Search PubMed⌕ Search

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.

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

At least 91 records · Page 5Linked to original sources
PubMed1977

Influence of histone H1 on chromatin structure.

Removal of histone H1 produces a transition in the structure of chromatin fibers as observed by electron microscopy. Chromatin containing all histone proteins appears as fibers with a diameter of about 250 A. The nucleosomes within these fibers are closely packed. If histone H1 is selectively removed with 50-100 mM NaCl in 50 mM sodium phosphate buffer (pH 7.0) in the presence of the ion-exchange resin AG 50 W - X2, chromatin appears as "beads-on-a-string" with the nucleosomes separated from each other by distances of about 150-200 A. If chromatin is treated in the presence of the resin with NaCl at concentrations of 650 mM or more, the structural organization of the chromatin is decreased, yielding fibers of irregular appearance.

Animals↗
PubMed2005

Repair of DNA lesions in chromosomal DNA impact of chromatin structure and Cockayne syndrome proteins.

Decondensation of chromatin is essential to facilitate access to DNA metabolizing processes such as transcription and DNA repair. Disruption of histone-DNA contacts by histone modification or by ATP dependent chromatin remodelling allows DNA-binding proteins to compete with histones for DNA. The efficiency of global genome nucleotide excision repair (GGR) that removes a variety of helix distorting DNA lesions is known to be affected by chromatin structure most notably demonstrated by the slow repair of heterochromatin. In addition, the efficiency of GGR to repair lesions in transcriptionally active genes requires functional CSA and B proteins. We found that repair of UV-photolesions in both strands of the active adenosine deaminase gene was delayed in CS cells when compared to normal human fibroblasts. We suggest that the lack of transcription recovery characteristic for CS cells exposed to DNA damaging agents, might lead to changes in the chromatin structure of active genes, causing less efficient repair of lesions in these genes when compared to normal cells.

Chromatin↗
PubMedDate not supplied

The ade6 gene of the fission yeast Schizosaccharomyces pombe has the same chromatin structure in the chromosome and in plasmids.

We have analysed the chromatin structure of the ade6 gene of Schizosaccharomyces pombe and its flanking regions both in the chromosome and in plasmids. The chromatin structure is independent of the chromosomal or extrachromosomal location. The ade6 gene contains eight precisely positioned nucleosomes on the 5' half, 'not positioned' nucleosomes around the 3' end and a nuclease-sensitive promoter region. Precisely positioned nucleosomes, but no nuclease-sensitive region were also detected on the ura4 gene in the chromosome and on a plasmid. The results show that S. pombe chromosomal and extrachromosomal genes have chromatin structures similar to those of S. cerevisiae and higher eukaryotes.

Chromatin↗
PubMed2004

ATP-dependent chromatin structural modulation by multiprotein complex including HMGB1.

High mobility group box protein 1, HMGB1, is a major nonhistone chromatin component in higher eukaryotic cells. HMGB1 is thought to be involved in the processes of global nuclear events such as transcription, recombination and repair, but the mechanism of these processes is unclear. Here, we show a concrete example of chromatin structural modulation by HMGB1 in HeLa S3 cells. A co-immunopurification experiment with Flag-tagged HMGB1 revealed that a portion of HMGB1 in HeLa S3 cells is included in a large-molecular-weight multiprotein complex. The multiprotein complex including HMGB1 showed ATP hydrolysis and ATP-dependent chromatin structural modulation activities that increased the susceptibility of chromatin to MNase digestion, while HMGB1 alone had no such activity. Thus, HMGB1 in the multiprotein complex is critical for expressing the chromatin structural modulation activity. These results suggest that HMGB1 is involved in chromatin structural modulation in global nuclear events through its interaction with a multiprotein complex in mammalian cells.

Adenosine Triphosphate↗
PubMed1998

Chromatin structure and cardiac gene expression.

