Old cogs, new tricks: the evolution of gene expression in a chromatin context

[1]  Andrei N Lupas,et al.  Histones predate the split between bacteria and archaea , 2018, Bioinform..

[2]  P. Forterre,et al.  Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes , 2018, Proceedings of the National Academy of Sciences.

[3]  Chunaram Choudhary,et al.  Functions and mechanisms of non-histone protein acetylation , 2018, Nature Reviews Molecular Cell Biology.

[4]  Ying Huang,et al.  Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch. , 2018, Journal of molecular biology.

[5]  Hongyu Wu,et al.  Merge and separation of NuA4 and SWR1 complexes control cell fate plasticity in Candida albicans , 2018, Cell Discovery.

[6]  Xing Fu,et al.  Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants , 2018, Nature Genetics.

[7]  P. L. Puri,et al.  Shaping Gene Expression by Landscaping Chromatin Architecture: Lessons from a Master. , 2018, Molecular cell.

[8]  E. O'Duibhir,et al.  Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription. , 2018, Molecular cell.

[9]  Lu Bai,et al.  Systematic Study of Nucleosome-Displacing Factors in Budding Yeast. , 2018, Molecular cell.

[10]  F. Berger,et al.  Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility , 2018, Nucleic acids research.

[11]  Wei Li,et al.  Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity , 2018, Cell Discovery.

[12]  J. Franco-Zorrilla,et al.  Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes. , 2018, Molecular plant.

[13]  Răzvan V Chereji,et al.  Major Determinants of Nucleosome Positioning. , 2018, Biophysical journal.

[14]  Barry P. Young,et al.  Viral proteins as a potential driver of histone depletion in dinoflagellates , 2018, Nature Communications.

[15]  Stephanie L. Johnson,et al.  The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h , 2018, eLife.

[16]  P. Forterre,et al.  Asgard archaea do not close the debate about the universal tree of life topology , 2018, PLoS genetics.

[17]  D. Thanos,et al.  The Histone Variant MacroH2A Blocks Cellular Reprogramming by Inhibiting Mesenchymal-to-Epithelial Transition , 2018, Molecular and Cellular Biology.

[18]  Srinivas Ramachandran,et al.  Precise genome-wide mapping of single nucleosomes and linkers in vivo , 2018, Genome Biology.

[19]  Bram Henneman,et al.  Structure and function of archaeal histones , 2018, PLoS genetics.

[20]  Ajith Harish.  What is an archaeon and are the Archaea really unique? , 2018, bioRxiv.

[21]  E. Nogales,et al.  Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes , 2018, Nature Structural & Molecular Biology.

[22]  S. Henikoff,et al.  Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates. , 2017, Molecular cell.

[23]  Ben P. Williams,et al.  Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit , 2017, Nature Communications.

[24]  H. Madhani,et al.  Ten principles of heterochromatin formation and function , 2017, Nature Reviews Molecular Cell Biology.

[25]  Matthew W. Brown,et al.  Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group , 2017, bioRxiv.

[26]  A. Erives.  Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance , 2017, Epigenetics & Chromatin.

[27]  D. Zilberman,et al.  DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes , 2017, eLife.

[28]  B. Strahl,et al.  Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain , 2017, Nucleic acids research.

[29]  G. Hager,et al.  Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo , 2017, Nucleic acids research.

[30]  M. Mannervik,et al.  CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II. , 2017, Molecular cell.

[31]  B. Cairns,et al.  Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming , 2017, Cell.

[32]  Katja E. Jaeger,et al.  Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. , 2017, Molecular plant.

[33]  A. Shilatifard,et al.  A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation , 2017, Genes & development.

[34]  E. Selker,et al.  Telomere repeats induce domains of H3K27 methylation in Neurospora , 2017, bioRxiv.

[35]  A. Ishihama.  Building a complete image of genome regulation in the model organism Escherichia coli. , 2017, The Journal of general and applied microbiology.

[36]  Karolin Luger,et al.  Structure of histone-based chromatin in Archaea , 2017, Science.

[37]  Katharine L. Diehl,et al.  ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference , 2017, Nature.

