Articles

High-throughput assessment of context-dependent effects of chromatin proteins

Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest....

Authors: Laura Brueckner, Joris van Arensbergen, Waseem Akhtar, Ludo Pagie and Bas van Steensel

EpiMINE, a computational program for mining epigenomic data

In epigenetic research, both the increasing ease of high-throughput sequencing and a greater interest in genome-wide studies have resulted in an exponential flooding of epigenetic-related data in public domai...

Authors: SriGanesh Jammula and Diego Pasini

Imprinted DNA methylation reconstituted at a non-imprinted locus

In mammals, tight regulation of cytosine methylation is required for embryonic development and cellular differentiation. The trans-acting DNA methyltransferases that catalyze this modification have been identifi...

Authors: David H. Taylor, Chelsea M. McLean, Warren L. Wu, Alex B. Wang and Paul D. Soloway

Nucleosome distortion as a possible mechanism of transcription activation domain function

After more than three decades since the discovery of transcription activation domains (ADs) in gene-specific activators, the mechanism of their function remains enigmatic. The widely accepted model of direct r...

Authors: Tamara Y. Erkina and Alexandre M. Erkine

Fine-tuning of chromatin composition and Polycomb recruitment by two Mi2 homologues during C. elegans early embryonic development

The nucleosome remodeling and deacetylase complex promotes cell fate decisions throughout embryonic development. Its core enzymatic subunit, the SNF2-like ATPase and Helicase Mi2, is well conserved throughout ...

Authors: Stéphanie Käser-Pébernard, Catherine Pfefferli, Caroline Aschinger and Chantal Wicky

Erratum to: CBP binding outside of promoters and enhancers in Drosophila melanogaster

Authors: Philge Philip, Ann Boija, Roshan Vaid, Allison M. Churcher, David J. Meyers, Philip A. Cole, Mattias Mannervik and Per Stenberg

Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers

Pax6 is a key regulator of the entire cascade of ocular lens formation through specific binding to promoters and enhancers of batteries of target genes. The promoters and enhancers communicate with each other ...

Authors: Jian Sun, Yilin Zhao, Rebecca McGreal, Yamit Cohen-Tayar, Shira Rockowitz, Carola Wilczek, Ruth Ashery-Padan, David Shechter, Deyou Zheng and Ales Cvekl

The cnidarian Hydractinia echinata employs canonical and highly adapted histones to pack its DNA

Cnidarians are a group of early branching animals including corals, jellyfish and hydroids that are renowned for their high regenerative ability, growth plasticity and longevity. Because cnidarian genomes are ...

Authors: Anna Török, Philipp H. Schiffer, Christine E. Schnitzler, Kris Ford, James C. Mullikin, Andreas D. Baxevanis, Antony Bacic, Uri Frank and Sebastian G. Gornik

The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements

A common aberration in cancer is the activation of germline-specific proteins. The DNA-binding proteins among them could generate novel chromatin states, not found in normal cells. The germline-specific transc...

Authors: Elena M. Pugacheva, Evgeny Teplyakov, Qiongfang Wu, Jingjing Li, Cheng Chen, Chengcheng Meng, Jian Liu, Susan Robinson, Dmitry Loukinov, Abdelhalim Boukaba, Andrew Paul Hutchins, Victor Lobanenkov and Alexander Strunnikov

Histone H3 and TORC1 prevent organelle dysfunction and cell death by promoting nuclear retention of HMGB proteins

How cells respond and adapt to environmental changes, such as nutrient flux, remains poorly understood. Evolutionarily conserved nutrient signaling cascades can regulate chromatin to contribute to genome regul...

Authors: Hongfeng Chen, Jason J. Workman, Brian D. Strahl and R. Nicholas Laribee

Epigenetic dynamics of monocyte-to-macrophage differentiation

Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to an...

