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Histone Code (0):
Recent article
Histone Code
Abstract
Our results indicated that there were 23 combinatorial patterns for 12 histone modifications investigated when a general Bayesian network was constructed. Meanwhile, different networks were also constructed for the genes with high transcript levels (H-network) and low transcript levels (L-network),...
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PMID: 21815215
PDF is available here.
PDF is available here.
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Science Signaling (4)157 2011
Abstract
Inheritance of DNA methylation patterns is a key mechanism involved in epigenetic cell memory transmission from mother cell to daughter cell. This occurs due to cooperation between the DNA methyltransferase DNMT1 and the ubiquitin ligase UHRF1 (ubiquitin-like, containing plant homeo...
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PMID: 21266713
PDF is available here.
PDF is available here.
Abstract
We applied the concept of adding a lysine mimic to an established inhibitor (BIX-01294) of histone H3 lysine 9 methyltransferases G9a and G9a-like protein by including a 5-aminopentyloxy moiety, which is inserted into the target lysine-binding channel and becomes methylated by G9a-like protein, albe...
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PMID: 20434463
PDF is available here.
PDF is available here.
Abstract
We turned to a mouse embryonic stem cell (ESC) model. Here we show that histone H3 is proteolytically cleaved at its N-terminus during ESC differentiation. We map the sites of H3 cleavage and identify Cathepsin L as a protease responsible for proteolytically processing the N-terminal H3 tail. In add...
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PMID: 18957203
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)31 2008
Abstract
Histone modifications modulate chromatin structure and function. A posttranslational modification-randomized, combinatorial library based on the first 21 residues of histone H4 was designed for systematic examination of proteins that interpret a histone code. The 800-member library represented all p...
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PMID: 18616348
PDF is available here.
PDF is available here.
Abstract
In this issue, two papers implicate histone H3 lysine 56 acetylation in histone deposition in chromatin. Li et al. (2008) show that acetylation of H3K56 promotes S phase chromatin assembly that is mediated by the histone chaperones CAF-1 and Rtt106. Chen et al. (2008) establish that the acetylation...
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PMID: 18662534
PDF is available here.
PDF is available here.
Abstract
We previously discovered a novel trans-tail histone code involving monomethylated histone H4 lysine 20 (H4K20) and H3 lysine 9 (H3K9); however, the mechanisms that establish this code and its function in transcription were unknown. In this report, we demonstrate that H3K9 monomethylation is dependen...
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PMID: 18474616
PDF is available here.
PDF is available here.
Trends in Genetics (24)6 2008
Abstract
The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II comprises multiple tandem conserved heptapeptide repeats, unique to this eukaryotic RNA polymerase. This unusual structure provides a docking platform for factors involved in various co-transcriptional events. Recruitment...
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PMID: 18457900
PDF is available here.
PDF is available here.
Genes to Cells (13)6 2008
Abstract
We analyzed the function of SMCY protein during spermatogenesis. Biochemical identification of the proteins with which it interacted showed that SMCY formed a distinct complex with MSH5, a critical meiosis-regulatory protein in the human testicular germ cell line, NEC8. As anticipated, histone H3K4...
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PMID: 18459961
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)20 2008
Abstract
We examined transcriptional and epigenetic mechanism(s) behind diminished skeletal muscle GLUT4 mRNA in intrauterine growth-restricted (IUGR) female rat offspring. An increase in MEF2D (inhibitor) with a decline in MEF2A (activator) and MyoD (co-activator) binding to the glut4 promoter in IUGR versu...
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PMID: 18326493
PDF is available here.
PDF is available here.
Molecular and Cellular Biochemistry (312)1-2 2008
Abstract
We demonstrate for the first time that 'histone code' of the entire approximately 50 kb genomic DNA encoding the alpha- and beta-MyHC genes and the intergenic DNA that generates anti-beta-MyHC RNA was uniquely modulated by pro- and anti-hypertrophy signals of IL-18 and CBHA, respectively....
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PMID: 18292970
PDF is available here.
PDF is available here.
Abstract
We demonstrate that FoxA1 cell type-specific functions rely primarily on differential recruitment to chromatin predominantly at distant enhancers rather than proximal promoters. This differential recruitment leads to cell type-specific changes in chromatin structure and functional collaboration with...
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PMID: 18358809
PDF is available here.
PDF is available here.
