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Chromatin Assembly and Disassembly (0):
Recent article
Chromatin Assembly and Disassembly
FEBS Journal (278)19 2011
Abstract
Chromatin remodelling is the ATP-dependent change in nucleosome organisation driven by Snf2 family ATPases. The biochemistry of this process depends on the behaviours of ATP-dependent motor proteins and their dynamic nucleosome substrates, which brings significant technical and conce...
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PMID: 21810178
PDF is available here.
PDF is available here.
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FEBS Journal (278)19 2011
Abstract
Through its capability to transiently pack and unpack our genome, chromatin is a key player in the regulation of gene expression. Single-molecule approaches have recently complemented conventional biochemical and biophysical techniques to decipher the complex mechanisms ruling chroma...
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PMID: 21810177
PDF is available here.
PDF is available here.
FEBS Journal (278)19 2011
Abstract
We discuss nucleosome dynamics from two angles. First, we describe the dynamical modes of nucleosomes in the absence of remodelers that are experimentally fairly well characterized and theoretically understood. Then, we discuss remodelers and describe recent insights about the possible schemes that...
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PMID: 21812931
PDF is available here.
PDF is available here.
Abstract
We show that the combined action of Isw1 and Chd1 nucleosome-spacing enzymes is required to maintain this organization. In the absence of these enzymes, regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome, and a subset...
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PMID: 21940898
PDF is available here.
PDF is available here.
Abstract
Inflammatory responses to microbial and non-microbial stimuli involve coordinate changes in the expression of hundreds of genes. The inflammatory gene expression programs display two important features: first, alternative stimuli affect both a large set of common genes and a variable number of stimul...
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PMID: 20857270
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1809)9 2011
Abstract
Nature Cell Biology (13)8 2011
Abstract
How the unique chromatin configuration of embryonic stem cells (ESCs) integrates inputs from exogenous stimuli to maintain pluripotency remains largely unknown. The ESC-specific ATP-dependent chromatin-remodelling (esBAF) complex maintains the accessibility of the target sites of Sta...
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PMID: 21808242
PDF is available here.
PDF is available here.
Mutation Research (714)1-2 2011
Abstract
To investigate the mechanisms of the therapeutic action and drug resistance to the nitrogen mustard melphalan, melphalan-induced DNA damage repair and chromatin structure were examined along the p53, N-ras and d-globin gene loci in cells carrying different repair activities. In nucle...
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PMID: 21762707
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1809)9 2011
Abstract
We review the available data and integrate the results with structural and biochemical studies of related enzymes to derive a model for Mot1's catalytic action consistent with the broad literature on enzymes in this family. We propose that the Mot1 ATPase domain is tethered to TBP by a flexible, spr...
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PMID: 21658482
PDF is available here.
PDF is available here.
Zoological Science (28)6 2011
Abstract
We focused on the nuclear morphologies and examined their changing processes in dimorphic spermiogenesis. Electron microscopic observation revealed that, in euspermatids, chromatin condensation first appeared as a mosaic pattern of moderate electrodense material in the peripheral region of the round...
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PMID: 21627454
PDF is available here.
PDF is available here.
Plant Biology (62)1 2011
Abstract
The epigenomic regulation of chromatin structure and genome stability is essential for the interpretation of genetic information and ultimately the determination of phenotype. High-resolution maps of plant epigenomes have been obtained through a combination of chromatin technologies...
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PMID: 21438682
PDF is available here.
PDF is available here.
PLoS Genetics (7)6 2011
Abstract
We investigate how chromatin structure is modified following UV irradiation to facilitate DNA repair in yeast. Using a combination of chromatin immunoprecipitation to measure histone acetylation levels, histone acetylase occupancy in chromatin, MNase digestion, or restriction enzyme endonuclease acc...
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PMID: 21698136
PDF is available here.
PDF is available here.
Abstract
Sponsored by the New York Academy of Sciences, the Warren Alpert Medical School of Brown University and the University of Massachusetts Boston, "Behavioral Epigenetics" was held on October 29-30, 2010 at the University of Massachusetts Boston Campus Center, Boston, Massachusetts. This meeting feature...
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PMID: 21615751
PDF is available here.
PDF is available here.
Abstract
Abstract
Members of the nuclear steroid/thyroid hormone receptor (NR) gene superfamily are DNA-binding transcription factors that regulate target genes in a spatiotemporal manner, depending on the promoter context. In vivo observations of ligand responses in NR-mediated gene regulation led to the identificati...
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PMID: 21315607
PDF is available here.
PDF is available here.
