Articles

An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo

The physiological function of eukaryotic DNA occurs in the context of nucleosomal arrays that can expose or obscure defined segments of the genome. Certain DNA sequences are capable of strongly positioning a n...

Authors: Lia E Gracey, Zhi-Ying Chen, Jay M Maniar, Anton Valouev, Arend Sidow, Mark A Kay and Andrew Z Fire

A combined HM-PCR/SNuPE method for high sensitive detection of rare DNA methylation

DNA methylation changes are widely used as early molecular markers in cancer detection. Sensitive detection and classification of rare methylation changes in DNA extracted from circulating body fluids or compl...

Authors: Sascha Tierling, Matthias Schuster, Reimo Tetzner and Jörn Walter

Extensive sequence-influenced DNA methylation polymorphism in the human genome

Epigenetic polymorphisms are a potential source of human diversity, but their frequency and relationship to genetic polymorphisms are unclear. DNA methylation, an epigenetic mark that is a covalent modificatio...

Authors: Asaf Hellman and Andrew Chess

Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation

X chromosome inactivation, the mechanism used by mammals to equalise dosage of X-linked genes in XX females relative to XY males, is triggered by chromosome-wide localisation of a cis-acting non-coding RNA, Xist....

Authors: Y Amy Tang, Derek Huntley, Giovanni Montana, Andrea Cerase, Tatyana B Nesterova and Neil Brockdorff

HP1γ function is required for male germ cell survival and spermatogenesis

HP1 proteins are conserved components of eukaryotic constitutive heterochromatin. In mammals, there are three genes that encode HP1-like proteins, termed HP1α, HP1β and HP1γ, which have a high degree of homolo...

Authors: Jeremy P Brown, Jörn Bullwinkel, Bettina Baron-Lühr, Mustafa Billur, Philipp Schneider, Heinz Winking and Prim B Singh

Histone variant macroH2A1 deletion in mice causes female-specific steatosis

Vertebrate heterochromatin contains a non-allelic variant of the histone H2A called macroH2A1, which has the characteristic of being three times the size of the canonical H2A. The macroH2A1 C-terminal extensio...

Authors: Mathieu Boulard, Sébastien Storck, Rong Cong, Rodrigo Pinto, Hélène Delage and Philippe Bouvet

Histone H1 variant-specific lysine methylation by G9a/KMT1C and Glp1/KMT1D

The linker histone H1 has a key role in establishing and maintaining higher order chromatin structure and in regulating gene expression. Mammals express up to 11 different H1 variants, with H1.2 and H1.4 being...

Authors: Thomas Weiss, Sonja Hergeth, Ulrike Zeissler, Annalisa Izzo, Philipp Tropberger, Barry M Zee, Miroslav Dundr, Benjamin A Garcia, Sylvain Daujat and Robert Schneider

A paucity of heterochromatin at functional human neocentromeres

Centromeres are responsible for the proper segregation of replicated chromatids during cell division. Neocentromeres are fully functional ectopic human centromeres that form on low-copy DNA sequences and permi...

Authors: Alicia Alonso, Dan Hasson, Fanny Cheung and Peter E Warburton

Roles for common MLL/COMPASS subunits and the 19S proteasome in regulating CIITA pIV and MHC class II gene expression and promoter methylation

Studies indicate that the 19S proteasome contributes to chromatin reorganization, independent of the role the proteasome plays in protein degradation. We have previously shown that components of the 19S protea...

Authors: Olivia I Koues, Ninad T Mehta, Agnieszka D Truax, R Kyle Dudley, Jeanne K Brooks and Susanna F Greer

Histone H3 lysine 4 methylation is associated with the transcriptional reprogramming efficiency of somatic nuclei by oocytes

When the nuclei of mammalian somatic cells are transplanted to amphibian oocytes in the first meiotic prophase, they are rapidly induced to begin transcribing several pluripotency genes, including Sox2 and Oct...