Authors: Stefan Wallner, Christopher Schröder, Elsa Leitão, Tea Berulava, Claudia Haak, Daniela Beißer, Sven Rahmann, Andreas S. Richter, Thomas Manke, Ulrike Bönisch, Laura Arrigoni, Sebastian Fröhler, Filippos Klironomos, Wei Chen, Nikolaus Rajewsky, Fabian Müller…

GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes

Genome-wide studies in higher eukaryotes have revealed the presence of paused RNA polymerase II (RNA-Pol) at about 30–50 bp downstream of the transcription start site of genes involved in developmental control...

Authors: Shih-Ying Tsai, Yuh-Long Chang, Krishna B. S. Swamy, Ruei-Lin Chiang and Der-Hwa Huang

Epigenetics and inheritance of phenotype variation in livestock

Epigenetic inheritance plays a crucial role in many biological processes, such as gene expression in early embryo development, imprinting and the silencing of transposons. It has recently been established that...

Authors: Kostas A. Triantaphyllopoulos, Ioannis Ikonomopoulos and Andrew J. Bannister

Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice

Changes to the epigenome with aging, and DNA modifications in particular, have been proposed as a central regulator of the aging process, a predictor of mortality, and a contributor to the pathogenesis of age-...

Authors: Niran Hadad, Dustin R. Masser, Sreemathi Logan, Benjamin Wronowski, Colleen A. Mangold, Nicholas Clark, Laura Otalora, Archana Unnikrishnan, Matthew M. Ford, Cory B. Giles, Jonathan D. Wren, Arlan Richardson, William E. Sonntag, David R. Stanford and Willard Freeman

Systemic epigenetic response to recombinant lentiviral vectors independent of proviral integration

Lentiviral vectors (LV) are widely used for various gene transfer or gene therapy applications. The effects of LV on target cells are expected to be limited to gene delivery. Yet, human hematopoietic CD34+ cel...

Authors: Tamas Aranyi, Daniel Stockholm, Roseline Yao, Catherine Poinsignon, Thibaut Wiart, Guillaume Corre, Nizar Touleimat, Jörg Tost, Anne Galy and Andràs Paldi

Chromatin variation associated with liver metabolism is mediated by transposable elements

Functional regulatory regions in eukaryotic genomes are characterized by the disruption of nucleosomes leading to accessible chromatin. The modulation of chromatin accessibility is one of the key mediators of ...

Authors: Juan Du, Amy Leung, Candi Trac, Michael Lee, Brian W. Parks, Aldons J. Lusis, Rama Natarajan and Dustin E. Schones

Epigenetic origin of adaptive phenotypic variants in the human blood fluke Schistosoma mansoni

Adaptive evolution is not possible without the generation of phenotypic variants. The origin of these variations has been a central topic in evolutionary biology. Up to now, it was commonly accepted that stand...

Authors: Sara Fneich, André Théron, Céline Cosseau, Anne Rognon, Benoit Aliaga, Jérôme Buard, David Duval, Nathalie Arancibia, Jérôme Boissier, David Roquis, Guillaume Mitta and Christoph Grunau

DNA methylation signature of human fetal alcohol spectrum disorder

Prenatal alcohol exposure is the leading preventable cause of behavioral and cognitive deficits, which may affect between 2 and 5 % of children in North America. While the underlying mechanisms of alcohol’s ef...

Authors: Elodie Portales-Casamar, Alexandre A. Lussier, Meaghan J. Jones, Julia L. MacIsaac, Rachel D. Edgar, Sarah M. Mah, Amina Barhdadi, Sylvie Provost, Louis-Philippe Lemieux-Perreault, Max S. Cynader, Albert E. Chudley, Marie-Pierre Dubé, James N. Reynolds, Paul Pavlidis and Michael S. Kobor

Profiling genome-wide DNA methylation

DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dy...

Authors: Wai-Shin Yong, Fei-Man Hsu and Pao-Yang Chen

Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells

During the process of spermatogenesis, male germ cells undergo dramatic chromatin reorganization, whereby most histones are replaced by protamines, as part of the pathway to compact the genome into the small n...