Abstract
We show that yeast INO80 facilitates these diverse processes at least in part by controlling genome-wide distribution of the histone variant H2A.Z. In the absence of INO80, H2A.Z nucleosomes are mislocalized, and H2A.Z levels at promoters show reduced responsiveness to transcriptional changes, sugge...
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PMID: 21241891
PDF is available here.
PDF is available here.
Abstract
We then describe methods that detect nucleosome positioning and occupancy levels using chromatin immunoprecipitation in combination with deep sequencing (ChIP-Seq), a strategy that is now straightforward and cost efficient. We then explore current strategies for converting the sequence information i...
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PMID: 21241889
PDF is available here.
PDF is available here.
Fortschritte der Arzneimittelforschung. Progress in drug research. Progres des recherches pharmaceutiques (67) 2011
Abstract
We discuss recent studies on epigenetic regulation in MR and explore the concept of epigenetic therapy for MR....
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PMID: 21141729
PDF is available here.
PDF is available here.
Abstract
We discuss recent studies that provide a genome-wide view of the chromatin structure signature in ES cells and iPS cells and that highlight the central role of histone modifiers and chromatin remodelers in pluripotency maintenance and induction....
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PMID: 21325400
PDF is available here.
PDF is available here.
Abstract
I and histone acetyltransferase I in both cell lines while NaBu had only small effect. CLB-induced increased gene expression was attenuated by NaBu in CLB-sensitive NCI-H929 cells but not in resistant LP-1 cells. These results suggest that chromatin modifying agents may have differential effects on...
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PMID: 21075074
PDF is available here.
PDF is available here.
Abstract
We report that chromatin regulator tripartite motif-containing 24 (TRIM24) functions in humans as a reader of dual histone marks by means of tandem plant homeodomain (PHD) and bromodomain (Bromo) regions. The three-dimensional structure of the PHD-Bromo region of TRIM24 revealed a single functional...
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PMID: 21164480
PDF is available here.
PDF is available here.
Nature Medicine (16)12 2010
Abstract
Abstract
We use nucleosomes methylated on DNA and on histone H3 in an affinity assay, in conjunction with a SILAC-based proteomic analysis, to identify "crosstalk" between these two distinct classes of modification. Our analysis reveals proteins whose binding to nucleosomes is regulated by methylation of CpG...
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PMID: 21029866
PDF is available here.
PDF is available here.
Nature Neuroscience (13)11 2010
Abstract
I discuss how extracellular cues, including synaptic activity and neurotrophic factors, influence epigenetic modifications and regulate the neuronal transcriptional response. I also summarize additional mechanisms that induce chromatin remodeling events by combinatorial assembly of multiprotein comp...
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PMID: 20975757
PDF is available here.
PDF is available here.
Nature Neuroscience (13)11 2010
Abstract
We describe the complex communication network between the brain-specific central clock and the tissue-specific peripheral clocks that serve to synchronize the organism to both external and internal demands. In addition, we discuss and speculate on how epigenetic processes are involved in creating tr...
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PMID: 20975756
PDF is available here.
PDF is available here.
Protein & Cell (1)11 2010
Abstract
We review studies on the dynamics of chromatin higher order structure and its relationship with gene transcription....
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PMID: 21153512
PDF is available here.
PDF is available here.
British Journal of Cancer (103)8 2010
Abstract
The majority of testicular germ cell cancers develop through a pre-invasive carcinoma in situ (CIS) stage. The CIS cell is a neoplastic counterpart of foetal germ cells. During their development, foetal germ cells undergo extensive and essential epigenetic modifications, but little is known about ep...
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PMID: 20823885
PDF is available here.
PDF is available here.
European Journal of Cancer (46)15 2010
Abstract
We have examined the contribution of epigenetic modulation of gene expression in the potentiation of etoposide-mediated cytotoxicity in neuroblastoma cells. Specifically, we studied the effects of histone deacetylase inhibition with valproic acid on topoisomerase II gene expression and apoptosis in...
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PMID: 20886683
PDF is available here.
PDF is available here.
Nature Biotechnology (28)10 2010
Abstract
Replete with investor funds, the Cambridge, Massachusetts–based epigenetics firm is taking aim at methylases anddemethylases linked to disease.
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PMID: 20944577
PDF is available here.
PDF is available here.
Nature Biotechnology (28)10 2010
Abstract
One of the biggest gaps in our knowledge about epigenomes is how their interplay with cellular signaling influences development, adult cellular differentiation and disease.
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PMID: 20944593
PDF is available here.
PDF is available here.
Andrologia (42)5 2010
Abstract
We sought to determine whether a similar link exists in spermatids by combining immunogold labelling with detection of DNA strand breaks, making use of gold particles of different sizes. DNA strand breaks were not detected in the vicinity of AcH4 chromatin, suggesting that this modified histone may...