[38]  M. Bulyk,et al.  Polycomb-like proteins link the PRC2 complex to CpG islands , 2017, Nature.

[39]  Janet M. Young,et al.  Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals , 2017, bioRxiv.

[40]  Konrad U. Förstner,et al.  GT‐rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes , 2017, The EMBO journal.

[41]  T. Hirano,et al.  Mitotic chromosome assembly despite nucleosome depletion in Xenopus egg extracts , 2017, Science.

[42]  Sandipan Brahma,et al.  INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers , 2017, Nature Communications.

[43]  Zbynek Bozdech,et al.  Epigenetic landscapes underlining global patterns of gene expression in the human malaria parasite, Plasmodium falciparum. , 2017, International journal for parasitology.

[44]  T. Baubec,et al.  Dynamics and Context-Dependent Roles of DNA Methylation. , 2017, Journal of molecular biology.

[45]  Janet Iwasa,et al.  Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes , 2017, Nature Reviews Molecular Cell Biology.

[46]  Michael P. Snyder,et al.  Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression , 2017, Nature Communications.

[47]  D. J. McKay,et al.  Hormone-dependent control of developmental timing through regulation of chromatin accessibility , 2017, Genes & development.

[48]  Masih Sherafatian,et al.  The origins and evolutionary history of human non-coding RNA regulatory networks , 2017, J. Bioinform. Comput. Biol..

[49]  F. Berger,et al.  Compartmentalization of DNA Damage Response between Heterochromatin and Euchromatin Is Mediated by Distinct H2A Histone Variants , 2017, Current Biology.

[50]  A. Shevchenko,et al.  Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos , 2017, bioRxiv.

[51]  H. Kurumizaka,et al.  Histone Variant H2A.L.2 Guides Transition Protein-Dependent Protamine Assembly in Male Germ Cells. , 2017, Molecular cell.

[52]  B. Garcia,et al.  Recognition of Histone H3K14 Acylation by MORF. , 2017, Structure.

[53]  Hyoung-Pyo Kim,et al.  Epigenome mapping highlights chromatin-mediated gene regulation in the protozoan parasite Trichomonas vaginalis , 2017, Scientific Reports.

[54]  Christoforos Nikolaou,et al.  Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae , 2017, Nucleic acids research.

[55]  T. Przytycka,et al.  Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. , 2017, Cell systems.

[56]  S. Bengtson,et al.  Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae , 2017, PLoS biology.

[57]  Crispin T. S. Little,et al.  Evidence for early life in Earth’s oldest hydrothermal vent precipitates , 2017, Nature.

[58]  Giulia Basile,et al.  Intragenic DNA methylation prevents spurious transcription initiation , 2017, Nature.

[59]  Dina Grohmann,et al.  Same same but different: The evolution of TBP in archaea and their eukaryotic offspring , 2017, Transcription.

[60]  Fei Ji,et al.  Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. , 2017, Molecular cell.

[61]  M. Wilkins,et al.  A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B , 2017, PLoS genetics.

[62]  Mary Gehring,et al.  DNA methylation and imprinting in plants: machinery and mechanisms , 2017, Critical reviews in biochemistry and molecular biology.

[63]  G. Narlikar,et al.  Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler , 2017, Science.

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

[65]  Thijs J. G. Ettema,et al.  Asgard archaea illuminate the origin of eukaryotic cellular complexity , 2017, Nature.

[66]  P. Filippakopoulos,et al.  Functions of bromodomain-containing proteins and their roles in homeostasis and cancer , 2017, Nature Reviews Molecular Cell Biology.

[67]  Ilya Lezhava,et al.  Lessons of the Master , 2017 .

[68]  Di Zhang,et al.  Metabolic regulation of gene expression through histone acylations , 2016, Nature Reviews Molecular Cell Biology.

[69]  Steven Henikoff,et al.  Histone variants on the move: substrates for chromatin dynamics , 2016, Nature Reviews Molecular Cell Biology.

[70]  Zhucheng Chen,et al.  Structure and regulation of the chromatin remodeller ISWI , 2016, Nature.

[71]  A. Nasir,et al.  Arguments Reinforcing the Three-Domain View of Diversified Cellular Life , 2016, Archaea.

