SEARCH · Search PubMed

Results for “Chromatin structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources

PubMed1983

Varigated chromatin structures of mouse ribosomal RNA genes.

We have employed a chromatin fractionation procedure on micrococcal nuclease-digested nuclei to examine the chromatin structure of mouse ribosomal RNA genes in two systems that differ by at least 14-fold in the level of ribosomal RNA transcription. In a cultured cell line enriched in transcriptionally active ribosomal chromatin, most ribosomal sequences are preferentially sensitive to digestion by micrococcal nuclease, reside in an insoluble chromatin fraction, and lack typical nucleosomal packaging; only minor amounts of ribosomal sequences are packaged into soluble, nucleosomal chromatin. By contrast, in adult liver, which is enriched in transcriptionally inactive ribosomal chromatin, the majority of ribosomal genes are packaged into soluble, nucleosomal chromatin. However, a significant fraction of liver ribosomal chromatin is insoluble and possesses a non-nucleosomal structure. Therefore, within a single cell population or tissue, mouse ribosomal RNA genes are organized into both nucleosomal and non-nucleosomal chromatin structures. We suggest that these structures have functional significance.

Animals↗

PubMed1995

Metaphase chromosome analysis by ligation-mediated PCR: heritable chromatin structure and a comparison of active and inactive X chromosomes.

We report that ligation-mediated PCR (LMPCR) can be used for high-resolution study of metaphase chromosomes, and we discuss the role of metaphase chromatin structure in the preservation of differentiated cell states. The X chromosome-linked human PGK1 (phosphoglycerate kinase 1) promoter region was investigated, and euchromatic active X chromosome (Xa) metaphase chromatin was compared with interphase Xa chromatin and to heterochromatic inactive X chromosome (Xi) metaphase and interphase chromatin. We find that (i) good-quality data at single-nucleotide resolution can be obtained by LMPCR analysis of dimethyl sulfate-treated intact metaphase cells; (ii) transcription factors present on the Xa promoter of interphase chromatin are not present on metaphase chromatin, establishing that the transcription complex on the PGK1 promoter must form de novo each cell generation; and (iii) the dimethyl sulfate reactivity pattern of Xa and Xi chromatin at metaphase is very similar to that of naked DNA. These results are discussed in the context of models for heritable chromatin structure and epigenetic mechanisms for cell memory, and they are also relevant to more general aspects of chromatin structure and differences between euchromatin and heterochromatin.

Animals↗

PubMed1993

Cell cycle-related changes in chromatin structure detected by flow cytometry using multiple DNA fluorochromes.

Three-color staining and sequential fluorescence analysis of the dyes bound to specific base regions and intercalating sites on DNA were used to detect alterations of chromatin organization in single cells. Two non-intercalating DNA-reactive fluorochromes, Hoechst 33342 (HO) with preferential binding to A-T and mithramycin (MI) which binds to G-C regions, were used for cell staining in combination with propidium iodide (PI), a dye that intercalates between DNA base pairs without base specificity. Blue (HO), green (MI), and red (PI) fluorescence intensities were quantitatively analyzed following sequential excitation of stained cells in a three-laser flow system (uv, 457 nm and 530 nm wavelengths). Competition for dye binding was not significant and, although energy transfer occurs, under appropriate conditions, DNA distribution profiles for exponentially growing cells exhibit relatively low coefficients of variation (CVs), G2 + M/G1 peak ratios near values of 2, and comparable percentages of cells in G1, S, and G2 + M for each of the three dyes. The fluorescence intensity of each dye is proportional to the relative number of specific base regions or intercalating sites accessible for dye binding in DNA. Electronic ratio analyses of blue to green and red to green fluorescence signals provided a measure of the correlation of A-T to G-C and intercalation to G-C sites, respectively, for dye-bound regions on the DNA. Ratio analyses were sensitive to conformational changes in chromatin structure that alter the relative proportion of different base regions in DNA accessible for dye binding. Using this method, rearrangements in chromatin structure were observed in synchronized CHO cells during progression through the cell cycle. The sensitivity of this method will make it useful in investigations on effects of various agents (i.e., drugs, irradiation, viruses) on chromatin structure in single cells. Also, the three-color DNA staining and analysis techniques have potential for improving chromosome resolution in flow karyotyping studies.

Animals↗

PubMed2007

Regulation of telomere movement by telomere chromatin structure.

