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

Major Determinants of Nucleosome Positioning

(2018) Răzvan V. Chereji et al.   BIOPHYSICAL JOURNAL

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

(2018) Patrick J. Murphy et al.   CELL

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

(2018) Matthew W Brown et al.   Genome Biology and Evolution

Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals

(2018) Antoine Molaro et al.   GENOME RESEARCH

The Histone Variant MacroH2A Blocks Cellular Reprogramming by Inhibiting Mesenchymal-to-Epithelial Transition

(2018) Maria Pliatska et al.   MOLECULAR AND CELLULAR BIOLOGY

Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription

(2018) Slawomir Kubik et al.   MOLECULAR CELL

Shaping Gene Expression by Landscaping Chromatin Architecture: Lessons from a Master

(2018) Vittorio Sartorelli et al.   MOLECULAR CELL

Systematic Study of Nucleosome-Displacing Factors in Budding Yeast

(2018) Chao Yan et al.   MOLECULAR CELL

Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes

(2018) Ángeles Gómez-Zambrano et al.   Molecular Plant

Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes

(2018) Simon Poepsel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility

(2018) Akihisa Osakabe et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes

(2018) Simon Poepsel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Asgard archaea do not close the debate about the universal tree of life topology

(2018) Violette Da Cunha et al.   PLoS Genetics

Telomere repeats induce domains of H3K27 methylation in Neurospora

(2018) Kirsty Jamieson et al.   eLife

The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h

(2018) Nathan Gamarra et al.   eLife

Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity

(2018) Chih-Chao Hsu et al.   Cell Discovery

Merge and separation of NuA4 and SWR1 complexes control cell fate plasticity in Candida albicans

(2018) Xiongjun Wang et al.   Cell Discovery

Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch

(2018) Ling Peng et al.   JOURNAL OF MOLECULAR BIOLOGY

Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants

(2018) Zicong Li et al.   NATURE GENETICS

Structure and function of archaeal histones

(2018) Bram Henneman et al.   PLoS Genetics

Histones predate the split between bacteria and archaea

(2018) Vikram Alva et al.   BIOINFORMATICS

Functions and mechanisms of non-histone protein acetylation

(2018) Takeo Narita et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

What is an archaeon and are the Archaea really unique?

(2018) Ajith Harish   PeerJ

Hormone-dependent control of developmental timing through regulation of chromatin accessibility

(2017) Christopher M. Uyehara et al.   GENES & DEVELOPMENT

A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation

(2017) Marc A.J. Morgan et al.   GENES & DEVELOPMENT

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

(2017) Benjamin J. E. Martin et al.   GENETICS

Epigenetic landscapes underlining global patterns of gene expression in the human malaria parasite, Plasmodium falciparum

(2017) Archana P Gupta et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Building a complete image of genome regulation in the model organism Escherichia coli

(2017) Akira Ishihama   JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY

Dynamics and Context-Dependent Roles of DNA Methylation

(2017) Christina Ambrosi et al.   JOURNAL OF MOLECULAR BIOLOGY

Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates

(2017) Srinivas Ramachandran et al.   MOLECULAR CELL

Histone Variant H2A.L.2 Guides Transition Protein-Dependent Protamine Assembly in Male Germ Cells

(2017) Sophie Barral et al.   MOLECULAR CELL

CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II

(2017) Ann Boija et al.   MOLECULAR CELL

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

(2017) Sharmistha Kundu et al.   MOLECULAR CELL

Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis

(2017) Sandra Cortijo et al.   Molecular Plant

Polycomb-like proteins link the PRC2 complex to CpG islands

(2017) Haojie Li et al.   NATURE

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference

(2017) Geoffrey P. Dann et al.   NATURE

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

Evidence for early life in Earth’s oldest hydrothermal vent precipitates

(2017) Matthew S. Dodd et al.   NATURE

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ten principles of heterochromatin formation and function

(2017) Robin C. Allshire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functions of bromodomain-containing proteins and their roles in homeostasis and cancer

(2017) Takao Fujisawa et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain

(2017) Brianna J Klein et al.   NUCLEIC ACIDS RESEARCH

Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae

(2017) Maria Tsochatzidou et al.   NUCLEIC ACIDS RESEARCH

Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo

(2017) Thomas A Johnson et al.   NUCLEIC ACIDS RESEARCH

Structure of histone-based chromatin in Archaea

(2017) Francesca Mattiroli et al.   SCIENCE

Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler

(2017) Kalyan K. Sinha et al.   SCIENCE

Mitotic chromosome assembly despite nucleosome depletion inXenopusegg extracts

(2017) Keishi Shintomi et al.   SCIENCE

Recognition of Histone H3K14 Acylation by MORF

(2017) Brianna J. Klein et al.   STRUCTURE

Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance

(2017) Albert J. Erives   Epigenetics & Chromatin

Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression

(2017) Kévin Contrepois et al.   Nature Communications

INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers

(2017) Sandipan Brahma et al.   Nature Communications

Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae

(2017) Stefan Bengtson et al.   PLOS BIOLOGY

A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B

(2017) Tatiana A. Soboleva et al.   PLoS Genetics

DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes

(2017) David B Lyons et al.   eLife

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

(2017) Benjamin J. E. Martin et al.   GENETICS

The origins and evolutionary history of human non-coding RNA regulatory networks

(2017) Masih Sherafatian et al.   Journal of Bioinformatics and Computational Biology