[72]  S. Svärd,et al.  Specific histone modifications play critical roles in the control of encystation and antigenic variation in the early-branching eukaryote Giardia lamblia. , 2016, The international journal of biochemistry & cell biology.

[73]  A. Travers,et al.  The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity , 2016, Biophysical Reviews.

[74]  Ziv Bar-Joseph,et al.  A transcription factor hierarchy defines an environmental stress response network , 2016, Science.

[75]  Ariel Kaplan,et al.  H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes , 2016, Nature Communications.

[76]  Michael D. Wilson,et al.  Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders , 2016, Genome Biology.

[77]  A. Chivas,et al.  Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures , 2016, Nature.

[78]  Carl Wu,et al.  Comment on “A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme” , 2016, Science.

[79]  Zhimin Liu,et al.  Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex , 2016, eLife.

[80]  P. Forterre,et al.  Giant viruses and the origin of modern eukaryotes. , 2016, Current opinion in microbiology.

[81]  Soumitra S Ghosh,et al.  Lysine acetylation of the Mycobacterium tuberculosis HU protein modulates its DNA binding and genome organization , 2016, Molecular microbiology.

[82]  Srinivas Ramachandran,et al.  Transcriptional Regulators Compete with Nucleosomes Post-replication , 2016, Cell.

[83]  J. Ausió,et al.  The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin , 2016, Epigenetics.

[84]  B. N. Devaiah,et al.  RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription , 2016, Cell.

[85]  K. Kaestner,et al.  The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. , 2016, Molecular cell.

[86]  J. Wouters,et al.  Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B. , 2016, Journal of structural biology.

[87]  Patrick Sobetzko.  Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes , 2016, Nucleic acids research.

[88]  T. Gabaldón,et al.  Late acquisition of mitochondria by a host with chimeric prokaryotic ancestry , 2016, Nature.

[89]  Chongsheng He,et al.  Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements , 2016, PLoS genetics.

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

[91]  Leonid A. Mirny,et al.  Super-resolution imaging reveals distinct chromatin folding for different epigenetic states , 2015, Nature.

[92]  N. Brockdorff,et al.  The interplay of histone modifications – writers that read , 2015, EMBO reports.

[93]  Daria A. Gaykalova,et al.  Structural analysis of nucleosomal barrier to transcription , 2015, Proceedings of the National Academy of Sciences.

[94]  D. J. McKay,et al.  Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo , 2015, Genome research.

[95]  S. Bowerman,et al.  Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations. , 2015, Biophysical journal.

[96]  Jürg Müller,et al.  Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation , 2015, Genes & development.

[97]  T. Hirano,et al.  Reconstitution of mitotic chromatids with a minimum set of purified factors , 2015, Nature Cell Biology.

[98]  I. Maraziotis,et al.  Composite macroH2A/NRF-1 Nucleosomes Suppress Noise and Generate Robustness in Gene Expression. , 2015, Cell reports.

[99]  Christopher M. Vockley,et al.  Epigenome editing by a CRISPR/Cas9-based acetyltransferase activates genes from promoters and enhancers , 2015, Nature Biotechnology.

[100]  B. Snel,et al.  The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history , 2015, BMC Evolutionary Biology.

[101]  Srinivas Ramachandran,et al.  Asymmetric nucleosomes flank promoters in the budding yeast genome , 2015, Genome research.

[102]  J. Yates,et al.  Product Binding Enforces the Genomic Specificity of a Yeast Polycomb Repressive Complex , 2015, Cell.

[103]  E. Verdin,et al.  50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond , 2014, Nature Reviews Molecular Cell Biology.

[104]  R. Paro,et al.  Transcriptional silencing by polycomb-group proteins. , 2014, Cold Spring Harbor perspectives in biology.

[105]  J. Tanny.  Chromatin modification by the RNA Polymerase II elongation complex , 2014, Transcription.

[106]  J. Filée.  Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: the visible part of the iceberg? , 2014, Virology.

[107]  Karolin Luger,et al.  The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis , 2014, Cell.