Gene activation is often preceded by or accompanied by a perturbation of the chromatin structure. Recently, several co-factors of transcription factors have been identified as histone acetyltransferases. In addition, retinoblastoma protein and some co-factors can form a complex with histone deacetylases. These discoveries provide direct evidence that modification of chromatin structure is crucial for gene activation. However, the role of chromatin structure in cardiac-specific expression has not yet been elucidated. The potential significance of chromatin structure in cardiac-specific gene expression is indicated by: (1) heterogeneous human SWI/SNF chromatin remodelling factors among various tissues; (2) several chromatin remodelling factors shown to be expressed preferentially in the heart; (3) the demonstration of chromatin remodelling of the cardiac beta-myosin heavy chain gene (MyHC) during cardiac development. We therefore propose to study cardiac-specific chromatin remodelling activity in order to elucidate mechanisms controlling the reactivation of the fetal heart genetic program in the hypertrophic heart.

Animals↗
PubMed1975

Electron microscopic and biochemical evidence that chromatin structure is a repeating unit.

Electron microscopic and biochemical studies demonstrate that the fundamental structure of chromatin depleted of lysine-rich histones is composed of a flexible chain of spherical particles (nucleosomes), about 125 A in diameter, connected by DNA filaments. Such a chromatin preparation can be separated by centrifugation into two fractions which differ in the spacing of the nucleosomes; In one fraction almost all of the DNA is condensed in nucleosomes, while the other fraction contains long stretches of free DNA connecting regions where the nucleosomes are closely packed. The isolated nucleosomes contain about 200 base pairs of DNA and the four histones F2alpha1, F2alpha2, and F2b, and F3 in an overall histone/DNA ratio of 0.97; In such a structure the DNA is compacted slightly more than five times from its extended length; The same basic structure can be visualized in chromatin spilling out of lysed nuclei. However, in this latter case the nucleosomes are very closely packed, suggesting that histone F1 is involved in the superpacking of DNA in chromosomes and nuclei. The chromatin fiber appears to be a self-assembling structure, since the nucleosomal arrangement can be reconstituted in vitro from DNA and the four histones F2alpha1, F2alpha2, F2b and F3 only, irrespective of their cellular origin.

Adenoviridae↗
PubMed1994

Insensitivity of the present hsp26 chromatin structure to a TATA box mutation in Drosophila.

The role of the TATA element in establishing the chromatin structure and inducible transcription of the Drosophila melanogaster hsp26 gene has been analyzed. An hsp26/lacZ fusion gene with a mutant promoter, in which the TATA box sequence TATAAA was changed to CCCAAA, was introduced into Drosophila by P-element transformation. The mutation had little effect on formation of the preset chromatin structure observed prior to induction. However, the mutation dramatically reduced transcription levels following heat shock. Northern analysis indicated that weak, inducible expression of the mutant promoter occurred within the same period of heat shock as for the normal promoter, suggesting that TFIID was associated with the mutant promoter prior to heat shock. Biochemical analysis showed that the mutant promoter still bound TFIID in vitro, but with 3-5-fold less affinity than the normal promoter. DNase I footprinting revealed that the conformation of the TFIID-DNA complex differed significantly from that of the normal promoter. These results indicate that alterations in the conformation or the stability of the TFIID-DNA complex drastically reduce the level of induction, but do not dramatically affect chromatin structure formation. Formation of the requisite chromatin structure is either independent of, or highly tolerant of, changes in the TFIID-DNA complex.

Animals↗
PubMed1999

Presetting of chromatin structure and transcription factor binding poise the human GADD45 gene for rapid transcriptional up-regulation.

GADD45 has been suggested to coordinate cell cycle regulation with the repair of DNA damage following ionizing radiation (IR). Although the GADD45 gene is transcriptionally up-regulated in response to IR, alterations in in vivo transcription factor (TF) binding or chromatin structure associated with up-regulation have not been defined. To understand how chromatin structure might influence TF binding and GADD45 up-regulation, key regulatory regions of the gene were identified by in vivo DNase I hypersensitivity (HS) analysis. Chromatin structure and in vivo TF binding in these regions were subsequently monitored in both non-irradiated and irradiated human ML-1 cells. In non-irradiated cells expressing basal levels of GADD45, the gene exhibited a highly organized chromatin structure with distinctly positioned nucleosomes. Also identified in non-irradiated cells were DNA-protein interactions at octamer binding motifs and a CCAAT box in the promoter and at consensus binding sites for AP-1 and p53 within intron 3. Upon irradiation and a subsequent 15-fold increase in GADD45 mRNA levels, neither the chromatin structure nor the pattern of TF binding in key regulatory regions was altered. These results suggest that the GADD45 gene is poised for up-regulation and can be rapidly induced independent of gross changes in chromatin structure or TF binding.