Authors: Lacey J. Luense, Xiaoshi Wang, Samantha B. Schon, Angela H. Weller, Enrique Lin Shiao, Jessica M. Bryant, Marisa S. Bartolomei, Christos Coutifaris, Benjamin A. Garcia and Shelley L. Berger

Genome-wide redistribution of MeCP2 in dorsal root ganglia after peripheral nerve injury

Methyl-CpG-binding protein 2 (MeCP2), a protein with affinity for methylated cytosines, is crucial for neuronal development and function. MeCP2 regulates gene expression through activation, repression and chro...

Authors: Melissa T. Manners, Adam Ertel, Yuzhen Tian and Seena K. Ajit

Inheritance of the CENP-A chromatin domain is spatially and temporally constrained at human centromeres

Chromatin containing the histone variant CENP-A (CEN chromatin) exists as an essential domain at every centromere and heritably marks the location of kinetochore assembly. The size of the CEN chromatin domain ...

Authors: Justyne E. Ross, Kaitlin Stimpson Woodlief and Beth A. Sullivan

Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells

Hematopoietic stem cell renewal and differentiation are regulated through epigenetic processes. The conversion of 5-methylcytosine into 5-hydroxymethylcytosine (5hmC) by ten-eleven-translocation enzymes provid...

Authors: Xavier Tekpli, Alfonso Urbanucci, Adnan Hashim, Cathrine B. Vågbø, Robert Lyle, Marianne K. Kringen, Anne Cathrine Staff, Ingunn Dybedal, Ian G. Mills, Arne Klungland and Judith Staerk

Abnormal X chromosome inactivation and sex-specific gene dysregulation after ablation of FBXL10

Almost all CpG-rich promoters in the mammalian genome are bound by the multidomain FBXL10 protein (also known as KDM2B, JHDM1B, CXXC2, and NDY1). FBXL10 is expressed as two isoforms: FBXL10-1, a longer form t...

Authors: Mathieu Boulard, John R. Edwards and Timothy H. Bestor

The chicken erythrocyte epigenome

Transcriptional regulation is impacted by multiple layers of genome organization. A general feature of transcriptionally active chromatin is sensitivity to DNase I and association with acetylated histones. How...

Authors: Sanzida Jahan, Wayne Xu, Shihua He, Carolina Gonzalez, Geneviève P. Delcuve and James R. Davie

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

The presence of histone 3 lysine 9 (H3K9) methylation on the mouse inactive X chromosome has been controversial over the last 15 years, and the functional role of H3K9 methylation in X chromosome inactivation...

Authors: Andrew Keniry, Linden J. Gearing, Natasha Jansz, Joy Liu, Aliaksei Z. Holik, Peter F. Hickey, Sarah A. Kinkel, Darcy L. Moore, Kelsey Breslin, Kelan Chen, Ruijie Liu, Catherine Phillips, Miha Pakusch, Christine Biben, Julie M. Sheridan, Benjamin T. Kile…

Distinct epigenetic features of differentiation-regulated replication origins

Eukaryotic genome duplication starts at discrete sequences (replication origins) that coordinate cell cycle progression, ensure genomic stability and modulate gene expression. Origins share some sequence featu...

Authors: Owen K. Smith, RyanGuk Kim, Haiqing Fu, Melvenia M. Martin, Chii Mei Lin, Koichi Utani, Ya Zhang, Anna B. Marks, Marc Lalande, Stormy Chamberlain, Maxwell W. Libbrecht, Eric E. Bouhassira, Michael C. Ryan, William S. Noble and Mirit I. Aladjem

Regulation of chaperone binding and nucleosome dynamics by key residues within the globular domain of histone H3

Nucleosomes have an important role in modulating access of DNA by regulatory factors. The role specific histone residues have in this process has been shown to be an important mechanism of transcription regula...

Authors: Sarah J. Hainer and Joseph A. Martens

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

Small molecule inhibitors of histone deacetylases (HDACi) hold promise as anticancer agents for particular malignancies. However, clinical use is often confounded by toxicity, perhaps due to indiscriminate hyp...

Authors: Christopher L. Frank, Dinesh Manandhar, Raluca Gordân and Gregory E. Crawford

The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing

The cohesin complex consists of multiple core subunits that play critical roles in mitosis and transcriptional regulation. The cohesin-associated protein Wapal plays a central role in off-loading cohesin to fa...

