Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis

[1]  Nir Friedman,et al.  Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C , 2015, Cell.

[2]  C. Millar,et al.  H2A.Z marks antisense promoters and has positive effects on antisense transcript levels in budding yeast , 2015, BMC Genomics.

[3]  C. Peterson,et al.  The Ino80 complex prevents invasion of euchromatin into silent chromatin , 2015, Genes & development.

[4]  Weifeng Gu,et al.  Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF , 2015, Genes & development.

[5]  A. Mosley,et al.  The Exosome Component Rrp6 Is Required for RNA Polymerase II Termination at Specific Targets of the Nrd1-Nab3 Pathway , 2015, PLoS genetics.

[6]  L. Boyer.  Faculty Opinions recommendation of H2A.Z-dependent crosstalk between enhancer and promoter regulates cyclin D1 expression. , 2014 .

[7]  T. Tsukiyama,et al.  ATP-dependent chromatin remodeling shapes the long noncoding RNA landscape , 2014, Genes & development.

[8]  J. Bähler,et al.  The RNA exosome promotes transcription termination of backtracked RNA polymerase II , 2014, Nature Structural &Molecular Biology.

[9]  Nam Pho,et al.  A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription , 2014, Cell.

[10]  K. Struhl,et al.  TFIIH phosphorylation of the Pol II CTD stimulates mediator dissociation from the preinitiation complex and promoter escape. , 2014, Molecular cell.

[11]  Judith B. Zaugg,et al.  Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast , 2014, Nucleic acids research.

[12]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[13]  Daniel Schulz,et al.  Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis , 2013, Cell.

[14]  Alexander van Oudenaarden,et al.  Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins , 2013, Proceedings of the National Academy of Sciences.

[15]  P. Cramer,et al.  Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels. , 2013, Molecular cell.

[16]  Peter J. Park,et al.  Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast , 2013, Molecular and Cellular Biology.

[17]  K. Bystricky,et al.  H2A.Z-dependent crosstalk between enhancer and promoter regulates Cyclin D1 expression , 2013, Oncogene.

[18]  Vincent L. Butty,et al.  H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation , 2013, PLoS genetics.

[19]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[20]  Dirk Eddelbuettel,et al.  Seamless R and C++ Integration with Rcpp , 2013 .

[21]  J. Pérez-Ortín,et al.  Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis , 2013, Cell.

[22]  O. Rando,et al.  A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme , 2013, Science.

[23]  K. Bystricky,et al.  TIP48/Reptin and H2A.Z Requirement for Initiating Chromatin Remodeling in Estrogen-Activated Transcription , 2013, PLoS genetics.

[24]  Kairong Cui,et al.  H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. , 2013, Cell stem cell.

[25]  L. Steinmetz,et al.  Extensive degradation of RNA precursors by the exosome in wild-type cells. , 2012, Molecular cell.

[26]  D. Tollervey,et al.  Transcriptome-wide Analysis of Exosome Targets , 2012, Molecular cell.

[27]  Judith B. Zaugg,et al.  Gene Loops Enhance Transcriptional Directionality , 2012, Science.

[28]  Alexander R. Pico,et al.  Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage , 2012, Cell.

[29]  Krishnamurthy Natarajan,et al.  Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes , 2012, Nature.

[30]  L. Steinmetz,et al.  Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins. , 2012, Molecular cell.

[31]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[32]  Pierre-Étienne Jacques,et al.  A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes. , 2012, Molecular cell.

[33]  S. Loeillet,et al.  XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast , 2011, Nature.

[34]  Albert E. Almada,et al.  Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome , 2011, Proceedings of the National Academy of Sciences.

[35]  Philip Lijnzaad,et al.  The specificity and topology of chromatin interaction pathways in yeast. , 2011, Molecular cell.

[36]  Hadley Wickham,et al.  The Split-Apply-Combine Strategy for Data Analysis , 2011 .

[37]  Wolfgang Huber,et al.  Antisense expression increases gene expression variability and locus interdependency , 2011, Molecular systems biology.