Abstract
We identified target promoters of nine transcription factors, including somatic cell reprogramming factors (Oct4, Sox2, Klf4, and c-Myc) and others (Nanog, Dax1, Rex1, Zpf281, and Nac1), on a global scale in mouse ES cells. We found that target genes fall into two classes: promoters bound by few fac...
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PMID: 18358816
PDF is available here.
PDF is available here.
Journal of Biochemistry (143)3 2008
Abstract
Recently, the existence of a 'histone code' has been proposed to explain the link between the covalent chemical modification of histone proteins and the epigenetic regulation of gene activity. Although the role of the four 'core' histones has been extensively studied, little is known about the invol...
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PMID: 18234717
PDF is available here.
PDF is available here.
Abstract
We review genome-wide approaches to studying epigenomic structure and the exciting findings that have been obtained using these technologies....
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PMID: 18250624
PDF is available here.
PDF is available here.
EMBO Journal (27)1 2008
Abstract
We report that 14-3-3 binding is modulated by combinatorial modifications of histone H3. S10 phosphorylation is necessary for an interaction, but additional H3K9 or H3K14 acetylation increases the affinity of 14-3-3 for histone H3. Histone H3 phosphoacetylation occurs concomitant with K9 methylation...
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PMID: 18059471
PDF is available here.
PDF is available here.
Mutation Research (658)3 2008
Abstract
Chromatin structure plays a key role in most processes involving DNA metabolism. Chromatin modifications implicated in transcriptional regulation are relatively well characterized and are thought to be the result of a code on the histone proteins (histone code). This code, involving phosphorylation,...
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PMID: 18296106
PDF is available here.
PDF is available here.
Abstract
Polycomb-group genes (PcG), identified by Drosophila genetics, are believed to maintain positional information by constituting a cellular memory system. Recently this system has been proved to be supported by epigenetic transcription regulation. PcG products comprise two distinct complexes, PcG comp...
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PMID: 18224410
PDF is available here.
PDF is available here.
Abstract
We propose that multivalent interactions on a single histone tail and beyond may have a significant, if not dominant, role in chromatin transactions....
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PMID: 18037899
PDF is available here.
PDF is available here.
Abstract
Abstract
We found that methyl H3K36 nucleosome recognition by Rpd3S also requires the plant homeobox domain (PHD) of its Rco1 subunit. Thus, the coupled chromo and PHD domains of Rpd3S specify recognition of the methyl H3K36 mark, demonstrating the first combinatorial domain requirement within a protein comp...
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PMID: 17510366
PDF is available here.
PDF is available here.
Abstract
We report an unexpected and general strategy that is based on the requirement for specific cohorts of inhibitory histone methyltransferases (HMTs) to impose gene-specific gatekeeper functions that prevent unliganded nuclear receptors and other classes of regulated transcription factors from binding...
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PMID: 17289570
PDF is available here.
PDF is available here.
Abstract
In this issue, Garcia-Bassets et al. (2007) show that spurious transcriptional activation by unliganded nuclear receptors is inhibited by histone lysine methylation. This inhibitory histone modification code is efficiently countered by the ligand-dependent recruitment of histone lysine demethylases,...
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PMID: 17289562
PDF is available here.
PDF is available here.
Abstract
We have utilized a linear regression of optimized sigmoidal functions to correlate transcription factor binding patterns to the acetylation profiles of 11 lysines in the four core histones measured at all S. cerevisiae promoters. The resulting associations are combined with large-scale protein-prote...
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PMID: 18091724
PDF is available here.
PDF is available here.
Chromosome Research (15)2 2007
Abstract
We show that H3.3S31P also occurs during mitosis of the urochordate Oikopleura dioica, suggesting this histone modification and its function in mitosis is already present at the invertebrate-vertebrate transition. The spatial pattern differed from that of H3 phosphorylation at serine 28 (H3S28P). H3...
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PMID: 17333540
PDF is available here.
PDF is available here.
Genome Biology (8)6 2007
Abstract
We have compared GC- and AT-rich isochores of yeast with respect to chromatin conformation, histone modification status and transcription. Using 3C analysis we show that, along chromosome III, GC-rich isochores have a chromatin structure that is characterized by lower chromatin interaction frequenci...
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PMID: 17577398
PDF is available here.
PDF is available here.