CCAAT-Enhancer-Binding Proteins↗
PubMed1999

Density gradient centrifugation and glass wool filtration of semen remove spermatozoa with damaged chromatin structure.

The ability of double-layered density gradient centrifugation (DGC) or glass wool filtration (GWF) of semen to remove spermatozoa with damaged chromatin structure was assessed by the flow cytometric sperm chromatin structure assay (SCSA), which measures the susceptibility to sperm nuclear denaturation in situ. Ejaculates from 26 men attending a university-affiliated assisted reproduction laboratory were processed by DGC and GWF. Unprocessed, DGC- and GWF-processed specimens were assessed by the SCSA and by conventional semen parameters. Changes in chromatin structure were compared with conventional semen parameters. Both sperm preparation techniques yielded sperm suspensions with improved sperm chromatin structure as well as motility (%), forward progression (1-4) and viability (%). DGC was superior to GWF in the efficiency of recovering motile, morphologically normal, mature sperm suspensions. However, GWF produced improved chromatin integrity (SDalpha(t)) and viability. Moderate correlations between SCSA and conventional sperm parameters were observed. Nevertheless, the SCSA provides additional information about the biochemical integrity of sperm DNA and may be used in future studies to provide insight into assisted reproduction technology outcomes not explained by conventional sperm parameters.

Cell Separation↗
PubMed1996

Chromatin structure of the yeast URA3 gene at high resolution provides insight into structure and positioning of nucleosomes in the chromosomal context.

To characterize nucleosome structure and positioning in the chromosomal context, the chromatin structure of the whole URA3 gene was studied in the genome and in a minichromosome by testing the accessibility of DNA to micrococcal nuclease and DNase I. The cutting patterns and hence the chromatin structures were almost indistinguishable in the genome and in the minichromosomes. The only notable exception was enhanced cutting between nucleosomes U3/U4 and U4/U5 in the minichromosomes. The results demonstrate that there is no severe constraint acting from outside the URA3 gene in chromosomes and minichromosomes. While low-resolution mapping showed six regions with a positioned nucleosome (U1 to U6), each region resolved in a complex pattern consistent with multiple overlapping positions. Some regions (U1, U4, U5 and U6) showed multiple positions with a dominant rotational setting (DNase I pattern), while U2 showed positioning within 10 bp but with no defined rotational setting, demonstrating that nucleosome positions were not in phase and not coordinately regulated. Reduced DNase I cutting from about 50 bp form the 5' end towards 3' end was common to all nucleosome regions. This polarity has been observed on isolated core particles. The results demonstrate that the DNase I pattern observed in vitro indeed reflects a structural property of nucleosomes in the chromosomal context. It is emphasized that despite the local heterogeneity revealed by high-resolution mapping, the low-resolution map is a reasonably accurate representation of the chromatin structure.

Base Sequence↗
PubMed2005

[Effects of extremely low frequency electromagnetic fields on DNA of testicular cells and sperm chromatin structure in mice].