Beyond their role in replication and chromosome end capping, telomeres are also thought to function in meiotic chromosome pairing, meiotic and mitotic chromosome segregation as well as in nuclear organization. Observations in both somatic and meiotic cells suggest that the positioning of telomeres within the nucleus is highly specific and believed to be dependent mainly on telomere interactions with the nuclear envelope either directly or through chromatin interacting proteins. Although little is known about the mechanism of telomere clustering, some studies show that it is an active process. Recent data have suggested a regulatory role for telomere chromatin structure in telomere movement. This review will summarize recent studies on telomere interactions with the nuclear matrix, telomere chromatin structure and factors that modify telomere chromatin structure as related to regulation of telomere movement.

Chromatin↗

PubMed2002

Protamine-like proteins: evidence for a novel chromatin structure.

Protamine-like (PL) proteins are DNA-condensing proteins that replace somatic-type histones during spermatogenesis. Their composition suggests a function intermediate to that of histones and protamines. Although these proteins have been well characterized at the chemical level in a large number of species, particularly in marine invertebrates, little is known about the specific structures arising from their interaction with DNA. Speculation concerning chromatin structure is complicated by the high degree of heterogeneity in both the number and size of these proteins, which can vary considerably even between closely related species. After careful examination and comparison of the protein sequences available to date for the PL proteins, we propose a model for a novel chromatin structure in the sperm of these organisms that is mediated by somatic-type histones, which are frequently found associated with these proteins. This structure supports the concept that the PL proteins may represent various evolutionary steps between a sperm-specific histone H1 precursor and true protamines. Potential post-translational modifications and the control of PL protein expression and deposition are also discussed.

Amino Acid Sequence↗

PubMed2004

Cbf1p modulates chromatin structure, transcription and repair at the Saccharomyces cerevisiae MET16 locus.

The presence of damage in the transcribed strand (TS) of active genes and its position in relation to nucleosomes influence nucleotide excision repair (NER) efficiency. We examined chromatin structure, transcription and repair at the MET16 gene of wild-type and cbf1Delta Saccharomyces cerevisiae cells under repressing or derepressing conditions. Cbf1p is a sequence-specific DNA binding protein required for MET16 chromatin remodelling. Irrespective of the level of transcription, repair at the MspI restriction fragment of MET16 exhibits periodicity in line with nucleosome positions in both strands of the regulatory region and the non-transcribed strand of the coding region. However, repair in the coding region of the TS is always faster, but exhibits periodicity only when MET16 is repressed. In general, absence of Cbf1p decreased repair in the sequences examined, although the effects were more dramatic in the Cbf1p remodelled area, with repair being reduced to the lowest levels within the nucleosome cores of this region. Our results indicate that repair at the promoter and coding regions of this lowly transcribed gene are dependent on both chromatin structure and the level of transcription. The data are discussed in light of current models relating NER and chromatin structure.

Basic Helix-Loop-Helix Leucine Zipper Transcriptio↗

PubMedDate not supplied

Chromatin structure in globozoospermia: a case report.

Sperm nuclear abnormalities in patients with globozoospermia have not been well characterized and may lead to the high rates of fertilization failure and embryo loss reported in patients with this form of teratozoospermia. This study used transmission electron microscopy (TEM), the sperm chromatin structure assay (SCSA), and single cell gel eletrophoresis assay (COMET) to assess if globozoospermia is associated with sperm chromatin structure abnormalities, DNA fragmentation, or both. The flow cytometric SCSA measures abnormal chromatin structure based on the susceptibility of sperm nuclear DNA to acid-induced denaturation in situ. COMET measures DNA fragmentation in individual sperm nuclei based upon gel electrophoretic patterns. Although sperm concentration (113 million/mL) and motility (66%) were normal in the patient, there was complete acrosome deficiency. TEM and SCSA data confirmed light microscopic examination that showed that sperm populations included a mixture of round and elongated sperm heads. Even though 100% of sperm had abnormal head morphology, only 13% demonstrated DNA denaturation (COMPalpha(t)), which is below our threshold of 15% COMPalpha(t), and consistent with high-fertility patients. Of interest, 13% of the sperm were also positive in the COMET assay, supporting our previous observations that SCSA-positive cells are also positive for DNA fragmentation. It was unexpected but of great interest that a human sperm population with 100% sperm morphology abnormalities had a chromatin integrity at the molecular level that is equivalent to sperm populations shown in previous studies to be highly fertile. These data are the first reported using SCSA and COMET assays to evaluate a patient with globozoospermia and support previous reports that intracytoplasmic sperm injection of globozoospermia may result in fertility/pregnancy. Lower success rates seen in some patients may be due to unrelated factors.

Adult↗

PubMed1992

Altered chromatin structure of cerebral nuclei in experimental diabetes mellitus.