Authors: Kazutaka Murata, Tony Kouzarides, Andrew J Bannister and John B Gurdon

Transcription-dependent silencing of inducible convergent transgenes in transgenic mice

Silencing of transgenes in mice is a common phenomenon typically associated with short multi-copy transgenes. We have investigated the regulation of the highly inducible human granulocyte-macrophage colony-sti...

Authors: Fernando J Calero-Nieto, Andrew G Bert and Peter N Cockerill

Distinguishing epigenetic marks of developmental and imprinting regulation

The field of epigenetics is developing rapidly, however we are only beginning to comprehend the complexity of its influence on gene regulation. Using genomic imprinting as a model we examine epigenetic profile...

Authors: Kirsten R McEwen and Anne C Ferguson-Smith

Differences in the epigenetic and reprogramming properties of pluripotent and extra-embryonic stem cells implicate chromatin remodelling as an important early event in the developing mouse embryo

During early mouse development, two extra-embryonic lineages form alongside the future embryo: the trophectoderm (TE) and the primitive endoderm (PrE). Epigenetic changes known to take place during these early...

Authors: Joana Santos, C Filipe Pereira, Aida Di-Gregorio, Thomas Spruce, Olivia Alder, Tristan Rodriguez, Véronique Azuara, Matthias Merkenschlager and Amanda G Fisher

Repressive and non-repressive chromatin at native telomeres in Saccharomyces cerevisiae

In Saccharomyces cerevisiae genes that are located close to a telomere can become transcriptionally repressed by an epigenetic process known as telomere position effect. There is large variation in the level of t...

Authors: Esther R Loney, Peter W Inglis, Sarah Sharp, Fiona E Pryde, Nicholas A Kent, Jane Mellor and Edward J Louis

Core promoter acetylation is not required for high transcription from the phosphoenolpyruvate carboxylase promoter in maize

Acetylation of promoter nucleosomes is tightly correlated and mechanistically linked to gene activity. However, transcription is not necessary for promoter acetylation. It seems, therefore, that external and e...

Authors: Ina Horst, Sascha Offermann, Bjoern Dreesen, Markus Niessen and Christoph Peterhansel

EZH2-dependent chromatin looping controls INK4a and INK4b, but not ARF, during human progenitor cell differentiation and cellular senescence

The INK4b-ARF-INK4a tumour suppressor locus controls the balance between progenitor cell renewal and cancer. In this study, we investigated how higher-order chromatin structure modulates differential expression o...

Authors: Sima Kheradmand Kia, Parham Solaimani Kartalaei, Elnaz Farahbakhshian, Farzin Pourfarzad, Marieke von Lindern and C Peter Verrijzer

Interaction of RNA polymerase II and the small RNA machinery affects heterochromatic silencing in Drosophila

Heterochromatin is the tightly packaged dynamic region of the eukaryotic chromosome that plays a vital role in cellular processes such as mitosis and meiotic recombination. Recent experiments in Schizosaccharomyc...

Authors: Harsh H Kavi and James A Birchler

The molecular basis for stability of heterochromatin-mediated silencing in mammals

The archetypal epigenetic phenomenon of position effect variegation (PEV) in Drosophila occurs when a gene is brought abnormally close to heterochromatin, resulting in stochastic silencing of the affected gene in...

Authors: Kyoko Hiragami-Hamada, Sheila Q Xie, Alexander Saveliev, Santiago Uribe-Lewis, Ana Pombo and Richard Festenstein

Epigenetics & Chromatin celebrates its first anniversary

Authors: Steven Henikoff and Frank Grosveld

ERG-associated protein with SET domain (ESET)-Oct4 interaction regulates pluripotency and represses the trophectoderm lineage

Pluripotency, the capacity for indefinite self-renewal and differentiation into diverse cell types is a unique state exhibited by embryonic stem (ES) cells. Transcriptional regulators, such as Oct4, are critic...

Authors: Leng-Siew Yeap, Katsuhiko Hayashi and M Azim Surani

Epigenetic inheritance of an inducibly nucleosome-depleted promoter and its associated transcriptional state in the apparent absence of transcriptional activators

Dynamic changes to the chromatin structure play a critical role in transcriptional regulation. This is exemplified by the Spt6-mediated histone deposition on to histone-depleted promoters that results in displ...