Authors: Cary Stelloh, Michael H. Reimer, Kirthi Pulakanti, Steven Blinka, Jonathan Peterson, Luca Pinello, Shuang Jia, Sergei Roumiantsev, Martin J. Hessner, Samuel Milanovich, Guo-Cheng Yuan and Sridhar Rao

The high mobility group protein HMO1 functions as a linker histone in yeast

Eukaryotic chromatin consists of nucleosome core particles connected by linker DNA of variable length. Histone H1 associates with the linker DNA to stabilize the higher-order chromatin structure and to modulat...

Authors: Arvind Panday and Anne Grove

Genome-wide methylation analysis demonstrates that 5-aza-2-deoxycytidine treatment does not cause random DNA demethylation in fragile X syndrome cells

Fragile X syndrome (FXS) is caused by CGG expansion over 200 repeats at the 5′ UTR of the FMR1 gene and subsequent DNA methylation of both the expanded sequence and the CpGs of the promoter region. This epigeneti...

Authors: Elisabetta Tabolacci, Giorgia Mancano, Stella Lanni, Federica Palumbo, Martina Goracci, Fabrizio Ferrè, Manuela Helmer-Citterich and Giovanni Neri

Application of recombinant TAF3 PHD domain instead of anti-H3K4me3 antibody

Histone posttranslational modifications (PTMs) represent a focal point of chromatin regulation. The genome-wide and locus-specific distribution and the presence of distinct histone PTMs is most commonly examin...

Authors: Goran Kungulovski, Rebekka Mauser, Richard Reinhardt and Albert Jeltsch

Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer

There is growing evidence that DNA methylation alterations contribute to carcinogenesis. While cancer tissue exhibits widespread DNA methylation changes, the proportion of tissue-specific versus tissue-indepe...

Authors: Yuting Chen, Charles E. Breeze, Shao Zhen, Stephan Beck and Andrew E. Teschendorff

Mutations that prevent or mimic persistent post-translational modifications of the histone H3 globular domain cause lethality and growth defects in Drosophila

Understanding the function of histone post-translational modifications is the key to deciphering how genomic activities are regulated. Among the least well-understood histone modifications in vivo are those t...

Authors: Hillary K. Graves, Pingping Wang, Matthew Lagarde, Zhihong Chen and Jessica K. Tyler

Molecular mechanism of the priming by jasmonic acid of specific dehydration stress response genes in Arabidopsis

Plant genes that provide a different response to a similar dehydration stress illustrate the concept of transcriptional ‘dehydration stress memory’. Pre-exposing a plant to a biotic stress or a stress-signalin...

Authors: Ning Liu and Zoya Avramova

Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase

DNA methylation is one way to encode epigenetic information and plays a crucial role in regulating gene expression during embryonic development. DNA methylation marks are established by the DNA methyltransfera...

Authors: Yun Liu, William Duong, Claudia Krawczyk, Nancy Bretschneider, Gábor Borbély, Mukesh Varshney, Christian Zinser, Primo Schär and Joëlle Rüegg

Profiling placental and fetal DNA methylation in human neural tube defects

The incidence of neural tube defects (NTDs) declined by about 40 % in Canada with the introduction of a national folic acid (FA) fortification program. Despite the fact that few Canadians currently exhibit fol...

Authors: E. Magda Price, Maria S. Peñaherrera, Elodie Portales-Casamar, Paul Pavlidis, Margot I. Van Allen, Deborah E. McFadden and Wendy P. Robinson

Chicken embryonic stem cells and primordial germ cells display different heterochromatic histone marks than their mammalian counterparts

Chromatin epigenetics participate in control of gene expression during metazoan development. DNA methylation and post-translational modifications (PTMs) of histones have been extensively characterised in cell ...

Authors: Clémence Kress, Guillaume Montillet, Christian Jean, Aurélie Fuet and Bertrand Pain

The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3

Regulation of gene expression by histone-modifying enzymes is essential to control cell fate decisions and developmental processes. Two histone-modifying enzymes, RPD3, a deacetylase, and dKDM5/LID, a demethyl...