OBJECTIVE: To study the effects of 50 Hz electromagnetic fields (EMFs) on DNA of testicular cells and sperm chromatin structure in mice. METHODS: Mice were exposed to 50 Hz, 0.2 mT or 6.4 mT electromagnetic fields for 4 weeks. DNA strand breakage in testicular cells was detected by single-cell gel electrophoresis assay. Sperm chromatin structure was analyzed by sperm chromatin structure assay with flow cytometry. RESULTS: After 50 Hz, 0.2 mT or 6.4 mT EMFs exposure, the percentage of cells with DNA migration in total testicular cells increased from the control level of 25.64% to 37.83% and 39.38% respectively. The relative length of comet tail and the percentage of DNA in comet tail respectively increased from the control levels of 13.06% +/- 12.38% and 1.52% +/- 3.25% to 17.86% +/- 14.60% and 2.32% +/- 4.26% after 0.2 mT exposure and to 17.88% +/- 13.71% and 2.35% +/- 3.87% after 6.4 mT exposure (P < 0.05). Exposure to EMFs had not induced significant changes in S.D.alphaT and XalphaT, but COMPalphaT (cells outside the main population of alpha t), the percentage of sperms with abnormal chromatin structure, increased in the two exposed groups. CONCLUSION: 50 Hz EMFs may have the potential to induce DNA strand breakage in testicular cells and sperm chromatin condensation in mice.

Animals↗
PubMed1990

Alternative chromatin structure at CpG islands.

Actively transcribed chromatin is structurally different from bulk inactive chromatin. It has been difficult to define the molecular basis of the difference, however, because purified fractions of active chromatin were not available. We have overcome this problem by releasing oligonucleosomes from the nonmethylated CpG-rich islands (CpG islands) of HeLa cell nuclei using restriction endonucleases. Since CpG islands very often include the promoters and 5' transcribed regions of genes, they represent a model for the "active" chromatin structure. CpG island chromatin differs in three respects from bulk chromatin prepared in the same way: histone H1 is present in very low amounts; histones H3 and H4 are highly acetylated; and nucleosome-free regions are present. Except for the latter regions, the average nucleosomal spacing is similar to that of bulk chromatin.

Base Sequence↗
PubMed1998

Nucleosome and chromatin structures and functions.

From the above discussion it can be appreciated that the major unknowns to advancing our understanding of nucleosome and chromatin structure and functions are: 1) the binding sites of the histone N- and C-terminal domains in native nucleosomes and in chromatin; 2) the effects of histone reversible chemical modifications of phosphorylations, acetylations and ubiquitinations on the binding of the histone N- and C-terminal domains in nucleosome and chromatin structures; 3) the path(s) of the linker DNA between nucleosome in the different orders of chromatin structure; 4) the position of the globular, N- and C-terminal domains of linker histones in the nucleosome and chromatin structures; and 5) the lack of a detailed structure for the 30 nm chromatin fiber. The above unknowns provide formidable challenges for future researchers.

Animals↗
PubMed1984

Gene expression in murine erythroleukemia cells. Transcriptional control and chromatin structure of the alpha 1-globin gene.

The transcriptional activation and chromatin structure of the alpha 1-globin gene was analyzed during induced erythroid differentiation in murine erythroleukemia cells (MELC). In uninduced MELC, a low level of alpha 1-globin, coding-strand-specific transcription is detectable. Hexamethylene bisacetamide (HMBA)-mediated MELC differentiation is associated with a 10 to 20-fold increase in the rate of alpha 1-globin gene transcription. In induced MELC, alpha 1-globin gene transcription initiated predominantly near the cap site, occurs only off the coding strand, and might terminate, or attenuate, in a region 50 to 250 base-pairs 3' of the polyadenylation site. Before transcriptional activation of the gene, chromatin surrounding the gene displays overlapping DNase I and S1 nuclease sensitive sites, which map to a region 100 to 200 base-pairs 5' of the cap site. After induction, the nuclease sensitivity of these pre-established, overlapping sites increases. In addition, induction generates novel, non-overlapping DNase I and S1 nuclease sensitive sites, which map to regions centered 300 base-pairs 5', and approximately coincident with the cap site, respectively. We compared the time-course of alpha 1-globin transcriptional activation to the chromatin structure changes. A twofold increase in gene transcription is detected within two cell cycles (approximately 24 hours) of exposure of cells synchronized in the G1/early S-phase to inducer. Transcription rates continue to increase for at least 48 hours in MELC cultured with HMBA (the latest time assayed). Chromatin structure changes appear nearly complete after two cell cycles.