Genome Biology (8)12 2007
Abstract
We have investigated the 'histone code' associated with the histone methyltransferases Suv39h1 and G9a by combining double immunopurification and mass spectrometry. Our results confirm the previously reported histone modifications associated with Suv39h1 and G9a. Moreover, this method allowed us to...
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PMID: 18096052
PDF is available here.
PDF is available here.
Abstract
We evaluate various published WCE buffers for their relative effectiveness in the detection of histone modifications by Western blot analysis. We also present a precise, yet time-efficient method for the detection of subtle changes in histone modification levels. Lastly, we present a protocol for th...
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PMID: 17101440
PDF is available here.
PDF is available here.
Abstract
We provide validated ChIP-on-chip methods for analyzing histone modification patterns at genome-scale in mammalian cells....
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PMID: 17101450
PDF is available here.
PDF is available here.
Abstract
I describe a simple and unbiased biochemical pull-down assay that allows for the identification of novel histone effector proteins and utilizes biotinylated histone peptides modified at various residues. I provide detailed protocols and suggestions for troubleshooting....
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PMID: 17101446
PDF is available here.
PDF is available here.
Cellular Microbiology (8)12 2006
Abstract
We describe in this review, such studies provide a unique vantage point of the evolutionary picture of eukaryotic cell development, and reveal unique phenomena that could be exploited pharmacologically to treat protozoal diseases....
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PMID: 17026479
PDF is available here.
PDF is available here.
Abstract
Genes & Development (20)18 2006
Abstract
We show that histone H4 Ser1 is phosphorylated (H4 S1ph) during sporulation, starting from mid-sporulation and persisting to germination, and is temporally distinct from earlier meiosis-linked H3 S10ph involved in chromosome condensation. A histone H4 S1A substitution mutant forms aberrant spores an...
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PMID: 16980586
PDF is available here.
PDF is available here.
Genes & Development (20)18 2006
Abstract
Genetika (Moskva) (42)9 2006
Abstract
Investigation of protein complexes, various types of protein modifications and the structure of the chromatin of specific chromosome regions, such as centromeres, telomeres, and adjacent heterochromatic regions, considerably complicated the notion on DNA, prevailing five decades ago, as molecules th...
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PMID: 17100088
PDF is available here.
PDF is available here.
Abstract
ACS Chemical Biology (1)4 2006
Abstract
Chemical modification of histones through a growing number of post-translational mechanisms is an integral part of transcription. A recent report provides exciting new evidence that conjugation of the ubiquitin-like protein SUMO to histones opposes acetylation and establishes SUMOylation as an impor...
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PMID: 17163672
PDF is available here.
PDF is available here.
Trends in Plant Science (11)4 2006
Abstract
The organization of DNA into chromatin regulates expression and maintenance (replication, repair, recombination, segregation) of genetic information in a dynamic manner. The N-terminal tails of the nucleosomal core histones are subjected to post-translational modifications such as acetylation, methy...
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PMID: 16546438
PDF is available here.
PDF is available here.
Nature Cell Biology (8)4 2006
Abstract
We report that all three HP1 isoforms can be extensively modified, similar to histones, suggesting that the silencing of gene expression may be further regulated beyond the histone code. To assess the potential impact of these modifications, we analysed the phosphorylation of HP1gamma at Ser 83 as a...
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PMID: 16531993
PDF is available here.
PDF is available here.
Abstract
Many plant species have evolved the ability to flower in the proper season by sensing environmental cues. The prolonged cold of winter is one such cue that certain plants use to acquire competence to flower the following spring. For example, biennials and winter annuals become established in one gro...
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PMID: 16980591
PDF is available here.
PDF is available here.
BMC Genomics (7)1 2006
Abstract
This involved a total of 13,000 PCR assays allowing for rigorous analysis by fitting a linear regression model to the data. Mutation analysis of HDAC1, HDAC2, SUV39H1, and SUV39H2 revealed only two out of 181 cancer samples (both cell lines) with significant coding-sequence alterations. Supervised a...
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PMID: 16638127
PDF is available here.
PDF is available here.
Abstract
We developed a model system whereby HP1 can be targeted to pericentric heterochromatin in ES cells lacking Suv(3)9h1/2 histone methyltransferase (HMTase) activities. HP1 so targeted can reconstitute tri-methylated lysine 9 of histone H3 (Me(3)K9H3) and tri-methylated lysine 20 of histone H4 (Me(3)K2...