[38]  A. van Hoof,et al.  Different nuclease requirements for exosome-mediated degradation of normal and nonstop mRNAs , 2011, Proceedings of the National Academy of Sciences.

[39]  Macarena Morillo-Huesca,et al.  The SWR1 Histone Replacement Complex Causes Genetic Instability and Genome-Wide Transcription Misregulation in the Absence of H2A.Z , 2010, PloS one.

[40]  J. Rine,et al.  Roles for H2A.Z and Its Acetylation in GAL1 Transcription and Gene Induction, but Not GAL1-Transcriptional Memory , 2010, PLoS biology.

[41]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[42]  Macarena Morillo-Huesca,et al.  The SWR 1 Histone Replacement Complex Causes Genetic Instability and Genome-Wide Transcription Misregulation in the Absence of H 2 A . Z , 2010 .

[43]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[44]  Ming Zhou,et al.  Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs , 2009, Nature.

[45]  M. Hampsey,et al.  Detection of gene loops by 3C in yeast. , 2009, Methods.

[46]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[47]  Sean R. Collins,et al.  Functional Organization of the S. cerevisiae Phosphorylation Network , 2009, Cell.

[48]  Christophe Malabat,et al.  Widespread bidirectional promoters are the major source of cryptic transcripts in yeast , 2009, Nature.

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

[50]  Edoardo M. Airoldi,et al.  Predicting Cellular Growth from Gene Expression Signatures , 2009, PLoS Comput. Biol..

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

[52]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[53]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[54]  Gene W. Yeo,et al.  Divergent Transcription from Active Promoters , 2008, Science.

[55]  R. Young,et al.  H2AZ Is Enriched at Polycomb Complex Target Genes in ES Cells and Is Necessary for Lineage Commitment , 2008, Cell.

[56]  N. Friedman,et al.  Cell Cycle– and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast , 2008, PLoS genetics.

[57]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[58]  J. Tyler,et al.  Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation , 2008, Proceedings of the National Academy of Sciences.

[59]  Guennaelle Dieppois,et al.  Antisense RNA Stabilization Induces Transcriptional Gene Silencing via Histone Deacetylation in S. cerevisiae , 2007, Cell.

[60]  M. Hampsey,et al.  A transcription-independent role for TFIIB in gene looping. , 2007, Molecular cell.

[61]  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.

[62]  Grant W. Brown,et al.  Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map , 2007, Nature.

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

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

[65]  J. Corden,et al.  Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. , 2006, Molecular cell.

[66]  D. Libri,et al.  Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. , 2006, Molecular cell.

[67]  Wolfgang Huber,et al.  Transcript mapping with high-density oligonucleotide tiling arrays , 2006, Bioinform..

[68]  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.

[69]  H. Green,et al.  An immortalized drug-resistant cell line established from 12-13-day mouse embryos for the propagation of human embryonic stem cells. , 2006, Differentiation; research in biological diversity.

[70]  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.

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

[72]  B. Séraphin,et al.  Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase , 2005, Cell.

[73]  M. Grunstein,et al.  Acetylation in Histone H3 Globular Domain Regulates Gene Expression in Yeast , 2005, Cell.

[74]  J. Strathern,et al.  Methods in yeast genetics : a Cold Spring Harbor Laboratory course manual , 2005 .

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

[76]  Michael Hampsey,et al.  Ssu72 Is an RNA polymerase II CTD phosphatase. , 2004, Molecular cell.

[77]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[78]  Wei-Hua Wu,et al.  ATP-Driven Exchange of Histone H2AZ Variant Catalyzed by SWR1 Chromatin Remodeling Complex , 2004, Science.

[79]  F. Netter,et al.  Supplemental References , 2002, We Came Naked and Barefoot.

[80]  W. Keller,et al.  A role for SSU72 in balancing RNA polymerase II transcription elongation and termination. , 2002, Molecular cell.

[81]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[82]  M. Hampsey,et al.  Functional Interaction between Ssu72 and the Rpb2 Subunit of RNA Polymerase II in Saccharomyces cerevisiae , 2000, Molecular and Cellular Biology.

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

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

[85]  G. Fink,et al.  Methods in yeast genetics , 1979 .