To determine whether diabetes alters chromatin structure in vivo, micrococcal nuclease digestion kinetics were analyzed in cerebral cortical and hepatic nuclei of streptozotocin-induced diabetic rats. Cerebral nuclei of diabetic rats maintained for 6 weeks were less susceptible to micrococcal nuclease digestion compared with control rats. Insulin treatment reversed diabetes-related changes in nuclease digestion kinetics. There were no changes in the kinetics of digestion in hepatic nuclei. The reduced digestibility of cerebral DNA in diabetes could not be attributed to altered DNA fluorescence spectra, or altered distribution of most abundant chromatin proteins that were either solubilized or that remained insoluble immediately following nuclease digestion. It is concluded that chronic, uncontrolled hyperglycemia can alter chromatin structure of some tissues in vivo, and this change is probably related to subtle alterations in DNA-protein interactions.

Animals↗

PubMed1996

Significance of the chromatin structure in expression of the rat prolactin gene.

To elucidate the mechanisms underlying cell type-specific expression of the growth hormone (GH) and prolactin (PRL) genes, we used rat pituitary-derived cell lines producing exclusively GH (GC cells) or PRL (235 cells), and examined the following: expression of transcription factors essential for GH and/or PRL gene expression; promoter/enhancer activity of the GH and PRL genes transiently introduced by transfection; and chromatin structures of the GH and PRL genes. Even in PRL-nonproducing GC cells, the PRL promoter/enhancer was more active than the GH promoter, and the transcription factors, Pit-1 and estrogen receptor (ER), essential for PRL gene expression were functional. The PRL promoter/enhancer of GC cells was normal. On DNase I sensitivity analysis of the chromatin structure, two hypersensitive sites were detected in PRL gene chromatin of PRL-producing 235 cells but none in that of GC cells. It thus follows that the major reason for absence of the expression of the endogenous PRL gene in GC cells is neither the lack of transcription factors necessary for PRL gene expression nor an anomaly of the PRL gene itself, but that the chromatin structure of the PRL gene differs in PRL-nonproducing and -producing cells. It was shown in this study that neither Pit-1 nor ER is required for conversion of the structure of PRL gene chromatin to a DNase I-hypersensitive state.

Animals↗

PubMed2004

NAD+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1.

PARP-1 is the most abundantly expressed member of a family of proteins that catalyze the transfer of ADP-ribose units from NAD+ to target proteins. Herein, we describe previously uncharacterized nucleosome binding properties of PARP-1 that promote the formation of compact, transcriptionally repressed chromatin structures. PARP-1 binds in a specific manner to nucleosomes and modulates chromatin structure through NAD+-dependent automodification, without modifying core histones or promoting the disassembly of nucleosomes. The automodification activity of PARP-1 is potently stimulated by nucleosomes, causing the release of PARP-1 from chromatin. The NAD+-dependent activities of PARP-1 are reversed by PARG, a poly(ADP-ribose) glycohydrolase, and are inhibited by ATP. In vivo, PARP-1 incorporation is associated with transcriptionally repressed chromatin domains that are spatially distinct from both histone H1-repressed domains and actively transcribed regions. Thus, PARP-1 functions both as a structural component of chromatin and a modulator of chromatin structure through its intrinsic enzymatic activity.

Adenosine Triphosphate↗

PubMed1984

The role of the central globular domain of histone H5 in chromatin structure.

Histone H5 contains three tyrosines in the central, apolar region of the molecule. All three tyrosines can be spin labeled at low ionic strength. When the central globular domain is folded at high ionic strength, only one tyrosine becomes accessible to the imidazole spin label. Spin labeling the buried tyrosines prevents the folding of the globular structure, which, in turn, affects the proper binding of the H5 molecule to stripped chromatin. Chromatin complexes reconstituted from such an extensively modified H5 molecule show a weaker protection of the 168 base pair chromatosome during nuclease digestion. However, when only the surface tyrosine of the H5 molecule is labeled, such a molecule can still bind correctly to stripped chromatin, yielding a complex very similar to that of native chromatin. Our data supports the idea that not just the presence of the linker histone H5, but the presence of an intact H5 molecule with a folded, globular central domain in essential in the recognition of its specific binding sites on the nucleosomes. Our data also show that during the chromatin condensation process, the tumbling environment of the spin label attached to the surface tyrosine in the H5 molecule is not greatly hindered but remains partially mobile. This suggests that either the labeled domain of the H5 molecule is not directly involved in the condensation process or the formation of the higher-order chromatin structure does not result is a more viscous or tighter environment around the spin label. The folded globular domain of H5 molecule serves in stabilizing the nucleosome structure, as well as the higher-order chromatin structure.