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PMID: 20860633
PDF is available here.
PDF is available here.
Biochemical Journal (431)2 2010
Abstract
We found that knockdown of hINO80 (human INO80) confers DNA-damage hypersensitivity and inefficient DSB repair. Microarray analysis and other experiments have identified the Rad54B and XRCC3 (X-ray repair complementing defective repair in Chinese-hamster cells 3) genes, implicated in DSB repair, to...
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PMID: 20687897
PDF is available here.
PDF is available here.
Genes & Development (24)16 2010
Abstract
We undertook a systematic investigation of chromatin reorganization during gametogenesis, using the model eukaryote Saccharomyces cerevisiae to examine sporulation, which has strong similarities with higher eukaryotic spermatogenesis. We established a mutational screen of histones H3 and H4 to uncov...
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PMID: 20713519
PDF is available here.
PDF is available here.
Epigenetics (5)6 2010
Abstract
Regulation of Set1-COMPASS-mediated H3K4 methylation and Dot1-mediated H3K79 methylation by H2BK123 ubiquitination (H2Bub1) is an evolutionarily conserved trans-histone crosstalk mechanism. How H2Bub1 impacts chromatin structure and affects Set1-COMPASS/Dot1 functions has not been fu...
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PMID: 20523115
PDF is available here.
PDF is available here.
Abstract
We investigated the remodeling of H3K27me3 in Bos taurus embryos obtained after in vitro fertilization (IVF) and SCNT. In this species, transfer-induced chromatin remodeling can be clearly separated from embryonic genome activation (EGA), which occurs at the 8-16-cell stage, and cloning by SCNT is 1...
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PMID: 20431250
PDF is available here.
PDF is available here.
Nature Reviews: Cancer (10)8 2010
Abstract
The molecular chaperone heat shock protein 90 (HSP90) has been used by cancer cells to facilitate the function of numerous oncoproteins, and it can be argued that cancer cells are 'addicted' to HSP90. However, although recent reports of the early clinical efficacy of HSP90 inhibitors are encouraging...
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PMID: 20651736
PDF is available here.
PDF is available here.
Abstract
Diabetes is associated with significantly accelerated rates of several debilitating microvascular complications such as nephropathy, retinopathy, and neuropathy, and macrovascular complications such as atherosclerosis and stroke. While several studies have been devoted to the evaluation of genetic f...
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PMID: 20462972
PDF is available here.
PDF is available here.
Molecular Immunology (47)11-12 2010
Abstract
We investigated the role of the ATP-dependent chromatin remodeling enzyme SNF2H in mouse T cells; to date, SNF2H has not been investigated in T cells. We found that SNF2H repressed expression of IL-2 and other cytokines in activated cells. By contrast, SNF2H activated expression of IL-3. The ISWI co...
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PMID: 20471682
PDF is available here.
PDF is available here.
Abstract
We set out to assess any role for epigenetic factors in the regulation of intestinal epithelial cell immune responses. Experiments were conducted using the HCT116 cell line, and a subclone was genetically engineered to lack DNA methyltransferases (DNMT). The induction of the chemokine interleukin-8...
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PMID: 20378831
PDF is available here.
PDF is available here.
Abstract
We show that DNA demethylation in the mouse PGCs is mechanistically linked to the appearance of single-stranded DNA (ssDNA) breaks and the activation of the base excision repair (BER) pathway, as is the case in the zygote where the paternal pronucleus undergoes active DNA demethylation shortly after...
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PMID: 20595612
PDF is available here.
PDF is available here.
Abstract
We have established that Pbx1 negatively regulates Hoxa10-mediated gene transcription in mesenchymal cells and identified components of a Pbx1 complex associated with genes in osteoblasts. Expression of Pbx1 impaired osteogenic commitment of C3H10T1/2 multipotent cells and differentiation of MC3T3-E...
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PMID: 20439491
PDF is available here.
PDF is available here.
Abstract
We sought to identify factors that mediate reprogramming with higher efficiency. We established an assay to screen nuclear fractions from extracts of pluripotent mouse cells based on Oct4 reactivation. Using proteomics, we identified components of the ATP-dependent BAF chromatin-remodeling complex,...
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PMID: 20550931
PDF is available here.
PDF is available here.
Abstract
We currently define as epigenetics evolved over time as our knowledge on DNA methylation and chromatin modifications and their effects on gene expression increased. The current explosion of research on epigenetics and the increasing documentation of the effects of various environmental factors on DN...
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PMID: 20381512
PDF is available here.
PDF is available here.
Abstract
The characteristics of epigenetic control, including the potential for long-lasting, stable effects on gene expression that outlive an initial transient signal, could be of singular importance for post-mitotic neurons, which are subject to changes with short- to long-lasting influence on their activ...