[108]  L. Aravind,et al.  Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics. , 2014, Cold Spring Harbor perspectives in biology.

[109]  Teresa M. Przytycka,et al.  DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide , 2014, International journal of molecular sciences.

[110]  D. Levens,et al.  DNA topology and transcription , 2014, Nucleus.

[111]  D. Zilberman,et al.  Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes , 2014, Cell.

[112]  Christopher M. Weber,et al.  Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. , 2014, Molecular cell.

[113]  S. Henikoff,et al.  Transcription-generated torsional stress destabilizes nucleosomes , 2013, Nature Structural &Molecular Biology.

[114]  L. Mirny,et al.  High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome , 2013, Science.

[115]  H. Madhani.  The Frustrated Gene: Origins of Eukaryotic Gene Expression , 2013, Cell.

[116]  S. Henikoff,et al.  Mot1 Redistributes TBP from TATA-Containing to TATA-Less Promoters , 2013, Molecular and Cellular Biology.

[117]  Karolin Luger,et al.  Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss , 2013, Nature Communications.

[118]  G. Mizuguchi,et al.  Nucleosome-free Region Dominates Histone Acetylation in Targeting SWR1 to Promoters for H2A.Z Replacement , 2013, Cell.

[119]  Mark C. Field,et al.  Molecular paleontology and complexity in the last eukaryotic common ancestor , 2013, Critical reviews in biochemistry and molecular biology.

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

[121]  K. Struhl,et al.  Determinants of nucleosome positioning , 2013, Nature Structural &Molecular Biology.

[122]  S. Cockroft,et al.  Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures , 2013, Nature Structural &Molecular Biology.

[123]  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.

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

[125]  B. Strahl,et al.  Tandem PHD fingers of MORF/MOZ acetyltransferases display selectivity for acetylated histone H3 and are required for the association with chromatin. , 2012, Journal of molecular biology.

[126]  Gary D Bader,et al.  Chromatin is an ancient innovation conserved between Archaea and Eukarya , 2012, eLife.

[127]  K. Basler,et al.  Transcription in the Absence of Histone H3.2 and H3K4 Methylation , 2012, Current Biology.

[128]  D. Coleman-Derr,et al.  Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes , 2012, PLoS genetics.

[129]  Ashok Patel,et al.  The basic linker of macroH2A stabilizes DNA at the entry/exit site of the nucleosome , 2012, Nucleic acids research.

[130]  J. R. Chubb,et al.  Dynamic acetylation of lysine-4-trimethylated histone H3 and H3 variant biology in a simple multicellular eukaryote , 2012, Nucleic acids research.

[131]  J. Baxter,et al.  A model for chromosome condensation based on the interplay between condensin and topoisomerase II. , 2012, Trends in genetics : TIG.

[132]  Patrick Cramer,et al.  Review Conservation between the Rna Polymerase I, Ii, and Iii Transcription Initiation Machineries , 2022 .

[133]  A. Hinck,et al.  The Growth-Suppressive Function of the Polycomb Group Protein Polyhomeotic Is Mediated by Polymerization of Its Sterile Alpha Motif (SAM) Domain* , 2012, The Journal of Biological Chemistry.

[134]  M. Grunstein,et al.  Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast , 2011, Proceedings of the National Academy of Sciences.

[135]  W. Sullivan,et al.  Canonical and variant histones of protozoan parasites. , 2011, Frontiers in bioscience.

[136]  Uma M. Muthurajan,et al.  The Linker Region of MacroH2A Promotes Self-association of Nucleosomal Arrays , 2011, The Journal of Biological Chemistry.

[137]  L. Mahadevan,et al.  Dynamic acetylation of all lysine-4 trimethylated histone H3 is evolutionarily conserved and mediated by p300/CBP , 2011, Proceedings of the National Academy of Sciences.

[138]  J. Diffley,et al.  Positive Supercoiling of Mitotic DNA Drives Decatenation by Topoisomerase II in Eukaryotes , 2011, Science.

[139]  O. Rando,et al.  Global Regulation of H2A.Z Localization by the INO80 Chromatin-Remodeling Enzyme Is Essential for Genome Integrity , 2011, Cell.

