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At least 235 records · Page 13Linked to original sources
PubMed2005

Uteroplacental insufficiency affects epigenetic determinants of chromatin structure in brains of neonatal and juvenile IUGR rats.

Intrauterine growth retardation (IUGR) increases the risk of neuroendocrine reprogramming. In the rat, IUGR leads to persistent changes in cerebral mRNA levels. This suggests lasting alterations in IUGR cerebral transcriptional regulation, which may result from changes in chromatin structure. Candidate nutritional triggers for these changes include altered cerebral zinc and one-carbon metabolite levels. We hypothesized that IUGR affects cerebral chromatin structure in neonatal and postnatal rat brains. Rats were rendered IUGR by bilateral uterine artery ligation; controls (Con) underwent sham surgery. At day of life 0 (d0), we measured cerebral DNA methylation, histone acetylation, expression of chromatin-affecting enzymes, and cerebral levels of one-carbon metabolites and zinc. At day of life 21 (d21), we measured cerebral DNA methylation and histone acetylation, as well as the caloric content of Con and IUGR rat breast milk. At d0, IUGR significantly decreased genome-wide and CpG island methylation, as well as increased histone 3 lysine 9 (H3/K9) and histone 3 lysine 14 (H3/K14) acetylation in the hippocampus and periventricular white matter, respectively. IUGR also decreased expression of the chromatin-affecting enzymes DNA methyltransferase 1 (DNMT1), methyl-CpG binding protein 2 (MeCP2), and histone deacetylase (HDAC)1 in association with increased cerebral levels of zinc. In d21 female IUGR rats, cerebral CpG DNA methylation remained lower, whereas H3/K9 and H3/K14 hyperacetylation persisted in hippocampus and white matter, respectively. In d21 male rats, IUGR decreased acetylation of H3/K9 and H3/K14 in these respective regions compared with controls. Despite these differences, caloric, fat, and protein content were similar in breast milk from Con and IUGR dams. We conclude that IUGR results in postnatal changes in cerebral chromatin structure and that these changes are sex specific.

Acetylation↗
PubMedDate not supplied

Chromatin structure and dynamics: functional implications.

In eucaryotes, DNA packaging into nucleosomes and its organization in a chromatin fiber generate constraints for all processes involving DNA, such as DNA-replication, -repair, -recombination, and -transcription. Transient changes in chromatin structure allow overcoming these constraints with different requirements in regions where processes described above are initiated. Mechanisms involved in chromatin dynamics are complex. Multiprotein complexes which can contain histone-acetyltransferase, -deacetylase, -methyltransferase or -kinase activities are targeted by regulatory factors to precise regions of the genome. These enzymes have been shown to modify histone-tails within specific nucleosomes. Post-translational modifications of histone-tails constitute a code that is thought to contribute to the nucleosome or to the chromatin fiber remodeling, either directly, or through the recruitment of other proteins. Other multiprotein complexes, such as ATP-dependent remodeling complexes, play an essential role in chromatin fiber dynamics allowing nucleosome sliding and redistribution on the DNA. We will focus here on the chromatin structure and its consequences for DNA damaging, replication, repair, and transcription and we will discuss the mechanisms of chromatin remodeling.

Acetyltransferases↗
PubMed1987

Sharp boundaries demarcate the chromatin structure of a yeast heat-shock gene.

In both induced and basally transcribed states, the chromatin structure of the yeast HSP82 heat-shock locus exhibits a remarkable degree of organization with respect to DNA sequence. The promoter region contains a constitutive DNase I hypersensitive site. The transcription unit is markedly sensitive to DNase I, and exhibits a sharp transition from a phased half- to a whole nucleosomal cleavage periodicity at the 3' end. Distant upstream and downstream regions are also organized into distinct arrays of phased nucleosomes. Each array is demarcated by DNase I hypersensitive sites that display internal protected regions, suggesting the presence of DNA binding proteins. In addition, since these sites are of mononucleosomal DNA length, they may acquire a nucleosomal structure under certain environmental conditions without disrupting flanking nucleosomal phasing frames. Thus, the HSP82 locus is organized into specific, phased, chromatin structures that appear to function in transcriptional initiation, RNA polymerase passage, transcriptional termination, and the establishment of chromatin-domain microenvironments.