Authors: Ryosuke Ohsawa, Melissa Adkins and Jessica K Tyler

Talking to chromatin: post-translational modulation of polycomb group function

Polycomb Group proteins are important epigenetic regulators of gene expression. Epigenetic control by polycomb Group proteins involves intrinsic as well as associated enzymatic activities. Polycomb target gene...

Authors: Hanneke EC Niessen, Jeroen A Demmers and Jan Willem Voncken

Essential role for Argonaute2 protein in mouse oogenesis

Argonaute2 protein (Ago2) is a key component of RNA-induced gene silencing complex, which is crucial for microRNA-mediated repression of target genes. The function of Ago2 in the mouse oocyte and early embryon...

Authors: Masahiro Kaneda, Fuchou Tang, Dónal O'Carroll, Kaiqin Lao and M Azim Surani

A role for non-coding Tsix transcription in partitioning chromatin domains within the mouse X-inactivation centre

Delimiting distinct chromatin domains is essential for temporal and spatial regulation of gene expression. Within the X-inactivation centre region (Xic), the Xist locus, which triggers X-inactivation, is juxtapos...

Authors: Pablo Navarro, Sophie Chantalat, Mario Foglio, Corinne Chureau, Sébastien Vigneau, Philippe Clerc, Philip Avner and Claire Rougeulle

Tissue-specific variation in DNA methylation levels along human chromosome 1

DNA methylation is a major epigenetic modification important for regulating gene expression and suppressing spurious transcription. Most methods to scan the genome in different tissues for differentially methy...

Authors: Cecilia De Bustos, Edward Ramos, Janet M Young, Robert K Tran, Uwe Menzel, Cordelia F Langford, Evan E Eichler, Li Hsu, Steve Henikoff, Jan P Dumanski and Barbara J Trask

DNA replication and the GINS complex: localization on extended chromatin fibers

The GINS complex is thought to be essential for the processes of initiation and elongation of DNA replication. This complex contains four subunits, one of which (Psf1) is proposed to bind to both chromatin and...

Authors: Stephanie M Cohen, Paul D Chastain II, Marila Cordeiro-Stone and David G Kaufman

The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly in development and spermatogenesis

Histone methylation is thought to be central to the epigenetic mechanisms that maintain and confine cellular identity in multi-cellular organisms. To examine epigenetic roles in cellular homeostasis, we condit...

Authors: Stefan Glaser, Sandra Lubitz, Kate L Loveland, Kazu Ohbo, Lorraine Robb, Frieder Schwenk, Jost Seibler, Daniela Roellig, Andrea Kranz, Konstantinos Anastassiadis and A Francis Stewart

Multiple sequence-directed possibilities provide a pool of nucleosome position choices in different states of activity of a gene

Genome-wide mappings of nucleosome occupancy in different species have shown presence of well-positioned nucleosomes. While the DNA sequences may help decide their locations, the observed positions in vivo are en...

Authors: Vinesh Vinayachandran, Rama-Haritha Pusarla and Purnima Bhargava

Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation

DNA methylation plays a vital role in normal cellular function, with aberrant methylation signatures being implicated in a growing number of human pathologies and complex human traits. Methods based on the mod...

Authors: Sophia J Docherty, Oliver SP Davis, Claire MA Haworth, Robert Plomin and Jonathan Mill

Yeast Sgf73/Ataxin-7 serves to anchor the deubiquitination module into both SAGA and Slik(SALSA) HAT complexes

Spinocerebellar ataxia (SCA) is a physically devastating, genetically inherited disorder characterized by abnormal brain function that results in the progressive loss of the ability to coordinate movements. Th...

Authors: Kenneth K Lee, Selene K Swanson, Laurence Florens, Michael P Washburn and Jerry L Workman

High-resolution mapping of heterochromatin redistribution in a Drosophila position-effect variegation model

Position-effect variegation (PEV) is the stochastic transcriptional silencing of a gene positioned adjacent to heterochromatin. white-mottled X-chromosomal inversions in Drosophila are classic PEV models that sho...

Authors: Maartje J Vogel, Ludo Pagie, Wendy Talhout, Marja Nieuwland, Ron M Kerkhoven and Bas van Steensel

Single-epitope recognition imaging of native chromatin

Direct visualization of chromatin has the potential to provide important insights into epigenetic processes. In particular, atomic force microscopy (AFM) can visualize single nucleosomes under physiological io...

Authors: Hongda Wang, Yamini Dalal, Steven Henikoff and Stuart Lindsay

Chromatin structure and DNA damage repair

The integrity of the genome is continuously challenged by both endogenous and exogenous DNA damaging agents. These damaging agents can induce a wide variety of lesions in the DNA, such as double strand breaks,...

Authors: Christoffel Dinant, Adriaan B Houtsmuller and Wim Vermeulen

Evidence for conserved DNA and histone H3 methylation reprogramming in mouse, bovine and rabbit zygotes

In mammals the parental genomes are epigenetically reprogrammed after fertilization. This reprogramming includes a rapid demethylation of the paternal (sperm-derived) chromosomes prior to DNA replication in zy...

Authors: Konstantin Lepikhov, Valeri Zakhartchenko, Ru Hao, Feikun Yang, Christine Wrenzycki, Heiner Niemann, Eckhard Wolf and Joern Walter

Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene

Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methyla...

Authors: Ida LM Candiloro, Thomas Mikeska, Peter Hokland and Alexander Dobrovic

Both telomeric and non-telomeric DNA damage are determinants of mammalian cellular senescence

Cellular senescence is a state reached by normal mammalian cells after a finite number of cell divisions and is characterized by morphological and physiological changes including terminal cell-cycle arrest. Th...

Authors: Asako J Nakamura, Y Jeffrey Chiang, Karen S Hathcock, Izumi Horikawa, Olga A Sedelnikova, Richard J Hodes and William M Bonner

The fungus Neurospora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9

Silencing of genes inserted near telomeres provides a model to investigate the function of heterochromatin. We initiated a study of telomeric silencing in Neurospora crassa, a fungus that sports DNA methylation, ...

Authors: Kristina M Smith, Gregory O Kothe, Cindy B Matsen, Tamir K Khlafallah, Keyur K Adhvaryu, Melissa Hemphill, Michael Freitag, Mohammad R Motamedi and Eric U Selker

Rapid telomere motions in live human cells analyzed by highly time-resolved microscopy

Telomeres cap chromosome ends and protect the genome. We studied individual telomeres in live human cancer cells. In capturing telomere motions using quantitative imaging to acquire complete high-resolution th...

Authors: Xueying Wang, Zvi Kam, Peter M Carlton, Lifeng Xu, John W Sedat and Elizabeth H Blackburn

Spatial and temporal plasticity of chromatin during programmed DNA-reorganization in Stylonychia macronuclear development

In this study we exploit the unique genome organization of ciliates to characterize the biological function of histone modification patterns and chromatin plasticity for the processing of specific DNA sequence...

Authors: Jan Postberg, Katharina Heyse, Marion Cremer, Thomas Cremer and Hans J Lipps

Dicer regulates Xist promoter methylation in ES cells indirectly through transcriptional control of Dnmt3a

X chromosome inactivation is the mechanism used in mammals to achieve dosage compensation of X-linked genes in XX females relative to XY males. Chromosome silencing is triggered in cis by expression of the non-co...

Authors: Tatyana B Nesterova, Bilyana C Popova, Bradley S Cobb, Sara Norton, Claire E Senner, Y Amy Tang, Thomas Spruce, Tristan A Rodriguez, Takashi Sado, Matthias Merkenschlager and Neil Brockdorff

Welcome to Epigenetics & Chromatin

Authors: Steven Henikoff and Frank Grosveld