 2012, PLoS genetics.

[22]  J Seth Strattan,et al.  Removal of promoter nucleosomes by disassembly rather than sliding in vivo. , 2004, Molecular cell.

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

[24]  T. Richmond,et al.  Structure and mechanism of the chromatin remodelling factor ISW1a , 2011, Nature.

[25]  B. Bartholomew,et al.  Regulating the chromatin landscape: structural and mechanistic perspectives. , 2014, Annual review of biochemistry.

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

[27]  E. Moran,et al.  Antagonistic Roles for BRM and BRG1 SWI/SNF Complexes in Differentiation , 2009, Journal of Biological Chemistry.

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

[29]  M. Petter,et al.  The Role of Bromodomain Proteins in Regulating Gene Expression , 2012, Genes.

[30]  T. Tsukiyama,et al.  Two Distinct Mechanisms of Chromatin Interaction by the Isw2 Chromatin Remodeling Complex In Vivo , 2005, Molecular and Cellular Biology.

[31]  Jerry L. Workman,et al.  ATP-Dependent Chromatin-Remodeling Complexes , 2000, Molecular and Cellular Biology.

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

[33]  B. Cairns,et al.  The biology of chromatin remodeling complexes. , 2009, Annual review of biochemistry.

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

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

[36]  N. Barkai,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Widespread remodeling of mid-coding sequence nucleosomes by Isw1 , 2010 .

[37]  Roger D Kornberg,et al.  Histone Octamer Transfer by a Chromatin-Remodeling Complex , 1999, Cell.

[38]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[39]  P. Grant,et al.  Histone H3 specific acetyltransferases are essential for cell cycle progression. , 2001, Genes & development.

[40]  Irene K. Moore,et al.  The DNA-encoded nucleosome organization of a eukaryotic genome , 2009, Nature.

[41]  N. Barkai,et al.  Two strategies for gene regulation by promoter nucleosomes. , 2008, Genome research.

[42]  B. Cairns,et al.  A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control. , 2001, Molecular cell.

[43]  L. Steinmetz,et al.  Bidirectional promoters generate pervasive transcription in yeast , 2009, Nature.

[44]  D. Moazed,et al.  Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA , 2013, Proceedings of the National Academy of Sciences.

[45]  Aviv Regev,et al.  Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. , 2011, Genome research.

[46]  P. Philippsen,et al.  Additional modules for versatile and economical PCR‐based gene deletion and modification in Saccharomyces cerevisiae , 1998, Yeast.

[47]  J. Raser,et al.  Control of Stochasticity in Eukaryotic Gene Expression , 2004, Science.

[48]  S. Henikoff,et al.  Regulation of nucleosome dynamics by histone modifications , 2013, Nature Structural &Molecular Biology.

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

[50]  H. A. Cole,et al.  RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast , 2014, Genome research.

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

[52]  C. Kooperberg,et al.  Yeast Isw1p Forms Two Separable Complexes In Vivo , 2003, Molecular and Cellular Biology.

[53]  C. Müller,et al.  Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. , 2003, Molecular cell.

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

[55]  Nicholas Proudfoot,et al.  Isw1 Chromatin Remodeling ATPase Coordinates Transcription Elongation and Termination by RNA Polymerase II , 2003, Cell.

[56]  B. Cairns,et al.  Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. , 2007, Molecular cell.

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

[58]  J. Palmer,et al.  Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. , 1999, Genes & development.

[59]  Brett Milash,et al.  Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping , 2008, Nature Genetics.

[60]  S. Smale,et al.  Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. , 2006, Genes & development.

[61]  T. Owen-Hughes,et al.  Histone Modifications Influence the Action of Snf2 Family Remodelling Enzymes by Different Mechanisms , 2007, Journal of molecular biology.

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

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

[64]  Poethig Rs,et al.  Life with 25,000 genes. , 2001 .

[65]  C. Kooperberg,et al.  Widespread Collaboration of Isw2 and Sin3-Rpd3 Chromatin Remodeling Complexes in Transcriptional Repression , 2001, Molecular and Cellular Biology.

[66]  T. Owen-Hughes,et al.  Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes , 2013, Cell.

[67]  M. L. Dechassa,et al.  SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. , 2010, Molecular cell.

[68]  H. Szerlong,et al.  Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14 , 2004, The EMBO journal.

[69]  M. Grunstein,et al.  Acetylation of yeast histone H4 lysine 16: a switch for protein interactions in heterochromatin and euchromatin. , 2004, Cold Spring Harbor symposia on quantitative biology.

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

[71]  Ian M. Fingerman,et al.  A charge-based interaction between histone H4 and Dot1 is required for H3K79 methylation and telomere silencing: identification of a new trans-histone pathway. , 2007, Genes & development.

[72]  Song Tan,et al.  Interplay of chromatin modifiers on a short basic patch of histone H4 tail defines the boundary of telomeric heterochromatin. , 2007, Molecular cell.

[73]  B. Cairns.  The logic of chromatin architecture and remodelling at promoters , 2009, Nature.

[74]  Stuart L Schreiber,et al.  Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. , 2003, Molecular cell.

[75]  Zhengjian Zhang,et al.  A Novel Mechanism of Antagonism between ATP-Dependent Chromatin Remodeling Complexes Regulates RNR3 Expression , 2009, Molecular and Cellular Biology.

[76]  S. Grewal,et al.  The Prevalence and Regulation of Antisense Transcripts in Schizosaccharomyces pombe , 2010, PloS one.