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome

(2017) Fedor Kouzine et al.   Cell Systems

Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations

(2016) Samuel Bowerman et al.   BIOPHYSICAL JOURNAL

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

Transcriptional Regulators Compete with Nucleosomes Post-replication

(2016) Srinivas Ramachandran et al.   CELL

Giant viruses and the origin of modern eukaryotes

(2016) Patrick Forterre et al.   CURRENT OPINION IN MICROBIOLOGY

The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin

(2016) Ciro Rivera-Casas et al.   Epigenetics

Specific histone modifications play critical roles in the control of encystation and antigenic variation in the early-branching eukaryote Giardia lamblia

(2016) Pedro G. Carranza et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B

(2016) Grégoire Rondelet et al.   JOURNAL OF STRUCTURAL BIOLOGY

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

Lysine acetylation of theMycobacterium tuberculosisHU protein modulates its DNA binding and genome organization

(2016) Soumitra Ghosh et al.   MOLECULAR MICROBIOLOGY

Structure and regulation of the chromatin remodeller ISWI

(2016) Lijuan Yan et al.   NATURE

Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry

(2016) Alexandros A. Pittis et al.   NATURE

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures

(2016) Allen P. Nutman et al.   NATURE

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Metabolic regulation of gene expression through histone acylations

(2016) Benjamin R. Sabari et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone variants on the move: substrates for chromatin dynamics

(2016) Paul B. Talbert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes

(2016) Patrick Sobetzko   NUCLEIC ACIDS RESEARCH

Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme"

(2016) F. Wang et al.   SCIENCE

A transcription factor hierarchy defines an environmental stress response network

(2016) L. Song et al.   SCIENCE

H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes

(2016) Sergei Rudnizky et al.   Nature Communications

Arguments Reinforcing the Three-Domain View of Diversified Cellular Life

(2016) Arshan Nasir et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex

(2016) Michael Tramantano et al.   eLife

The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history

(2015) Lidija Berke et al.   BMC EVOLUTIONARY BIOLOGY

Product Binding Enforces the Genomic Specificity of a Yeast Polycomb Repressive Complex

(2015) Phillip A. Dumesic et al.   CELL

The interplay of histone modifications - writers that read

(2015) T. Zhang et al.   EMBO REPORTS

Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation

(2015) Ana Raquel Pengelly et al.   GENES & DEVELOPMENT

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the earlyDrosophilaembryo

(2015) Katharine N. Schulz et al.   GENOME RESEARCH

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Reconstitution of mitotic chromatids with a minimum set of purified factors

(2015) Keishi Shintomi et al.   NATURE CELL BIOLOGY

Structural analysis of nucleosomal barrier to transcription

(2015) Daria A. Gaykalova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composite macroH2A/NRF-1 Nucleosomes Suppress Noise and Generate Robustness in Gene Expression

(2015) Matthieu D. Lavigne et al.   Cell Reports

Diversity and Divergence of Dinoflagellate Histone Proteins

(2015) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

(2014) Jason T. Huff et al.   CELL

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

(2014) Ramesh Yelagandula et al.   CELL

Asymmetric nucleosomes flank promoters in the budding yeast genome

(2014) Srinivas Ramachandran et al.   GENOME RESEARCH

DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide

(2014) Laura Baranello et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

(2014) Christopher M. Weber et al.   MOLECULAR CELL

50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond

(2014) Eric Verdin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: The visible part of the iceberg?

(2014) Jonathan Filée   VIROLOGY

Transcriptional Silencing by Polycomb-Group Proteins

(2014) U. Grossniklaus et al.   Cold Spring Harbor Perspectives in Biology

Protein and DNA Modifications: Evolutionary Imprints of Bacterial Biochemical Diversification and Geochemistry on the Provenance of Eukaryotic Epigenetics

(2014) L. Aravind et al.   Cold Spring Harbor Perspectives in Biology

DNA topology and transcription

(2014) Fedor Kouzine et al.   Nucleus

The Frustrated Gene: Origins of Eukaryotic Gene Expression

(2013) Hiten D. Madhani   CELL

Nucleosome-free Region Dominates Histone Acetylation in Targeting SWR1 to Promoters for H2A.Z Replacement

(2013) Anand Ranjan et al.   CELL

Molecular paleontology and complexity in the last eukaryotic common ancestor

(2013) V. Lila Koumandou et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Mot1 Redistributes TBP from TATA-Containing to TATA-Less Promoters

