Articles

Genome-wide methylation data mirror ancestry information

Genetic data are known to harbor information about human demographics, and genotyping data are commonly used for capturing ancestry information by leveraging genome-wide differences between populations. In con...

Authors: Elior Rahmani, Liat Shenhav, Regev Schweiger, Paul Yousefi, Karen Huen, Brenda Eskenazi, Celeste Eng, Scott Huntsman, Donglei Hu, Joshua Galanter, Sam S. Oh, Melanie Waldenberger, Konstantin Strauch, Harald Grallert, Thomas Meitinger, Christian Gieger…

The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes

The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function—the storage, expression, and replication of genetic information—is still one of the central i...

Authors: Tobias A. Knoch, Malte Wachsmuth, Nick Kepper, Michael Lesnussa, Anis Abuseiris, A. M. Ali Imam, Petros Kolovos, Jessica Zuin, Christel E. M. Kockx, Rutger W. W. Brouwer, Harmen J. G. van de Werken, Wilfred F. J. van IJcken, Kerstin S. Wendt and Frank G. Grosveld

Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells

Genome organization into subchromosomal topologically associating domains (TADs) is linked to cell-type-specific gene expression programs. However, dynamic properties of such domains remain elusive, and it is ...

Authors: Malte Wachsmuth, Tobias A. Knoch and Karsten Rippe

“Gap hunting” to characterize clustered probe signals in Illumina methylation array data

The Illumina 450k array has been widely used in epigenetic association studies. Current quality-control (QC) pipelines typically remove certain sets of probes, such as those containing a SNP or with multiple m...

Authors: Shan V. Andrews, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen and M. Daniele Fallin

Targeted bisulfite sequencing of the dynamic DNA methylome

The ability to measure DNA methylation precisely and efficiently continues to drive our understanding of this modification in development and disease. Whole genome bisulfite sequencing has the advantage of the...

Authors: Michael J. Ziller, Elena K. Stamenova, Hongcang Gu, Andreas Gnirke and Alexander Meissner

HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205

The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation....

Authors: Ajay S. Labade, Krishanpal Karmodiya and Kundan Sengupta

Widespread recovery of methylation at gametic imprints in hypomethylated mouse stem cells following rescue with DNMT3A2

Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated reg...

Authors: Avinash Thakur, Sarah-Jayne Mackin, Rachelle E. Irwin, Karla M. O’Neill, Gareth Pollin and Colum Walsh

Protein kinase Msk1 physically and functionally interacts with the KMT2A/MLL1 methyltransferase complex and contributes to the regulation of multiple target genes

The KMT2A/MLL1 lysine methyltransferase complex is an epigenetic regulator of selected developmental genes, in part through the SET domain-catalysed methylation of H3K4. It is essential for normal embryonic de...

Authors: Maaike Wiersma, Marianne Bussiere, John A. Halsall, Nil Turan, Robert Slany, Bryan M. Turner and Karl P. Nightingale

Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance

Long noncoding RNAs (lncRNAs) are a class of ubiquitous noncoding RNAs and have been found to act as tumor suppressors or oncogenes, which dramatically altered our understanding of cancer. Naked mole rat (NMR, He...

Authors: Jian-Jun Jiang, Le-Hua Cheng, Huan Wu, Yong-Han He and Qing-Peng Kong

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits

Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understandin...

Authors: Suhn Kyong Rhie, Yu Guo, Yu Gyoung Tak, Lijing Yao, Hui Shen, Gerhard A. Coetzee, Peter W. Laird and Peggy J. Farnham

Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq

The robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: They are non-renewable, vary in performance betw...

Authors: Michele Busby, Catherine Xue, Catherine Li, Yossi Farjoun, Elizabeth Gienger, Ido Yofe, Adrianne Gladden, Charles B. Epstein, Evan M. Cornett, Scott B. Rothbart, Chad Nusbaum and Alon Goren

Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia

A comprehensive assessment of the epigenetic dynamics in cancer cells is the key to understanding the molecular mechanisms underlying cancer and to improving cancer diagnostics, prognostics and treatment. By c...

Authors: Michiel E. Adriaens, Peggy Prickaerts, Michelle Chan-Seng-Yue, Twan van den Beucken, Vivian E. H. Dahlmans, Lars M. Eijssen, Timothy Beck, Bradly G. Wouters, Jan Willem Voncken and Chris T. A. Evelo

Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells

During meiosis, the X and Y chromosomes are transcriptionally silenced. The persistence of repressive chromatin marks on the sex chromatin after meiosis initially led to the assumption that XY gene silencing ...

Authors: Charlotte Moretti, Daniel Vaiman, Frederic Tores and Julie Cocquet

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3

Trimethylation at histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) controls gene activity during development and differentiation. Whether H3K4me3 and H3K27me3 changes dynamically in response to altered m...

Authors: Peggy Prickaerts, Michiel E. Adriaens, Twan van den Beucken, Elizabeth Koch, Ludwig Dubois, Vivian E. H. Dahlmans, Caroline Gits, Chris T. A. Evelo, Michelle Chan-Seng-Yue, Bradly G. Wouters and Jan Willem Voncken

Histone macroH2A1.2 promotes metabolic health and leanness by inhibiting adipogenesis

Obesity has tremendous impact on the health systems. Its epigenetic bases are unclear. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1.1 and macroH2A1.2, reg...

Authors: Valerio Pazienza, Concetta Panebianco, Francesca Rappa, Domenico Memoli, Michela Borghesan, Sara Cannito, Asami Oji, Giuseppe Mazza, Domenico Tamburrino, Giuseppe Fusai, Rosario Barone, Giulia Bolasco, Francesc Villarroya, Joan Villarroya, Kiyotaka Hatsuzawa, Francesco Cappello…

An H4K16 histone acetyltransferase mediates decondensation of the X chromosome in C. elegans males

In C. elegans, in order to equalize gene expression between the sexes and balance X and autosomal expression, two steps are believed to be required. First, an unknown mechanism is hypothesized to upregulate the X...

Authors: Alyssa C. Lau, Kevin P. Zhu, Elizabeth A. Brouhard, Michael B. Davis and Györgyi Csankovszki

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

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

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

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

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

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

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

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