Animals↗

PubMed1986

Effect of N-hydroxyparacetamol on DNA, RNA, and protein synthesis and chromatin structure.

N-Hydroxyparacetamol treatment of lymphoblastoid cells gave rise to a dose-dependent decrease in DNA, RNA, and protein synthesis. Inhibition of DNA synthesis was less marked in medium at pH 6.5 than at pH 9.0. N-Hydroxyparacetamol appeared to inhibit DNA synthesis at least in part through alterations to chromatin structure. This compound produced a dose-dependent and time-dependent loss in the superhelix density of DNA as determined by nucleoid sedimentation analysis. Alkaline elution data as well as sucrose gradient analysis revealed that this decrease in sedimentation did not arise through single strand breakage to DNA. The structural alterations to chromatin caused by N-hydroxyparacetamol appeared to have been repaired after 6 hr. However, sedimentation of "repaired" nucleoids in the presence of ethidium bromide was markedly different from sedimentation of untreated nucleoids. These results suggested that some N-hydroxyparacetamol remained associated with nucleo-protein, thus interfering with the binding of ethidium. Furthermore, both RNA and protein synthesis were markedly inhibited by N-hydroxyparacetamol, demonstrating a major effect on cell function. The widespread effects of N-hydroxyparacetamol could be accounted for by changes to chromatin structure or by a more general effect on cellular metabolism. Either of these effects could account for the dramatic cytotoxicity of this compound. A concentration of 2.5 mM reduced cell viability by 96% after 3 days.

Acetaminophen↗

PubMedDate not supplied

Effects of heat stress on mouse testicular cells and sperm chromatin structure.

Scrotal regions of mice were exposed to a 38.0, 40.0, or 42.0 degrees C (+/-0.1) H2O bath for 60 minutes to determine the effects of elevated temperatures on testicular cells and sperm chromatin structure. Mice were killed on various days after exposure, and ratios of acridine orange-stained testicular cell populations were determined by flow cytometry. Testicular weights of mice exposed to 42.0 degrees C decreased significantly day 1 (P < 0.01) through 35 (P < 0.001). Also, a significant relative decrease in testicular haploid cells was seen on days 3-35 (P < 0.001) with a corresponding increase in the diploid population (P < 0.001). Testicular analyses of mice exposed to 38.0 degrees C were not significantly different from control values. Testis weights of mice exposed to 40.0 degrees C were not affected, but a relative decrease in percent haploid cells occurred on days 11 and 14 (P < 0.001). The sperm chromatin structure assay (SCSA) was used to measure the susceptibility of cauda epididymal sperm DNA to in situ denaturation at low pH. Caudal epididymides of mice exposed to 42.0 degrees C had no sperm. Caudal epididymal sperm from mice exposed to 40.0 degrees C were most susceptible to acid-induced DNA denaturation on days 3 (P < 0.05), 7, 11, and 14 (all P < 0.001). The 38.0 degrees C exposed mice showed some minor sperm chromatin abnormalities at later time points (days 11-35). When compared to sperm head morphology measurements, SCSA parameters were more sensitive indicators of heat-induced sperm abnormalities. These results show that mouse spermatogenesis is disrupted by scrotal exposure to environmental temperatures several degrees over normal physiological temperature and, of more biological interest, that some thermal ranges above normal allowed production of sperm with compromised nuclear chromatin structure.

Acridine Orange↗

PubMedDate not supplied

Studies on sperm chromatin structure alterations and cytogenetic damage of mouse sperm following in vitro incubation. Studies on in vitro-incubated mouse sperm.

Mouse epididymal sperm incubated in Tyrode's T6 fertilization media were analyzed over time for chromosome damage by two methods. First, cytogenetic analysis was done on paternal pronuclei metaphase chromosomes. After 6 hours incubation 11% of the cells demonstrated chromosome structural abnormalities. Secondly, sperm nuclei were measured by the sperm chromatin structure assay, which is a measure of the susceptibility of sperm DNA to the nuclei demonstrated an increased susceptibility to DNA denaturation, reaching near 100% by 48 hours. Changes in chromatin structure at the molecular level may lead to chromosome breaks seen in pronuclear chromosomes.

Animals↗

PubMed1989

Chromatin structure and levels of expression and DNA methylation in the E3 region of chromosomally integrated adenovirus type 12 DNA.

Integrated adenovirus type 12 (Ad12) genes in Ad12-transformed cell lines were investigated for chromatin structure, expression levels and states of DNA methylation. The E3 region in the Ad12-transformed cell line HA12/7 is hypermethylated and not expressed. The same region in the Ad12-transformed hamster cell lines T637 and A2497-3 is transcribed and undermethylated (Kruczek, I. and Doerfler, W. (1982) EMBO J. 1, 409-414). There was no significant difference in the DNase I sensitivity of the E3 region when nuclei of the aforementioned cell lines were incubated with this nuclease. In contrast, incubation of these nuclei with the restriction endonuclease PstI and subsequent cleavage of the DNA with BamHI generated an additional 0.9 kbp fragment in T637 and A2497-3 DNA which was not observed after treating HA12/7 nuclei and DNA in the same way. This finding was interpreted as indicative of differences in the chromatin structure of the E3 region depending on its state of transcriptional activity and its level of methylation. The E1 and major late promoter regions, which were transcriptionally active and inactive, respectively, in all three cell lines investigated, did not exhibit differences in sensitivity towards DNase I or PstI treatment of nuclei. More refined technology will be required to compare the chromatin structure of active versus inactive genes.

Adenovirus Early Proteins↗

PubMed1986

Formation of stable chromatin structures on the histone H4 gene during differentiation in Tetrahymena thermophila.

The relationship between chromatin structure and the transcriptional activity of the histone H4-I gene of Tetrahymena thermophila was explored. Indirect end-labeling studies demonstrated that major DNase I- and micrococcal nuclease-hypersensitive sites flank the active macronuclear genes but not the inactive micronuclear genes. Runon transcription experiments with isolated macronuclei indicated that histone gene transcription rates decreased when cells were starved. However, macronuclear nuclease-hypersensitive sites persisted upon starvation. Thus, one level of transcriptional control of the H4-I gene results in altered chromatin structure and is established during nuclear differentiation. The rate of transcription is also controlled, but not through hypersensitive site-associated structures.

Cell Differentiation↗

PubMed2001

p53 targets chromatin structure alteration to repress alpha-fetoprotein gene expression.

Many of the functions ascribed to p53 tumor suppressor protein are mediated through transcription regulation. We have shown that p53 represses hepatic-specific alpha-fetoprotein (AFP) gene expression by direct interaction with a composite HNF-3/p53 DNA binding element. Using solid-phase, chromatin-assembled AFP DNA templates and analysis of chromatin structure and transcription in vitro, we find that p53 binds DNA and alters chromatin structure at the AFP core promoter to regulate transcription. Chromatin assembled in the presence of hepatoma extracts is activated for AFP transcription with an open, accessible core promoter structure. Distal (-850) binding of p53 during chromatin assembly, but not post-assembly, reverses transcription activation concomitant with promoter inaccessibility to restriction enzyme digestion. Inhibition of histone deacetylase activity by trichostatin-A (TSA) addition, prior to and during chromatin assembly, activated chromatin transcription in parallel with increased core promoter accessibility. Chromatin immunoprecipitation analyses showed increased H3 and H4 acetylated histones at the core promoter in the presence of TSA, while histone acetylation remained unchanged at the site of distal p53 binding. Our data reveal that p53 targets chromatin structure alteration at the core promoter, independently of effects on histone acetylation, to establish repressed AFP gene expression.

Acetylation↗

PubMed1989

Radiation damage and chromatin structure.

The recent advances made in the knowledge of chromatin structure have important implications in molecular and cellular radiobiology. There are now many lines of evidence that the chromatin organization can affect the production, the distribution and the repair of radiation-induced damage in DNA. Experiments with polynucleosomes show that DNA double strand breaks (dsb) are not randomly distributed along the DNA molecule. Rather, they are preferentially localized in linker regions, while core regions are more resistant. Isolated DNA is about 4-fold more susceptible to dsb than DNA irradiated as a part of polynucleosomes. This differential radiosensitivity is apparently due to the close association of DNA with proteins. The analysis of DNA single strand breaks production and repair in a human erythroleukemic cell line that can be induced to differentiate in vitro, showed that the repair kinetics in differentiated cells appears significantly slower than in undifferentiated ones. This can be interpreted as a decrease in the genome accessibility to repair enzymes due to the presence of more structured regions in chromatin after differentiation. It appears that a high degree of genome compactness could imply, on one hand, a high DNA radioresistance and, on the other hand, a slow DNA repair so that the identification of chromatin domains which are critical, from the structural point of view, in determining cellular effects such as cell killing and mutation, should take into account a sort of balance between the amount of damage and the extent of repair.

Animals↗