Chromatin↗
PubMed2001

Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation.

Silencing of tumor-suppressor genes by hypermethylation of promoter CpG islands is well documented in human cancer and may be mediated by methyl-CpG-binding proteins, like MeCP2, that are associated in vivo with chromatin modifiers and transcriptional repressors. However, the exact dynamic between methylation and chromatin structure in the regulation of gene expression is not well understood. In this study, we have analyzed the methylation status and chromatin structure of three CpG islands in the p14(ARF)/p16(INK4A) locus in a series of normal and cancer cell lines using methylation-sensitive digestion, MspI accessibility in intact nuclei and chromatin immunoprecipitation (ChIP) assays. We demonstrate the existence of an altered chromatin structure associated with the silencing of tumor-suppressor genes in human cancer cell lines involving CpG island methylation, chromatin condensation, histone deacetylation and MeCP2 binding. The data showed that MeCP2 could bind to methylated CpG islands in both promoters and exons; MeCP2 does not interfere with transcription when bound at an exon, suggesting a more generalized role for the protein beyond transcriptional repression. In the absence of methylation, it is demonstrated that CpG islands located in promoters versus exons display marked differences in the levels of acetylation of associated histone H3, suggesting that chromatin remodeling can be achieved by methylation-independent processes and perhaps explaining why non-promoter CpG islands are more susceptible to de novo methylation than promoter islands.

Acetylation↗
PubMed1993

Chromatin structures of Kluyveromyces lactis centromeres in K. lactis and Saccharomyces cerevisiae.

We have investigated the chromatin structure of Kluyveromyces lactis centromeres in isolated nuclei of K. lactis and Saccharomyces cerevisiae by using micrococcal nuclease and DNAse I digestion. The protected region found in K. lactis is approximately 270 bp long and encompasses the centromeric DNA elements, KlCDEI, KlCDEII, and KlCDEIII, but not KlCDE0. Halving KlCDEII to 82 bp impaired centromere function and led to a smaller protected structure (210 bp). Likewise, deletion of 5 bp from KlCDEI plus adjacent flanking sequences resulted in a smaller protected region and a decrease in centromere function. The chromatin structures of KlCEN2 and KlCEN4 present on plasmids were found to be similar to the structures of the corresponding centromeres in their chromosomal context. A different protection pattern of KlCEN2 was detected in S. cerevisiae, suggesting that KlCEN2 is not properly recognized by at least one of the centromere binding proteins of S. cerevisiae. The difference is mainly found at the KlCDEIII side of the structure. This suggests that one of the components of the ScCBF3-complex is not able to bind to KlCDEIII, which could explain the species specificity of K. lactis and S. cerevisiae centromeres.

Base Sequence↗
PubMed1996

Repression and activation by multiprotein complexes that alter chromatin structure.

Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.

Adenosine Triphosphate↗
PubMed1994

Activation of cAMP-dependent protein kinase alters the chromatin structure of the urokinase-type plasminogen activator gene promoter.

In LLC-PK1 cells, the urokinase-type plasminogen activator (uPA) gene is induced by two of the major signal transduction pathways, the protein kinase C (PKC) and the cAMP-dependent protein kinase (PKA) pathways. We have analyzed the chromatin structure of 26 kb of the uPA gene locus and have shown that PKA activation but not PKC activation induce major chromatin structural alterations in the uPA gene promoter. In uninduced cells, several DNase I hypersensitive (HS) sites were detected in the 5' and 3' flanking regions but not in the transcribed region. Two of the sites correspond to previously characterized regulatory sites: a cAMP responsive site at nucleotide position -3500 with respect to the initiation site, and the PEA3/AP1 site at -2100 that mediates PKC activation. After the activation of PKA but not PKC, a strong HS site was induced at -2600. Functional analysis of this region revealed cAMP responsive activity. Chromatin structural alterations again brought about specifically by PKA but not by PKC were were also detected in the upstream of the promoter by topoisomerase I cleavage site analysis, with two prominent sites appearing at -2800 and -3300. These results suggest that the strong cAMP induction of the uPA gene requires structural alterations that permit cooperative interactions between the multiple cAMP responsive sites.