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PMID: 20535202
PDF is available here.
PDF is available here.
Abstract
We developed new scoring functions to predict nucleosome positioning. There are three principal differences between our approach and earlier studies: (i) we assume that the length of nucleosomal DNA varies from 146 to 147 bp; (ii) we consider the anisotropic flexibility of pyrimidine-purine (YR) dim...
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PMID: 20232936
PDF is available here.
PDF is available here.
Abstract
We focus on DNA conformational signals found in the growing library of known high-resolution core-particle structures and the ways in which these features may contribute to the positioning of nucleosomes on specific DNA sequences. We survey the chemical composition of the protein-DNA assemblies and...
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PMID: 20232929
PDF is available here.
PDF is available here.
Abstract
Nucleosome positioning has been the subject of intense study for many years. The properties of micrococcal nuclease, the enzyme central to these studies, are discussed. The various methods used to determine nucleosome positions in vitro and in vivo are reviewed critically. These include the traditio...
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PMID: 20232933
PDF is available here.
PDF is available here.
Epigenetics (5)4 2010
Abstract
We have investigated possible mechanisms by which UV-B could reactivate Mu transposons by monitoring transcript abundance, epigenetic DNA marks, and chromatin factors associated with these elements. We demonstrate that both mudrA and B transcripts are expressed at higher levels after an 8 h-UV-B tre...
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PMID: 20421734
PDF is available here.
PDF is available here.
médecine/sciences (26)5 2010
Abstract
Abstract
The transcription factor RUNX1 is essential for definitive hematopoiesis and is required for the expression of a number of important hematopoietic regulator genes. It was recently shown that RUNX1 acts within a narrow developmental window during which it cannot be replaced by other members of the RU...
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PMID: 20194037
PDF is available here.
PDF is available here.
Abstract
We report significant amounts of H3.3-H4 tetramers split in vivo, whereas most H3.1-H4 tetramers remained intact. Inhibiting DNA replication-dependent deposition greatly reduced the level of splitting events, which suggests that (i) the replication-independent H3.3 deposition pathway proceeds largel...
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PMID: 20360108
PDF is available here.
PDF is available here.
Abstract
Abstract
The paradoxical effects of ovarian hormones in both the promotion and prevention of breast cancer have been debated for over 30 years. Genetic studies have demonstrated that ovarian hormones act through NF-kappaB to stimulate proliferation and ductal elongation, whereas the p53 tumor suppressor prot...
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PMID: 20238478
PDF is available here.
PDF is available here.
Abstract
Chromatin remodeling guided by non-coding RNA (ncRNA) contributes mechanistically to the establishment of chromatin structure and to the maintenance of epigenetic memory. Various ncRNAs have been identified as regulators of chromatin structure and gene expression. The widespread occurrence of antise...
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PMID: 20373265
PDF is available here.
PDF is available here.
Abstract
We are to have a clear view of the molecular biology of the cell and aspire to manipulate genomes and gene expression to our advantage. To bring together scientists working in this fast-developing field, the Biochemical Society held a Focused Meeting, 'Machines on Genes: Enzymes that Make, Break and...
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PMID: 20298187
PDF is available here.
PDF is available here.
Gastroenterology (138)3 2010
Abstract
Our study uncovers a novel mechanism regulating cell growth and identifies the NFAT/ELK complex as modulators of early stages of mitogen-stimulated proliferation in pancreatic cancer cells.
Copyright 2010 AGA Institute. Published by Elsevier Inc. All rights reserved....
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PMID: 19900447
PDF is available here.
PDF is available here.
Abstract
Plant Cell Online (22)3 2010
Abstract
We report the isolation of several independent mutants of MGOUN1 (MGO1) as genetic suppressors of ectopic WUS activity and enhancers of stem cell defects in hypomorphic wus alleles. mgo1 mutants have previously been reported to result in a delayed progression of meristem cells into differentiating o...
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PMID: 20228247
PDF is available here.
PDF is available here.
Toxicology In Vitro (24)2 2010
Abstract
Manganese, an essential trace nutrient in human beings, has been widely used in the steel industry to improve hardness, stiffness, and strength. With the increased applications of manganese compounds, discharge into the environment has rapidly increased and may exert adverse effects on human health....
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PMID: 19815061
PDF is available here.
PDF is available here.
Biosystems (99)3 2010
Abstract
We propose a stochastic computational model that captures such fluctuations. We incorporate the physiological properties of the process through parametric microevents. Each microevent is then associated with a stochastic model that couples its random temporal and spatial dynamics with the energy lan...
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PMID: 19945504
PDF is available here.
PDF is available here.