Viral proteins as a potential driver of histone depletion in dinoflagellates

[1]  Barry P. Young,et al.  Histone Acetylation, Not Stoichiometry, Regulates Linker Histone Binding in Saccharomyces cerevisiae , 2017, Genetics.

[2]  A. Place,et al.  Transcriptome Analysis of Core Dinoflagellates Reveals a Universal Bias towards “GC” Rich Codons , 2017, Marine drugs.

[3]  Julie Brind’Amour,et al.  Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae , 2017, Genetics.

[4]  C. Delwiche,et al.  Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics , 2016, Proceedings of the National Academy of Sciences.

[5]  P. Cramer,et al.  Nucleosomal arrangement affects single-molecule transcription dynamics , 2016, Proceedings of the National Academy of Sciences.

[6]  M. Weitzman,et al.  A core viral protein binds host nucleosomes to sequester immune danger signals , 2016, Nature.

[7]  M. Lynch,et al.  Diversity and Divergence of Dinoflagellate Histone Proteins , 2015, G3: Genes, Genomes, Genetics.

[8]  Mohammad M. Karimi,et al.  An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations , 2015, Nature Communications.

[9]  Adam P. Rosebrock,et al.  Cell cycle-regulated oscillator coordinates core histone gene transcription through histone acetylation , 2014, Proceedings of the National Academy of Sciences.

[10]  Wei Li,et al.  Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging , 2014, Genes & development.

[11]  B. Andrews,et al.  Regulation of histone gene transcription in yeast , 2014, Cellular and Molecular Life Sciences.

[12]  Vishwanath R. Iyer,et al.  Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements , 2014, Nucleic acids research.

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

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

[15]  S. Sugano,et al.  Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure , 2013, Current Biology.

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

[17]  Zhaoyu Li,et al.  DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing , 2013, Genome research.

[18]  S. Malik,et al.  Mediator-regulated transcription through the +1 nucleosome. , 2012, Molecular cell.

[19]  S. Henikoff,et al.  Chromatin: Packaging without Nucleosomes , 2012, Current Biology.

[20]  Kristina L. Ford,et al.  Loss of Nucleosomal DNA Condensation Coincides with Appearance of a Novel Nuclear Protein in Dinoflagellates , 2012, Current Biology.

[21]  Julia M. Schulze,et al.  Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae , 2012, Proceedings of the National Academy of Sciences.

[22]  Matthew J. Higgins,et al.  Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models , 2012, Nature Genetics.

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

[24]  Kristin R Brogaard,et al.  A base pair resolution map of nucleosome positions in yeast , 2012, Nature.

[25]  J. Lieb,et al.  In Vivo Effects of Histone H3 Depletion on Nucleosome Occupancy and Position in Saccharomyces cerevisiae , 2012, PLoS genetics.

[26]  D. Clark,et al.  Regulation of Histone Gene Expression in Budding Yeast , 2012, Genetics.

[27]  Sougata Roy,et al.  A Full Suite of Histone and Histone Modifying Genes Are Transcribed in the Dinoflagellate Lingulodinium , 2012, PloS one.

[28]  F. Winston,et al.  Chromatin and Transcription in Yeast , 2012, Genetics.

[29]  Senjie Lin,et al.  Spliced Leader RNAs, Mitochondrial Gene Frameshifts and Multi-Protein Phylogeny Expand Support for the Genus Perkinsus as a Unique Group of Alveolates , 2011, PloS one.

[30]  J. Pitula,et al.  Identification of Two Spliced Leader RNA Transcripts from Perkinsus marinus , 2011, The Journal of eukaryotic microbiology.

[31]  J. Gill,et al.  Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates , 2010, Proceedings of the National Academy of Sciences.

[32]  Timothy R. Hughes,et al.  G+C content dominates intrinsic nucleosome occupancy , 2009, BMC Bioinformatics.

[33]  J. Butler,et al.  TRAMP Complex Enhances RNA Degradation by the Nuclear Exosome Component Rrp6* , 2009, The Journal of Biological Chemistry.

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

[35]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

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

[37]  J. Hiscox,et al.  Nucleolar targeting: the hub of the matter , 2009, EMBO reports.

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

[39]  D. Hernandez-Verdun,et al.  Nucleolus: the fascinating nuclear body , 2007, Histochemistry and Cell Biology.

[40]  T. Gaasterland,et al.  Spliced leader RNA trans-splicing in dinoflagellates , 2007, Proceedings of the National Academy of Sciences.

[41]  Judith L Campbell,et al.  Contribution of Trf4/5 and the Nuclear Exosome to Genome Stability Through Regulation of Histone mRNA Levels in Saccharomyces cerevisiae , 2007, Genetics.

[42]  F. Delsuc,et al.  The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  S. Khorasanizadeh.  The Nucleosome From Genomic Organization to Genomic Regulation , 2004, Cell.

[44]  A. Gunjan,et al.  A Rad53 Kinase-Dependent Surveillance Mechanism that Regulates Histone Protein Levels in S. cerevisiae , 2003, Cell.

[45]  Craig D. Kaplan,et al.  Transcription Elongation Factors Repress Transcription Initiation from Cryptic Sites , 2003, Science.

[46]  Mark D. Robinson,et al.  FunSpec: a web-based cluster interpreter for yeast , 2002, BMC Bioinformatics.

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

[48]  Stephen P. Jackson,et al.  A role for Saccharomyces cerevisiae histone H2A in DNA repair , 2000, Nature.

[49]  V. Kushnirov.  Rapid and reliable protein extraction from yeast , 2000, Yeast.

[50]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

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

[52]  Fred Winston,et al.  Functional Organization of the Yeast SAGA Complex: Distinct Components Involved in Structural Integrity, Nucleosome Acetylation, and TATA-Binding Protein Interaction , 1999, Molecular and Cellular Biology.

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

[54]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[55]  P. Huitorel,et al.  Isolation of the major basic nuclear protein and its localization on chromosomes of the dinoflagellate, Oxyrrhis marina , 1997, Biology of the cell.

[56]  B. Dujon,et al.  New vectors for combinatorial deletions in yeast chromosomes and for gap‐repair cloning using ‘split‐marker’ recombination , 1996, Yeast.

[57]  M. Tesar,et al.  Foot-and-mouth disease virus protease 3C inhibits cellular transcription and mediates cleavage of histone H3. , 1990, Virology.

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

[59]  Roger D. Kornberg,et al.  Synthetic peptides as nuclear localization signals , 1986, Nature.

[60]  P. J. Rizzo,et al.  Chromosomal Proteins in the Dinoflagellate Alga Gyrodinium cohnii , 1972, Science.

[61]  R. D. Gietz,et al.  Yeast transformation by the LiAc/SS carrier DNA/PEG method. , 2014, Methods in molecular biology.

[62]  T. Mullen,et al.  Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. , 2008, Genes & development.

[63]  A. Tong,et al.  Synthetic genetic array analysis in Saccharomyces cerevisiae. , 2006, Methods in molecular biology.

[64]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[65]  S. Bell,et al.  Nucleosomes positioned by ORC facilitate the initiation of DNA replication. , 2001, Molecular cell.

[66]  R. Müller,et al.  Regulatable promoters of Saccharomyces cerevisiae: comparison of transcriptional activity and their use for heterologous expression. , 1994, Nucleic acids research.

[67]  B. Haarer,et al.  Fluorescence microscopy methods for yeast. , 1989, Methods in cell biology.

[68]  M. Sun.  Debate rages over breast cancer study. , 1988, Science.