Animals↗
PubMed1996

Molecular analysis of a recombinational hotspot adjacent to Lmp2 gene in the mouse MHC: fine location and chromatin structure.

Meiotic recombinations in the proximal region of the mouse major histocompatibility complex (MHC) are clustered within certain segments of chromosome, known as hotspots. In this study, we found that one of such hotspots, previously mapped between the Pb and Ob genes, is located very close to the 3' end of the Lmp2 gene, which encodes a subunit of a proteolytic proteasome. To analyze the molecular basis of the site specificity of hotspots, we examined the structure of the chromatin around this Lmp2 hotspot and another one located in the MHC class II Eb gene, by monitoring DNase I-hypersensitive sites (DHSSs) of the chromatin. DHSSs were detected at the both hotspots in the somatic cells. In the meiotic cells, DHSS was detected within the Eb hotspot, as previously reported, but not in the Lmp2 hotspot. Thus, open structure of chromatin during meiosis, as monitored by hypersensitivity to DNase I, is not a general feature of mouse recombinational hotspots, contrasting the case of the lower eukaryote, S. cerevisiae, in which hotspots are always associated with DHSSs.

Animals↗
PubMed1995

The bulk chromatin structure of a murine transgene does not vary with its transcriptional or DNA methylation status.

The DNA methylation status of HRD, a murine transgene, can be controlled by the genetic background upon which it is carried. We found the transgene to be transcribed in competent tissues only when undermethylated. Chromatin structure over the transgene was assayed by nuclear accessibility with DNase I, MspI, and PstI. While the transgene was up to fivefold more resistant to MspI when methylated than when not methylated, we observed no such difference with DNase I or PstI. We suggest that methyl-CpG-binding proteins are responsible for the difference observed with MspI, but that the chromatin structures are otherwise similarly compacted. Methylation could, therefore, play a regulatory role in gene expression beyond that which can be accomplished by bulk chromatin structure alone.

5-Methylcytosine↗
PubMed1985

Chromatin structure and de novo methylation of sperm DNA: implications for activation of the paternal genome.

The chromatin structure characteristic of constitutively expressed genes, tissue-specific genes, and inactive genes is absent in chicken sperm chromatin. However, point sites of undermethylation in sperm DNA within constitutively expressed genes, but not within globin genes or an inactive gene, correspond to the location of regions of altered chromatin structure (hypersensitive sites) in somatic tissue and spermatogonial cells. A de novo methylation process whereby regions within and flanking these genes become methylated, but which excludes the methylation of sequences within hypersensitive sites, occurs between the spermatogonial stage and the first meiotic prophase. These undermethylated regions may play a role in the activation of the paternal genome during embryogenesis.

Animals↗
PubMed1987

Roles of cis-acting elements and chromatin structure in Drosophila alcohol dehydrogenase gene expression.

The alcohol dehydrogenase (Adh) gene of D. melanogaster is transcribed from two different promoters during fly development: the distal (adult) and the proximal (embryonic-larval). Certain aspects of Adh gene regulation are represented in Drosophila continuous cell lines. We have used Drosophila tissue culture cells in an in vivo transient expression assay to delimit cis-acting sequences affecting Adh expression, and to investigate the role of chromatin structure in Adh gene regulation. These studies show that positive cis-acting elements of the distal promoter can exist in at least 2 alternative chromatin configurations. There is a close correlation between specific transcriptional activity of the Adh distal promoter and a defined, localized chromatin structural change that indicates altered DNA-protein interactions. Thus, chromatin structure appears to play a role in regulating the accessibility of defined positive cis-acting regulatory sequences of Adh to transcription factors and the transcription machinery.

Alcohol Dehydrogenase↗
PubMedDate not supplied

Glutathione depletion potentiates ethyl methanesulfonate-induced damage to sperm chromatin structure.