[140]  K. Murakami,et al.  Archaeal RNA polymerase and transcription regulation , 2011, Critical reviews in biochemistry and molecular biology.

[141]  L. Mularoni,et al.  INAUGURAL ARTICLE by a Recently Elected Academy Member:DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo , 2010 .

[142]  D. Zilberman,et al.  Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex , 2010, Current Biology.

[143]  H. Cerutti,et al.  Origin of the polycomb repressive complex 2 and gene silencing by an E(z) homolog in the unicellular alga Chlamydomonas , 2010, Epigenetics.

[144]  Steven Henikoff,et al.  Histone variants — ancient wrap artists of the epigenome , 2010, Nature Reviews Molecular Cell Biology.

[145]  E. Geiduschek,et al.  Transcriptional activation in the context of repression mediated by archaeal histones , 2010, Proceedings of the National Academy of Sciences.

[146]  L. Aravind,et al.  Diversity and evolution of chromatin proteins encoded by DNA viruses. , 2010, Biochimica et biophysica acta.

[147]  E. Pérez-Rueda,et al.  Identification and Genomic Analysis of Transcription Factors in Archaeal Genomes Exemplifies Their Functional Architecture and Evolutionary Origin , 2010, Molecular biology and evolution.

[148]  Julia M. Schulze,et al.  Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation , 2009, Proceedings of the National Academy of Sciences of the United States of America.

[149]  M. Shirakawa,et al.  Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain , 2009, EMBO reports.

[150]  Dustin E. Schones,et al.  Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes , 2009, Cell.

[151]  J. Shabanowitz,et al.  Acetylation of vertebrate H2A.Z and its effect on the structure of the nucleosome. , 2009, Biochemistry.

[152]  M. Pellegrini,et al.  Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana , 2009, Genome Biology.

[153]  David Fenyo,et al.  Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. , 2009, Genes & development.

[154]  D. Sumner,et al.  Late Archean molecular fossils from the Transvaal Supergroup record the antiquity of microbial diversity and aerobiosis , 2009 .

[155]  P. Forterre,et al.  Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms , 2009, Nucleic acids research.

[156]  Dmitri A. Nusinow,et al.  MacroH2A allows ATP-dependent chromatin remodeling by SWI/SNF and ACF complexes but specifically reduces recruitment of SWI/SNF. , 2008, Biochemistry.

[157]  Fan Zhang,et al.  Structure of a RSC–nucleosome complex and insights into chromatin remodeling , 2008, Nature Structural &Molecular Biology.

[158]  S. Henikoff,et al.  Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks , 2008, Nature.

[159]  R. Aebersold,et al.  An Essential Switch in Subunit Composition of a Chromatin Remodeling Complex during Neural Development , 2007, Neuron.

[160]  Z. Avramova,et al.  Origin of the bacterial SET domain genes: vertical or horizontal? , 2007, Molecular biology and evolution.

[161]  C. Peterson,et al.  Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage. , 2006, Genes & development.

[162]  Marcel Geertz,et al.  Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome , 2006, EMBO reports.

[163]  J. William Schopf,et al.  Fossil evidence of Archaean life , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[164]  Geoffrey J. Barton,et al.  Identification of multiple distinct Snf2 subfamilies with conserved structural motifs , 2006, Nucleic acids research.

[165]  B. Franklin Pugh,et al.  Genome-Wide Relationships between TAF1 and Histone Acetyltransferases in Saccharomyces cerevisiae , 2006, Molecular and Cellular Biology.

[166]  Eugene V Koonin,et al.  Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. , 2006, Virus research.

[167]  R. Roeder,et al.  Mechanism of Polymerase II Transcription Repression by the Histone Variant macroH2A , 2006, Molecular and Cellular Biology.

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

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

[170]  Wen-Hsiung Li,et al.  Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. , 2005, Molecular biology and evolution.

[171]  L. Aravind,et al.  The many faces of the helix-turn-helix domain: transcription regulation and beyond. , 2005, FEMS microbiology reviews.

[172]  J. Lieb,et al.  Evidence for nucleosome depletion at active regulatory regions genome-wide , 2004, Nature Genetics.