(2013) G. E. Zentner et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-generated torsional stress destabilizes nucleosomes

(2013) Sheila S Teves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme

(2013) S. Watanabe et al.   SCIENCE

Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss

(2013) Maxim Y. Sheinin et al.   Nature Communications

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

(2012) Gangqing Hu et al.   Cell Stem Cell

Loss of Nucleosomal DNA Condensation Coincides with Appearance of a Novel Nuclear Protein in Dinoflagellates

(2012) Sebastian G. Gornik et al.   CURRENT BIOLOGY

Transcription in the Absence of Histone H3.2 and H3K4 Methylation

(2012) Martina Hödl et al.   CURRENT BIOLOGY

The Growth-Suppressive Function of the Polycomb Group Protein Polyhomeotic Is Mediated by Polymerization of Its Sterile Alpha Motif (SAM) Domain

(2012) Angela K. Robinson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tandem PHD Fingers of MORF/MOZ Acetyltransferases Display Selectivity for Acetylated Histone H3 and Are Required for the Association with Chromatin

(2012) Muzaffar Ali et al.   JOURNAL OF MOLECULAR BIOLOGY

Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries

(2012) Alessandro Vannini et al.   MOLECULAR CELL

Dynamic acetylation of lysine-4-trimethylated histone H3 and H3 variant biology in a simple multicellular eukaryote

(2012) Duen-Wei Hsu et al.   NUCLEIC ACIDS RESEARCH

The basic linker of macroH2A stabilizes DNA at the entry/exit site of the nucleosome

(2012) Srinivas Chakravarthy et al.   NUCLEIC ACIDS RESEARCH

A model for chromosome condensation based on the interplay between condensin and topoisomerase II

(2012) Jonathan Baxter et al.   TRENDS IN GENETICS

Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes

(2012) Devin Coleman-Derr et al.   PLoS Genetics

Chromatin is an ancient innovation conserved between Archaea and Eukarya

(2012) Ron Ammar et al.   eLife

Global Regulation of H2A.Z Localization by the INO80 Chromatin-Remodeling Enzyme Is Essential for Genome Integrity

(2011) Manolis Papamichos-Chronakis et al.   CELL

Archaeal RNA polymerase and transcription regulation

(2011) Sung-Hoon Jun et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Canonical and variant histones of protozoan parasites

(2011) Maria Carolina Dalmasso   Frontiers in Bioscience-Landmark

The Linker Region of MacroH2A Promotes Self-association of Nucleosomal Arrays

(2011) Uma M. Muthurajan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast

(2011) A. S. Sperling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic acetylation of all lysine-4 trimethylated histone H3 is evolutionarily conserved and mediated by p300/CBP

(2011) N. T. Crump et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Positive Supercoiling of Mitotic DNA Drives Decatenation by Topoisomerase II in Eukaryotes

(2011) J. Baxter et al.   SCIENCE

Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex

(2010) Assaf Zemach et al.   CURRENT BIOLOGY

Origin of the polycomb repressive complex 2 and gene silencing by an E(z) homolog in the unicellular alga Chlamydomonas

(2010) Scott Shaver et al.   Epigenetics

Identification and Genomic Analysis of Transcription Factors in Archaeal Genomes Exemplifies Their Functional Architecture and Evolutionary Origin

(2010) E. Perez-Rueda et al.   MOLECULAR BIOLOGY AND EVOLUTION

Histone variants — ancient wrap artists of the epigenome

(2010) Paul B. Talbert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo

(2010) S. Gangadharan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional activation in the context of repression mediated by archaeal histones

(2010) S. P. Wilkinson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acetylation of Vertebrate H2A.Z and Its Effect on the Structure of the Nucleosome

(2009) Toyotaka Ishibashi et al.   BIOCHEMISTRY

Diversity and evolution of chromatin proteins encoded by DNA viruses

(2009) Robson F. de Souza et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain

(2009) Junji Otani et al.   EMBO REPORTS

Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei

(2009) T. N. Siegel et al.   GENES & DEVELOPMENT

Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms

(2009) P. Forterre et al.   NUCLEIC ACIDS RESEARCH

Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation

(2009) A. Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MacroH2A Allows ATP-Dependent Chromatin Remodeling by SWI/SNF and ACF Complexes but Specifically Reduces Recruitment of SWI/SNF†

(2008) Evelyn Y. Chang et al.   BIOCHEMISTRY

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

(2008) Daniel Zilberman et al.   NATURE

Structure of a RSC–nucleosome complex and insights into chromatin remodeling

(2008) Yuriy Chaban et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Late Archean molecular fossils from the Transvaal Supergroup record the antiquity of microbial diversity and aerobiosis

(2008) Jacob R. Waldbauer et al.   PRECAMBRIAN RESEARCH

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

(2007) Lakshminarayan M. Iyer et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY