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Articles
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Citation: Epigenetics & Chromatin 2013 6(Suppl 1):P66
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A permissive chromatin structure is adopted prior to site-specific DNA demethylation of developmentally expressed genes involved in macronuclear differentiation
DNA methylation and demethylation are important epigenetic regulatory mechanisms in eukaryotic cells and, so far, only partially understood. We exploit the minimalistic biological ciliate system to understand ...
Citation: Epigenetics & Chromatin 2013 6:5 -
Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array
Measurement of genome-wide DNA methylation (DNAm) has become an important avenue for investigating potential physiologically-relevant epigenetic changes. Illumina Infinium (Illumina, San Diego, CA, USA) is a c...
Citation: Epigenetics & Chromatin 2013 6:4 -
Functional characterization of EZH2β reveals the increased complexity of EZH2 isoforms involved in the regulation of mammalian gene expression
Histone methyltransferase enhancer of zeste homologue 2 (EZH2) forms an obligate repressive complex with suppressor of zeste 12 and embryonic ectoderm development, which is thought, along with EZH1, to be prim...
Citation: Epigenetics & Chromatin 2013 6:3 -
Epigenetics & Chromatin: interactions and processes
On 11 to 13 March 2013, BioMed Central will be hosting its inaugural conference, Epigenetics & Chromatin: Interactions and Processes, at Harvard Medical School, Boston, MA, USA. Epigenetics & Chromatin has now la...
Citation: Epigenetics & Chromatin 2013 6:2 -
Crosstalk between SET7/9-dependent methylation and ARTD1-mediated ADP-ribosylation of histone H1.4
Different histone post-translational modifications (PTMs) fine-tune and integrate different cellular signaling pathways at the chromatin level. ADP-ribose modification of histones by cellular ADP-ribosyltransf...
Citation: Epigenetics & Chromatin 2013 6:1 -
Tracking the mechanical dynamics of human embryonic stem cell chromatin
A plastic chromatin structure has emerged as fundamental to the self-renewal and pluripotent capacity of embryonic stem (ES) cells. Direct measurement of chromatin dynamics in vivo is, however, challenging as hig...
Citation: Epigenetics & Chromatin 2012 5:20 -
Mediator regulates non-coding RNA transcription at fission yeast centromeres
In fission yeast, centromeric heterochromatin is necessary for the fidelity of chromosome segregation. Propagation of heterochromatin in dividing cells requires RNA interference (RNAi) and transcription of cen...
Citation: Epigenetics & Chromatin 2012 5:19 -
Erratum to: HP1gamma function is required for male germ cell survival and spermatogenesis
Citation: Epigenetics & Chromatin 2012 5:18 -
HIRA dependent H3.3 deposition is required for transcriptional reprogramming following nuclear transfer to Xenopus oocytes
Nuclear reprogramming is potentially important as a route to cell replacement and drug discovery, but little is known about its mechanism. Nuclear transfer to eggs and oocytes attempts to identify the mechanis...
Citation: Epigenetics & Chromatin 2012 5:17 -
Spatial organization of the chicken beta-globin gene domain in erythroid cells of embryonic and adult lineages
The β-globin gene domains of vertebrate animals constitute popular models for studying the regulation of eukaryotic gene transcription. It has previously been shown that in the mouse the developmental switchin...
Citation: Epigenetics & Chromatin 2012 5:16 -
Deacetylation of H4-K16Ac and heterochromatin assembly in senescence
Cellular senescence is a stress response of mammalian cells leading to a durable arrest of cell proliferation that has been implicated in tumor suppression, wound healing, and aging. The proliferative arrest i...
Citation: Epigenetics & Chromatin 2012 5:15 -
Selected imprinting of INS in the marsupial
In marsupials, growth and development of the young occur postnatally, regulated by milk that changes in composition throughout the long lactation. To initiate lactation in mammals, there is an absolute require...
Citation: Epigenetics & Chromatin 2012 5:14 -
Cohesin is required for expression of the estrogen receptor-alpha (ESR1) gene
In conjunction with posttranslational chromatin modifications, proper arrangement of higher order chromatin structure appears to be important for controlling transcription in the nucleus. Recent genome-wide st...
Citation: Epigenetics & Chromatin 2012 5:13 -
MK3 controls Polycomb target gene expression via negative feedback on ERK
Gene-environment interactions are mediated by epigenetic mechanisms. Polycomb Group proteins constitute part of an epigenetic cellular transcriptional memory system that is subject to dynamic modulation during...
Citation: Epigenetics & Chromatin 2012 5:12 -
The influence of DNA sequence on epigenome-induced pathologies
Clear cause-and-effect relationships are commonly established between genotype and the inherited risk of acquiring human and plant diseases and aberrant phenotypes. By contrast, few such cause-and-effect relat...
Citation: Epigenetics & Chromatin 2012 5:11 -
Rapid genome-scale mapping of chromatin accessibility in tissue
The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. C...
Citation: Epigenetics & Chromatin 2012 5:10 -
Genome-wide DNA methylation profiling of non-small cell lung carcinomas
Non-small cell lung carcinoma (NSCLC) is a complex malignancy that owing to its heterogeneity and poor prognosis poses many challenges to diagnosis, prognosis and patient treatment. DNA methylation is an impor...
Citation: Epigenetics & Chromatin 2012 5:9 -
The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner
CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types. In conjunction with cohesin, it organizes chromatin into loops, thereby regulating gene expression and epigen...
Citation: Epigenetics & Chromatin 2012 5:8 -
A unified phylogeny-based nomenclature for histone variants
Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conven...
Citation: Epigenetics & Chromatin 2012 5:7 -
A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci
Chromatin structure at a given site can differ between chromosome copies in a cell, and such imbalances in chromatin structure have been shown to be important in understanding the molecular mechanisms controll...
Citation: Epigenetics & Chromatin 2012 5:6 -
The conformational flexibility of the C-terminus of histone H4 promotes histone octamer and nucleosome stability and yeast viability
The protein anti-silencing function 1 (Asf1) chaperones histones H3/H4 for assembly into nucleosomes every cell cycle as well as during DNA transcription and repair. Asf1 interacts directly with H4 through the...
Citation: Epigenetics & Chromatin 2012 5:5 -
ATP-dependent chromatin remodeling in the DNA-damage response
The integrity of DNA is continuously challenged by metabolism-derived and environmental genotoxic agents that cause a variety of DNA lesions, including base alterations and breaks. DNA damage interferes with v...
Citation: Epigenetics & Chromatin 2012 5:4 -
Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells
DNA methylation, histone modifications and nucleosome occupancy act in concert for regulation of gene expression patterns in mammalian cells. Recently, G9a, a H3K9 methyltransferase, has been shown to play a r...
Citation: Epigenetics & Chromatin 2012 5:3 -
Knockdown of menin affects pre-mRNA processing and promoter fidelity at the interferon-gamma inducible IRF1 gene
The tumor suppressor menin (MEN1) is mutated in the inherited disease multiple endocrine neoplasia type I, and has several documented cellular roles, including the activation and repression of transcription effec...
Citation: Epigenetics & Chromatin 2012 5:2 -
Enhancers and silencers: an integrated and simple model for their function
Regulatory DNA elements such as enhancers, silencers and insulators are embedded in metazoan genomes, and they control gene expression during development. Although they fulfil different roles, they share speci...
Citation: Epigenetics & Chromatin 2012 5:1 -
Enhancer-driven chromatin interactions during development promote escape from silencing by a long non-coding RNA
Gene regulation in eukaryotes is a complex process entailing the establishment of transcriptionally silent chromatin domains interspersed with regions of active transcription. Imprinted domains consist of clus...
Citation: Epigenetics & Chromatin 2011 4:21 -
Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells
A proposed role for Myc in maintaining mouse embryonic stem (ES) cell pluripotency is transcriptional repression of key differentiation-promoting genes, but detail of the mechanism has remained an important op...
Citation: Epigenetics & Chromatin 2011 4:20 -
A proteomic approach for the identification of novel lysine methyltransferase substrates
Signaling via protein lysine methylation has been proposed to play a central role in the regulation of many physiologic and pathologic programs. In contrast to other post-translational modifications such as ph...
Citation: Epigenetics & Chromatin 2011 4:19 -
Proliferating cell nuclear antigen is required for loading of the SMCX/KMD5C histone demethylase onto chromatin
Histone methylation is regulated by a large number of histone methyltransferases and demethylases. The recently discovered SMCX/KMD5C demethylase has been shown to remove methyl residues from lysine 4 of histo...
Citation: Epigenetics & Chromatin 2011 4:18 -
Pluripotency factor binding and Tsix expression act synergistically to repress Xist in undifferentiated embryonic stem cells
Expression of Xist, the master regulator of X chromosome inactivation, is extinguished in pluripotent cells, a process that has been linked to programmed X chromosome reactivation. The key pluripotency transcript...
Citation: Epigenetics & Chromatin 2011 4:17 -
Chromatin regulated interchange between polycomb repressive complex 2 (PRC2)-Ezh2 and PRC2-Ezh1 complexes controls myogenin activation in skeletal muscle cells
Polycomb group (PcG) genes code for chromatin multiprotein complexes that are responsible for maintaining gene silencing of transcriptional programs during differentiation and in adult tissues. Despite the lar...
Citation: Epigenetics & Chromatin 2011 4:16 -
Histone H1 interphase phosphorylation becomes largely established in G1 or early S phase and differs in G1 between T-lymphoblastoid cells and normal T cells
Histone H1 is an important constituent of chromatin, and is involved in regulation of its structure. During the cell cycle, chromatin becomes locally decondensed in S phase, highly condensed during metaphase, ...
Citation: Epigenetics & Chromatin 2011 4:15 -
Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene
Random monoallelic expression contributes to phenotypic variation of cells and organisms. However, the epigenetic mechanisms by which individual alleles are randomly selected for expression are not known. Taki...
Citation: Epigenetics & Chromatin 2011 4:14 -
The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization
Transcription initiation RNAs (tiRNAs) are nuclear localized 18 nucleotide RNAs derived from sequences immediately downstream of RNA polymerase II (RNAPII) transcription start sites. Previous reports have show...
Citation: Epigenetics & Chromatin 2011 4:13 -
H3K9me3-binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral silencing
Endogenous retroviruses (ERVs) are parasitic sequences whose derepression is associated with cancer and genomic instability. Many ERV families are silenced in mouse embryonic stem cells (mESCs) via SETDB1-depo...
Citation: Epigenetics & Chromatin 2011 4:12 -
Methylation of H2AR29 is a novel repressive PRMT6 target
Covalent histone modifications are central to all DNA-dependent processes. Modifications of histones H3 and H4 are becoming well characterised, but knowledge of how H2A modifications regulate chromatin dynamic...
Citation: Epigenetics & Chromatin 2011 4:11 -
Genome-wide mapping of imprinted differentially methylated regions by DNA methylation profiling of human placentas from triploidies
Genomic imprinting is an important epigenetic process involved in regulating placental and foetal growth. Imprinted genes are typically associated with differentially methylated regions (DMRs) whereby one of t...
Citation: Epigenetics & Chromatin 2011 4:10 -
Generation of bivalent chromatin domains during cell fate decisions
In self-renewing, pluripotent cells, bivalent chromatin modification is thought to silence (H3K27me3) lineage control genes while 'poising' (H3K4me3) them for subsequent activation during differentiation, impl...
Citation: Epigenetics & Chromatin 2011 4:9 -
Erratum to: Multiple sequence-directed possibilities provide a pool of nucleosome position choices in different states of activity of a gene
Citation: Epigenetics & Chromatin 2011 4:8 -
Extensive epigenetic reprogramming in human somatic tissues between fetus and adult
Development of human tissue is influenced by a combination of intrinsic biological signals and extrinsic environmental stimuli, both of which are mediated by epigenetic regulation, including DNA methylation. H...
Citation: Epigenetics & Chromatin 2011 4:7 -
Role of the ATPase/helicase maleless (MLE) in the assembly, targeting, spreading and function of the male-specific lethal (MSL) complex of Drosophila
The male-specific lethal (MSL) complex of Drosophila remodels the chromatin of the X chromosome in males to enhance the level of transcription of most X-linked genes, and thereby achieve dosage compensation. The ...
Citation: Epigenetics & Chromatin 2011 4:6 -
Heterogeneity in the kinetics of nuclear proteins and trajectories of substructures associated with heterochromatin
Protein exchange kinetics correlate with the level of chromatin condensation and, in many cases, with the level of transcription. We used fluorescence recovery after photobleaching (FRAP) to analyse the kineti...
Citation: Epigenetics & Chromatin 2011 4:5 -
Quantitative analysis of polycomb response elements (PREs) at identical genomic locations distinguishes contributions of PRE sequence and genomic environment
Polycomb/Trithorax response elements (PREs) are cis-regulatory elements essential for the regulation of several hundred developmentally important genes. However, the precise sequence requirements for PRE function...
Citation: Epigenetics & Chromatin 2011 4:4 -
Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning
Unique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions. The histone H3 variant CENH3 (centromeric histone H3) is viewed as the ke...
Citation: Epigenetics & Chromatin 2011 4:3 -
Dot1 binding induces chromatin rearrangements by histone methylation-dependent and -independent mechanisms
Methylation of histone H3 lysine 79 (H3K79) by Dot1 is highly conserved among species and has been associated with both gene repression and activation. To eliminate indirect effects and examine the direct cons...
Citation: Epigenetics & Chromatin 2011 4:2 -
Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue
Genes subject to genomic imprinting are mono-allelically expressed in a parent-of-origin dependent manner. Each imprinted locus has at least one differentially methylated region (DMR) which has allele specific...
Citation: Epigenetics & Chromatin 2011 4:1 -
Global turnover of histone post-translational modifications and variants in human cells
Post-translational modifications (PTMs) on the N-terminal tails of histones and histone variants regulate distinct transcriptional states and nuclear events. Whereas the functional effects of specific PTMs are...
Citation: Epigenetics & Chromatin 2010 3:22 -
Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and its denucleation
Brahma-related gene 1 (Brg1, also known as Smarca4 and Snf2β) encodes an adenosine-5'-triphosphate (ATP)-dependent catalytical subunit of the (switch/sucrose nonfermentable) (SWI/SNF) chromatin remodeling complex...
Citation: Epigenetics & Chromatin 2010 3:21 -
Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae
Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed toward...
Citation: Epigenetics & Chromatin 2010 3:20
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