Acetamides↗
PubMed1997

The first exon of the rat aldolase C gene is essential for restoring the chromatin structure in transgenic mice.

A 13-kb fragment of the rat aldolase C gene contains sufficient information for gene expression. Transgenic mice carrying the 13-kb fragment showed restoration of chromatin structure and tissue-specific, copy number-dependent expression. To localize the regulatory elements responsible for restoring chromatin structure, several mutated constructs were used to produce transgenic mice. Three activities were examined: recreation of DNase hypersensitive sites, restoration of methylation status, and copy number-dependent expression. Deletions of the 3'-flanking region did not affect those activities. Deletion of seven introns affected the mRNA levels but not the restoration of the chromatin structure. The insertion of the LacZ gene into the first exon of the transgene interfered with both the restoration of the chromatin structure and the copy number-dependent expression in transgenic mice. DNase I footprinting assays revealed that brain-specific factors bind to the sequence disrupted by the LacZ insertion. These results suggest that the sequence in the first exon is essential for restoring the chromatin structure of the rat aldolase C gene.

Animals↗
PubMed1989

Chromatin structure of the 5' flanking region of the yeast LEU2 gene.

The chromatin structure of the LEU2 gene and its flanks has been studied by means of nuclease digestion, both with micrococcal nuclease and DNase I. The gene is organized in a array of positioned nucleosomes. Within the promoter region, the nucleosome positioning places the regulatory sequences, putative TATA box and upstream activator sequence outside the nucleosomal cores. The tRNA3Leu gene possesses a characteristic structure and is protected against nucleases. Most of the 5' flank is sensitive to DNase I digestion, although no clear hypersensitive sites were found. The chromatin structure is independent of either the transcriptional state of the gene or the chromosomal or episomal location. Finally, in the plasmid pJDB207, which lacks most of the promoter, we have found that the chromatin structure of the coding region is similar to that of the wild-type allele.

3-Isopropylmalate Dehydrogenase↗
PubMed2003

Hierarchical chromatin structure of Schizosaccharomyces pombe revealed by atomic force microscopy.

Many structural studies on higher eukaryotic chromatin have been carried out, but chromatin structure in fungi remains unclear. Schizosaccharomyces pombe has been used for investigations of chromosome function; however, the structural details of S. pombe chromatin have not been clarified owing to its small nucleus. We used atomic force microscopy for nano-scale imaging of chromatin isolated from S. pombe. Topographic images indicated that nuclear chromatin contained at least three hierarchical structures: large-scale chromatin fibers, spherical domains in the fibers, and nodules in the domains. The average diameters of the domain and the nodule were 363 +/- 85.2 nm and 46.2 +/- 9.30 nm. Each structure comprising the hierarchy was similar to higher eukaryotic chromatin thus far observed, despite definite differences in chromatin organization at the nucleosomal level. The presence of histone H1 suggested that there might be an alternative to compensate for histone H1 lacking in S. pombe.

Cell Cycle↗
PubMed1978

Effects of shearing on chromatin structure.

The effects of mechanical shearing on chromatin structure were investigated by using thermal denaturation and circular dichroism (CD) spectroscopy. Under ordinary conditions of mechanical shearing used for preparation of soluble chromatin, we observed only minor changes (less than 10%) of chromatin properties with respect to (a) absorption melting curves, (b) CD spectra, (c) CD melting curves and (d) histone transfer from chromatin to exogenous DNA. Such small pertubation of structural properties could be due to the generation of free ends when a large chromatin was cut into smaller fragments and by weakening the binding of histones to DNA near these free ends. In addition to mechanical shearing, sonication was used to shear some samples of chromatin. The effect of sonication on chromatin structure was investigated by the same physical methods used for mechanically sheared chromatin. The results indicate that sonication only slightly changes the chromatin properties with respect to CD spectra, similar to the results obtained by mechanical shearing, but sonication at high settings has a greater effect on the thermal denaturation property of chromatin as contrasted to our results from mechanically sheared chromatin.

Animals↗