[173]  J. Reeve,et al.  Transcription by an Archaeal RNA Polymerase Is Slowed but Not Blocked by an Archaeal Nucleosome , 2004, Journal of bacteriology.

[174]  Paul Tempst,et al.  Different EZH2-containing complexes target methylation of histone H1 or nucleosomal histone H3. , 2004, Molecular cell.

[175]  Steven Henikoff,et al.  Phylogenomics of the nucleosome , 2003, Nature Structural Biology.

[176]  A. Sivolob,et al.  Linker histone-dependent organization and dynamics of nucleosome entry/exit DNAs. , 2003, Journal of molecular biology.

[177]  J. Reeve,et al.  Conserved Eukaryotic Histone-Fold Residues Substituted into an Archaeal Histone Increase DNA Affinity but Reduce Complex Flexibility , 2003, Journal of bacteriology.

[178]  Hiten D. Madhani,et al.  Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin , 2003, Cell.

[179]  S. Jacobsen,et al.  Role of CG and Non-CG Methylation in Immobilization of Transposons in Arabidopsis , 2003, Current Biology.

[180]  Stepanka Vanacova,et al.  Molecular biology of the amitochondriate parasites, Giardia intestinalis, Entamoeba histolytica and Trichomonas vaginalis. , 2003, International journal for parasitology.

[181]  D. Reinberg,et al.  Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. , 2002, Genes & development.

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

[183]  Brigitte Wild,et al.  Histone Methyltransferase Activity of a Drosophila Polycomb Group Repressor Complex , 2002, Cell.

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

[185]  M. F. White,et al.  The Interaction of Alba, a Conserved Archaeal Chromatin Protein, with Sir2 and Its Regulation by Acetylation , 2002, Science.

[186]  F. Robert,et al.  H2A.Z Is Required for Global Chromatin Integrity and for Recruitment of RNA Polymerase II under Specific Conditions , 2001, Molecular and Cellular Biology.

[187]  Huntington F. Willard,et al.  Histone variant macroH2A contains two distinct macrochromatin domains capable of directing macroH2A to the inactive X chromosome , 2001, Nucleic Acids Res..

[188]  J. Workman,et al.  Recruitment of HAT Complexes by Direct Activator Interactions with the ATM-Related Tra1 Subunit , 2001, Science.

[189]  J. Dacks,et al.  Origin of H1 linker histones , 2001, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[190]  D. Lilley,et al.  Generation of Superhelical Torsion by ATP-Dependent Chromatin Remodeling Activities , 2000, Cell.

[191]  J. Widom,et al.  Effects of Histone Tail Domains on the Rate of Transcriptional Elongation through a Nucleosome , 2000, Molecular and Cellular Biology.

[192]  N. Butterfield,et al.  Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes , 2000, Paleobiology.

[193]  K. Struhl.  Fundamentally Different Logic of Gene Regulation in Eukaryotes and Prokaryotes , 1999, Cell.

[194]  Purificación López-García,et al.  Symbiosis Between Methanogenic Archaea and δ-Proteobacteria as the Origin of Eukaryotes: The Syntrophic Hypothesis , 1998, Journal of Molecular Evolution.

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

[196]  林继红,et al.  古细菌(Archaebacteria)表面糖蛋白 , 1990 .

[197]  C R Woese,et al.  Mitochondrial origins. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[198]  W. Earnshaw,et al.  Topoisomerase II is a structural component of mitotic chromosome scaffolds , 1985, The Journal of cell biology.

[199]  W. Doolittle,et al.  Has the endosymbiont hypothesis been proven? , 1982, Microbiological reviews.

[200]  C. Woese,et al.  Phylogenetic structure of the prokaryotic domain: The primary kingdoms , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[201]  Y. W. Alice,et al.  保存Yaf9 YEATSドメインのAsf1様構造とH2A.Z沈着とアセチル化における役割 , 2009 .

[202]  L. Aravind,et al.  Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. , 2008, International journal for parasitology.

[203]  L. Aravind,et al.  The many faces of the helix-turn-helix domain : Transcription regulation and beyond q , 2005 .