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PMID: 16213461
PDF is available here.
PDF is available here.
Annals of Botany (96)7 2005
Abstract
BACKGROUND: Epigenetics has rapidly evolved in the past decade to form an exciting new branch of biology. In modern terms, 'epigenetics' studies molecular pathways regulating how the genes are packaged in the chromosome and expressed, with effects that are heritable between cell divisions and even a...
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PMID: 16254022
PDF is available here.
PDF is available here.
Abstract
Epigenetics is the study of meiotically and mitotically heritable changes in gene expression which are not coded for in the DNA. Three distinct mechanisms appear intricately related in initiating and sustaining epigenetic modifications: RNA-associated silencing, DNA methylation and histone modificat...
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PMID: 16314933
PDF is available here.
PDF is available here.
Genes & Development (19)21 2005
Abstract
We describe a mutation in a recently identified Histone H2A kinase, nhk-1, in Drosophila that leads to female sterility due to defects in the formation of the meiotic chromosomal structures. The metaphase I arrest and the karyosome, a critical prophase I chromosomal structure, require nucleosomal hi...
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PMID: 16230526
PDF is available here.
PDF is available here.
European Journal of Cancer (41)16 2005
Abstract
We focus on several families of transcription activators and repressors that catalyse histone post-translational modifications (acetylation, methylation, phosphorylation, ubiquitination and SUMOylation); and how these enzymatic activities might alter the correct cell proliferation program, leading t...
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PMID: 16226460
PDF is available here.
PDF is available here.
Abstract
We provide evidence that the p53-inducible gene 14-3-3sigma is a new example of a gene important to human cancer, where epigenetic mechanisms participate in the control of normal cell type-specific expression, as well as aberrant gene silencing in cancer cells. Like a previously identified cell type...
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PMID: 16229802
PDF is available here.
PDF is available here.
Abstract
EMBO Reports (6)5 2005
Abstract
We show that the repressed state of an endogenous retinoic acid-regulated gene is quickly re-established after ligand removal. As expected, repression is characterized by recruitment of N-CoR/SMRT-HDAC3 (histone deacetylase 3) co-repressor complexes, leading to local histone hypoacetylation. The ach...
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PMID: 15832170
PDF is available here.
PDF is available here.
Abstract
Medical Principles and Practice (14 Suppl 1) 2005
Abstract
Derangement of DNA synthesis occurred due to an impaired de novo pathway of thymidylate synthesis in both vitamin-B12- and folate-deficient human megaloblastic bone marrows as well as in the bone marrows of rhesus monkeys and rats with experimentally induced folate deficiency. Interestingly, folate-...
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PMID: 16103708
PDF is available here.
PDF is available here.
Human Molecular Genetics (13)19 2004
Abstract
We examined histone modifications throughout the mouse and human Igf2r/IGF2R using chromatin immuno-precipitation (ChIP) assays in combination with quantitative real time PCR. Methylation of Lys4 and Lys9 of histone H3 in the promoter regions marks the active and silenced alleles, respectively. We m...
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PMID: 15294879
PDF is available here.
PDF is available here.
Nature Biotechnology (22)8 2004
Abstract
We apply a combination of SAGE and chromatin immunoprecipitation (ChIP) protocols to determine the distribution of hyperacetylated histones H3 and H4 in the Saccharomyces cerevisiae genome. We call this approach genome-wide mapping technique (GMAT). Using GMAT, we find that the highest acetylation l...
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PMID: 15235610
PDF is available here.
PDF is available here.
Current Biology (14)14 2004
Abstract
Trends in Cell Biology (14)6 2004
Abstract
Physiology (66) 2004
Abstract
Nuclear receptors (also known as nuclear hormone receptors) are hormone-regulated transcription factors that control many important physiological and developmental processes in animals and humans. Defects in receptor function result in disease. The diverse biological roles of these receptors reflect...
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PMID: 14977406
PDF is available here.
PDF is available here.
Abstract
Traditionally, molecular geneticists have studied the genome, that is, DNA. This has included its sequencing, with identification of promoters, enhancers, introns, exons, and mutations. During the last 10 to 15 years, it has become clear that this study of "naked" DNA imposed major limitations on ou...
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PMID: 14626483
PDF is available here.
PDF is available here.