Male rats were treated with phorone at dosages previously shown to reduce glutathione in rodent reproductive tracts, followed by a single challenge with ethyl methanesulfonate, a known mutagenic and clastogenic agent. Epididymal sperm collected 8 and 15 days after exposure from phorone pretreated animals had a significantly greater alteration of sperm chromatin structure, defined as an increased susceptibility to DNA denaturation in situ, relative to sperm obtained from animals injected with saline alone or saline+EMS (50, 100, 150, or 200 mg/kg bw). These data support the hypothesis that ethyl methanesulfonate-induced alkylation of developing sperm chromatin protamines causes a significant stress on chromatin structure leading to increased DNA damage. This is the first report showing that glutathione depletion potentiates EMS-induced chromatin structural alterations that are likely related to dominant lethal mutations.

Animals↗
PubMed2004

Two distinct methods analyzing chromatin structure using centrifugation and antibodies to modified histone H3: both provide similar chromatin states of the Rit1/Bcl11b gene.

Chromatin state of a 2-Mb region harboring Rit1/Bcl11b on mouse chromosome 12 was examined using two distinct methods. One is ChIP assay examining the degree of enrichment with histone H3 methylated at lysine 9 (H3-mLys9) in chromatin and the other is H/E (heterochromatin/euchromatin) assay that measures a chromatin condensation state by using centrifugation. The ChIP assay showed that a 50-kb interval covering the gene and an upstream region constituted chromatin enriched with unmethylated H3-mLys9 in cells expressing Rit1 compared to cells not expressing Rit1. In contrast, regions other than the 50-kb interval did not show much difference in the enrichment between the two different types of cells. On the other hand, H/E assay of two expressing and two non-expressing tissues provided compatible fractionation patterns, suggesting that the chromatin condensation state detected by H/E assay is correlated with the chromatin state controlled by histone H3 tail modification linked to gene expression. These results indicate that the centrifugation-based H/E assay should provide a new approach to the regulation of chromatin structure with respect to its condensation state, complementing ChIP assays.

Animals↗
PubMed2006

Chromatin structure exhibits spatio-temporal heterogeneity within the cell nucleus.

Local chromatin compaction undergoes dynamic perturbations to regulate genetic processes. To address this, the direct measurement of the fluidity of chromatin structure is carried out in single live cells using steady-state anisotropy imaging and polarization modulation microscopy. Fluorescently tagged core and linker histones are used to probe different structural aspects of chromatin compaction. A graded spatial heterogeneity in compaction is observed for the chromatin besides the distinct positional ordering of core and linker histones. These spatio-temporal features are maintained by active processes and perturbed during death. With cell cycle, the distribution in compaction heterogeneity continually changes maximizing during M-G1 transition where it displays bimodal behavior. Such measurements of spatio-temporal chromatin fluidity could have broader implications in understanding chromatin remodeling within living cells.

Adenosine Triphosphate↗
PubMed2002

Thymocyte apoptosis induced by phosphorylation of histones is associated with the change in chromatin structure to allow easy accessibility of DNase.

The inhibitors of protein phosphatase such as calyculin A and okadaic acid induce the apoptotic cell death in rat thymocytes. To clarify the molecular mechanism of these inhibitor-induced apoptosis, the effect of calyculin A on DNA fragmentation in the isolated nuclei were studied. A significant increase in DNA fragmentation was observed in the nuclei prepared from the cells treated with calyculin A that caused histone hyperphosphorylation. No changes of the activities of caspase-8 and -3 were observed in the extract from the cells treated with calyculin A. The circular dichroism analysis of soluble chromatin from calyculin A-treated thymocyte nuclei indicated that phosphorylation of histones decreased its alpha-helical content. Thus, the change in the chromatin structure may be due to the chemical modification of histones. Moreover, the structural change in chromatin preceded DNA fragmentation in the nuclei. Therefore, these results suggest that the change of chromatin structure allow easy accessibility of nuclear DNase to chromosomal DNA.

Animals↗
PubMed1991

The chromatin structure of centromeres from fission yeast: differentiation of the central core that correlates with function.

