Global reorganization of budding yeast chromosome conformation in different physiological conditions

Movement of the GAL locus to the nuclear periphery is part of a large-scale rearrangement of chromosome architecture induced by glucose withdrawal and is regulated by the activities of histone acetyltransferases and histone deacetylases.

[1]  P. Grant,et al.  Role of the Ada2 and Ada3 Transcriptional Coactivators in Histone Acetylation* , 2002, The Journal of Biological Chemistry.

[2]  Oreto Antúnez,et al.  Sus1, a Functional Component of the SAGA Histone Acetylase Complex and the Nuclear Pore-Associated mRNA Export Machinery , 2004, Cell.

[3]  K. Thorn,et al.  Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae , 2004, Yeast.

[4]  Sara Ahmed,et al.  DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery , 2010, Nature Cell Biology.

[5]  R. Sikorski,et al.  A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. , 1989, Genetics.

[6]  M. Rosbash,et al.  The nuclear exosome and adenylation regulate posttranscriptional tethering of yeast GAL genes to the nuclear periphery. , 2008, Molecular cell.

[7]  Christophe Zimmer,et al.  A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus , 2012, Current Biology.

[8]  L. Pillus,et al.  The SAGA Subunit Ada2 Functions in Transcriptional Silencing , 2009, Molecular and Cellular Biology.

[9]  S. Gasser,et al.  Modules for cloning‐free chromatin tagging in Saccharomyces cerevisae , 2008, Yeast.

[10]  K. Nasmyth,et al.  Cohesins: Chromosomal Proteins that Prevent Premature Separation of Sister Chromatids , 1997, Cell.

[11]  Bing Li,et al.  Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. , 2011, Molecular cell.

[12]  Christophe Zimmer,et al.  Systematic characterization of the conformation and dynamics of budding yeast chromosome XII , 2013, The Journal of cell biology.

[13]  J. Brickner,et al.  Cdk Phosphorylation of a Nucleoporin Controls Localization of Active Genes through the Cell Cycle , 2010, Molecular biology of the cell.

[14]  N. Amariglio,et al.  The nuclear-envelope protein and transcriptional repressor LAP2β interacts with HDAC3 at the nuclear periphery, and induces histone H4 deacetylation , 2005, Journal of Cell Science.

[15]  Fan Zhang,et al.  Gcn5 promotes acetylation, eviction, and methylation of nucleosomes in transcribed coding regions. , 2007, Molecular cell.

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

[17]  W. E. Moerner,et al.  Correlations of three-dimensional motion of chromosomal loci in yeast revealed by the double-helix point spread function microscope , 2014, Molecular biology of the cell.

[18]  Uwe Sauer,et al.  Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates , 2010, BMC Systems Biology.

[19]  Christophe Zimmer,et al.  Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres , 2010, Proceedings of the National Academy of Sciences.

[20]  Y. Gruenbaum Faculty Opinions recommendation of The nuclear-envelope protein and transcriptional repressor LAP2beta interacts with HDAC3 at the nuclear periphery, and induces histone H4 deacetylation. , 2005 .

[21]  Jean-Christophe Olivo-Marin,et al.  Nuclear pore complexes in the organization of silent telomeric chromatin , 2000, Nature.

[22]  E. Hurt,et al.  Yeast Ataxin-7 links histone deubiquitination with gene gating and mRNA export , 2008, Nature Cell Biology.

[23]  E. Seto,et al.  The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men , 2008, Nature Reviews Molecular Cell Biology.

[24]  Margaret Werner-Washburne,et al.  The genomics of yeast responses to environmental stress and starvation , 2002, Functional & Integrative Genomics.

[25]  P. Walter,et al.  Gene Recruitment of the Activated INO1 Locus to the Nuclear Membrane , 2004, PLoS biology.

[26]  R. Sternglanz,et al.  Esc1, a Nuclear Periphery Protein Required for Sir4-Based Plasmid Anchoring and Partitioning , 2002, Molecular and Cellular Biology.

[27]  M Wilm,et al.  The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. , 2001, Genes & development.

[28]  S. Dent,et al.  Multiple faces of the SAGA complex. , 2010, Current opinion in cell biology.

[29]  P. Silver,et al.  Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. , 2008, Genes & development.

[30]  Bas van Steensel,et al.  Genome Architecture: Domain Organization of Interphase Chromosomes , 2013, Cell.

[31]  F. Alber,et al.  Physical tethering and volume exclusion determine higher-order genome organization in budding yeast , 2012, Genome research.

[32]  K. Mechtler,et al.  A Dam1-based artificial kinetochore is sufficient to promote chromosome segregation in budding yeast , 2009, Nature Cell Biology.

[33]  Michael R. Green,et al.  Redundant roles for the TFIID and SAGA complexes in global transcription , 2000, Nature.