Authors: Ambikai Gajan, Valerie L. Barnes, Mengying Liu, Nirmalya Saha and Lori A. Pile

A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans

Environmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human. The capacity and mechanism of such phenomena are poorly understood. In C. elegans, siRNA ...

Authors: Julie Zhouli Ni, Natallia Kalinava, Esteban Chen, Alex Huang, Thi Trinh and Sam Guoping Gu

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis

Human histone H3.5 is a non-allelic H3 variant evolutionally derived from H3.3. The H3.5 mRNA is highly expressed in human testis. However, the function of H3.5 has remained poorly understood.

Authors: Takashi Urahama, Akihito Harada, Kazumitsu Maehara, Naoki Horikoshi, Koichi Sato, Yuko Sato, Koji Shiraishi, Norihiro Sugino, Akihisa Osakabe, Hiroaki Tachiwana, Wataru Kagawa, Hiroshi Kimura, Yasuyuki Ohkawa and Hitoshi Kurumizaka

Roles of cofactors and chromatin accessibility in Hox protein target specificity

The regulation of specific target genes by transcription factors is central to our understanding of gene network control in developmental and physiological processes yet how target specificity is achieved is s...

Authors: Ching Yew Beh, Sherif El-Sharnouby, Aikaterini Chatzipli, Steven Russell, Siew Woh Choo and Robert White

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

Considerable progress towards an understanding of complex diseases has been made in recent years due to the development of high-throughput genotyping technologies. Using microarrays that contain millions of si...

Authors: Yu Gyoung Tak and Peggy J. Farnham

A continuous kinetic assay for protein and DNA methyltransferase enzymatic activities

Methyltransferases (MTs) catalyze the S-adenosylmethionine (SAM)-dependent methylation of a wide variety of protein and DNA substrates. Methylation of lysine, arginine or cytosine regulates a variety of biologica...

Authors: Shai Duchin, Zlata Vershinin, Dan Levy and Amir Aharoni

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors

The capacity for plasticity in the adult brain is limited by the anatomical traces laid down during early postnatal life. Removing certain molecular brakes, such as histone deacetylases (HDACs), has proven to ...

Authors: Andreas Lennartsson, Erik Arner, Michela Fagiolini, Alka Saxena, Robin Andersson, Hazuki Takahashi, Yukihiko Noro, Judy Sng, Albin Sandelin, Takao K. Hensch and Piero Carninci

Genetic and epigenetic variation among inbred mouse littermates: identification of inter-individual differentially methylated regions

Phenotypic variability among inbred littermates reared in controlled environments remains poorly understood. Metastable epialleles refer to loci that intrinsically behave in this way and a few examples have be...

Authors: Harald Oey, Luke Isbel, Peter Hickey, Basant Ebaid and Emma Whitelaw

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia

Precise nucleosome positioning is an increasingly recognized feature of promoters and enhancers, reflecting complex contributions of DNA sequence, nucleosome positioning, histone modification and transcription...

Authors: Jennifer N. Wu, Luca Pinello, Elinor Yissachar, Jonathan W. Wischhusen, Guo-Cheng Yuan and Charles W. M. Roberts

ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay

DNA methylation at cytosine nucleotides constitutes epigenetic gene regulation impacting cellular development and a wide range of diseases. Cytosine bases of the DNA are converted to 5-methylcytosine by the me...

Authors: Jens Preussner, Julia Bayer, Carsten Kuenne and Mario Looso

A rapid passage through a two-active-X-chromosome state accompanies the switch of imprinted X-inactivation patterns in mouse trophoblast stem cells

In female mice, while the presence of two-active X-chromosomes characterises pluripotency, it is not tolerated in most other cellular contexts. In particular, in the trophoblastic lineage, impairment of patern...

Authors: Julie Prudhomme, Agnès Dubois, Pablo Navarro, Danielle Arnaud, Philip Avner and Céline Morey