We have examined the chromatin structure of centromere regions from the fission yeast Schizosaccharomyces pombe. The large and complex centromere regions of the S. pombe chromosomes encompass many kilobase pairs of DNA and contain several classes of tandemly repeated DNA sequences. The repeated sequences are further organized into a large inverted repeat flanking a central core, a conserved structural feature among all three centromeres in S. pombe. The nucleosomal configuration of the centromere regions is nonuniform and highly varied. Most of the centromere-specific repeated DNA sequences are packaged into nucleosomes typical of bulk chromatin. However, the central core and core-associated repeated sequences from the centromere regions of chromosomes I (cen1) and II (cen2), when present in S. pombe, show an altered chromatin structure, with little or no evidence of regular nucleosomal packaging. The atypical chromatin organization of the cen2 central core is not due to transcription, as no transcripts from this region were detected. These same DNA sequences, however, are packaged into nucleosomes typical of bulk chromatin when present in a nonfunctional environment on a minichromosome in the budding yeast Saccharomyces cerevisiae. Because the cen2 central core sequences themselves do not preclude regular nucleosomal packaging, we speculate that in S. pombe they constitute a specialized site of kinetochore protein assembly. The atypical nucleosomal pattern of the cen2 central core remains constant during the cell cycle, with only minor differences observed for some sequences. We propose that the unusual chromatin organization of the core region forms the basis of a higher order structural differentiation that distinguishes the centromere from the chromosome arms and specifies the essential structure for centromere function.

Blotting, Northern↗
PubMed2005

Influence of chromatin structure and radical scavengers on yields of radiation-induced 8-oxo-dG and DNA strand breaks in cellular model systems.

Radiation-induced formation of 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG) and DNA strand breaks was studied in cultured cells with normal or modified chromatin structure. Human fibroblasts were irradiated as cellular monolayers (intact cells), nuclear monolayers (permeabilized cells with intact chromatin structure), and nucleoid monolayers (permeabilized and salt-treated cells with histone-free DNA). 8-oxo-dG was assayed with reverse-phase HPLC coupled to an electrochemical detector and strand breaks with the alkali unwinding assay. Depletion of low-molecular-weight nuclear components increased the radiation-induced formation of 8-oxo-dG fivefold compared to twofold for the formation of strand breaks. Removal of both low-molecular-weight components and histones increased the yield of 8-oxo-dG 46-fold and the yield of strand breaks 43-fold. Removal of only the histones thus leads to a two times greater increase in the yield of strand breaks compared to 8-oxo-dG. Addition of radical scavengers to nuclear and nucleoid monolayers provided a significantly better protection against the formation of 8-oxo-dG relative to the formation of strand breaks. These results suggest that in intact cells, 8-oxo-dG is preferentially formed in histone-free structures of chromatin, indicating a larger role for the indirect effect of radiation in the formation of 8-oxo-dG than in the formation of strand breaks.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed1996

Pituitary-specific chromatin structure of the rat prolactin distal enhancer element.

The location of target DNA sequences within chromatin may affect the ability of trans-acting factors to bind cis-elements and regulate gene transcription. To examine the effect of chromatin structure on the ability of the estrogen-estrogen receptor complex (E2R) to bind its respective DNA binding element within the rat prolactin (rPRL) gene and modulate rPRL gene expression, we have developed cell lines derived from the rPRL-expressing (rPRL+) rat pituitary cell line GH3 and the rPRL-non- expressing (rPRL-) rat embryo fibroblast cell line Rat1. These cell lines contain mini-chromosomes composed of the 5' upstream regulatory region of the rPRL gene driving expression of a reporter gene, Tn5, within a bovine papillomavirus (BPV) vector. The rPRL-Tn5 gene retains the characteristics of cell-specific expression and estrogen inducibility of transcription displayed by the endogenous rPRL gene. The distal enhancer region, which contains an estrogen response element, was found to exist in a nucleosome-free region in pituitary-derived cells even in the absence of estrogen. In contrast, the rPRL distal enhancer in fibroblast cells was found to be randomly packaged into nucleosomes. These results indicate that DNA sequence is not sufficient to position nucleosomes in the rPRL gene. Rather, it suggests that cell-specific factors are present in pituitary cells that modify the chromatin structure of the distal enhancer which allow E2R to bind to its response element.

Animals↗