[34]  M. Rosbash,et al.  3′‐end formation signals modulate the association of genes with the nuclear periphery as well as mRNP dot formation , 2006, The EMBO journal.

[35]  M. Bezanilla,et al.  Myosin VIII associates with microtubule ends and together with actin plays a role in guiding plant cell division , 2014, eLife.

[36]  J. Olivo-Marin,et al.  Nuclear architecture and spatial positioning help establish transcriptional states of telomeres in yeast , 2002, Nature Cell Biology.

[37]  Adam J. Koch,et al.  The Nuclear Envelope Protein Emerin Binds Directly to Histone Deacetylase 3 (HDAC3) and Activates HDAC3 Activity* , 2012, The Journal of Biological Chemistry.

[38]  K. Weis,et al.  A negative feedback loop at the nuclear periphery regulates GAL gene expression , 2012, Molecular biology of the cell.

[39]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[40]  Taddel Angela,et al.  Reversible Disruption of pericentric Heterochromatin and Centromere Function by Inhibiting Deacetylases , 2001 .

[41]  M. Johnston,et al.  Feasting, fasting and fermenting. Glucose sensing in yeast and other cells. , 1999, Trends in genetics : TIG.

[42]  E. Valkov,et al.  Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export , 2014, Nucleic acids research.

[43]  Y. Barral,et al.  Role of SAGA in the asymmetric segregation of DNA circles during yeast ageing , 2014, eLife.

[44]  U. K. Laemmli,et al.  Chromatin Boundaries in Budding Yeast The Nuclear Pore Connection , 2002, Cell.

[45]  Michael P. Rout,et al.  Simple kinetic relationships and nonspecific competition govern nuclear import rates in vivo , 2006, The Journal of cell biology.

[46]  Pamela A. Silver,et al.  Genome-Wide Localization of the Nuclear Transport Machinery Couples Transcriptional Status and Nuclear Organization , 2004, Cell.

[47]  A. Pombo,et al.  Three-dimensional genome architecture: players and mechanisms , 2015, Nature Reviews Molecular Cell Biology.

[48]  Jean-Christophe Olivo-Marin,et al.  SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope , 2006, Nature.

[49]  P. Philippsen,et al.  Heterologous modules for efficient and versatile PCR‐based gene targeting in Schizosaccharomyces pombe , 1998, Yeast.

[50]  Jean-Christophe Olivo-Marin,et al.  High-resolution statistical mapping reveals gene territories in live yeast , 2008, Nature Methods.

[51]  Charles Boone,et al.  16 High-Throughput Strain Construction and Systematic Synthetic Lethal Screening in Saccharomycescerevisiae , 2007 .

[52]  J. Fuchs,et al.  Centromere clustering is a major determinant of yeast interphase nuclear organization. , 2000, Journal of cell science.

[53]  Susan M. Gasser,et al.  Live Imaging of Telomeres yKu and Sir Proteins Define Redundant Telomere-Anchoring Pathways in Yeast , 2002, Current Biology.

[54]  Barry P. Young,et al.  Balony: a software package for analysis of data generated by synthetic genetic array experiments , 2013, BMC Bioinformatics.

[55]  B. Aronow,et al.  Modulation of chromatin position and gene expression by HDAC4 interaction with nucleoporins , 2011, The Journal of cell biology.

[56]  O. Ozier-Kalogeropoulos,et al.  A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. , 1993, Nucleic acids research.

[57]  Andrew W. Murray,et al.  GFP tagging of budding yeast chromosomes reveals that protein–protein interactions can mediate sister chromatid cohesion , 1996, Current Biology.

[58]  F. Hediger,et al.  Nuclear pore association confers optimal expression levels for an inducible yeast gene , 2006, Nature.

[59]  Florence Hediger,et al.  Separation of silencing from perinuclear anchoring functions in yeast Ku80, Sir4 and Esc1 proteins , 2004, The EMBO journal.

[60]  Guennaelle Dieppois,et al.  Cotranscriptional Recruitment to the mRNA Export Receptor Mex67p Contributes to Nuclear Pore Anchoring of Activated Genes , 2006, Molecular and Cellular Biology.

[61]  Ben M. Webb,et al.  Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies , 2012, PLoS biology.

[62]  Florence Hediger,et al.  Myosin-like proteins 1 and 2 are not required for silencing or telomere anchoring, but act in the Tel1 pathway of telomere length control. , 2002, Journal of structural biology.

[63]  A. Corbett,et al.  Actively Transcribed GAL Genes Can Be Physically Linked to the Nuclear Pore by the SAGA Chromatin Modifying Complex* , 2007, Journal of Biological Chemistry.

[64]  D. Lohr,et al.  Yeast chromatin structure and regulation of GAL gene expression. , 2001, Progress in nucleic acid research and molecular biology.