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PubMed2005

Chromatin structure of human chromosomal fragile sites.

Cytological appearance of fragile sites as non-staining gaps in metaphase chromosomes suggests an abnormality in chromatin structure. Studies of fragile sites at three levels of chromosome organization: (1) examining the ability of DNA derived from fragile sites to form nucleosomes-the basic structural element of chromosomes, (2) probing the arrangement of nucleosome arrays over fragile sites in fragile site-expressing cell lines, and (3) visualizing fragile sites in higher-order chromatin organization, reveal an unusual chromatin structure associated with fragile sites. This fragile site-associated chromatin structure might play an active role in DNA metabolic processes such as replication, transcription, repair and recombination, which are closely linked to the instability of fragile sites.

Animals↗
PubMed2003

Relationship between the outcomes of assisted reproductive techniques and sperm DNA fragmentation as measured by the sperm chromatin structure assay.

OBJECTIVE: To investigate how moderate and/or high levels of DNA fragmentation (DFI), as measured by the sperm chromatin structure assay (SCSA), affect either IVF or IVF with intracytoplasmic sperm injection (ICSI) fertilization, cleavage, blastulation, implantation, and pregnancy. DESIGN: Retrospective clinical study. SETTING: Academic human reproduction laboratory. PATIENT(S): Eighty-nine couples undergoing IVF with conventional fertilization or ICSI. INTERVENTION(S): Sperm chromatin structure assay testing (SCSA) of semen aliquot taken from ejaculate used for assisted reproductive technology (ART). MAIN OUTCOME MEASURE(S): Related DFI to conventional semen parameters and cycle-specific outcomes after ART. RESULT(S): No patients achieved clinical pregnancy if SCSA values exceeded the DFI (27%, P<.01), moderate DFI (15%, P<.01), or high DFI (15%, P<.05) thresholds. Dividing the DFI sperm population into moderate-fragmentation and high-fragmentation categories did not improve the prognostic value of the SCSA. No coefficient of determination (r(2)) between SCSA parameters and conventional parameters exceeded 0.29. CONCLUSION(S): Sperm chromatin structure assay identified thresholds for negative pregnancy outcome after ART not identified using conventional semen parameters. This is the first study analyzing the clinical value of sperm DFI to [1] include a large number of ART patients (n = 89), [2] perform SCSA analysis on a semen aliquot from the ejaculate used for ART, and [3] examine how the extent (moderate and high DFI) of DFI influenced ART outcomes.

Chromatin↗
PubMed1998

Conserved elements containing NF-E2 and tandem GATA binding sites are required for erythroid-specific chromatin structure reorganization within the human beta-globin locus control region.

Proper expression of the genes of the human beta-globin gene locus requires the associated locus control region (LCR). Structurally, the LCR is defined by the presence of four domains of erythroid-specific chromatin structure. These domains, which have been characterized as DNase I hypersensitive sites (HSs), comprise the active elements of the LCR. The major focus of this research is to define the cis -acting elements which are required for the formation of these domains of unique chromatin structure. Our previous investigations on the formation of LCR HS4 demonstrated that NF-E2 and tandem, inverted GATA binding sites are required for the formation of the native HS. Similarly arranged NF-E2 and tandem GATA sites are present within the core regions of the other human LCR HSs and are evolutionarily conserved. Using site-directed mutagenesis of human HSs 2 and 3 we have tested the hypothesis that these NF-E2 and GATA sites are common requirements for the formation of all LCR HSs. We find that mutation of these elements, and particularly the GATA elements, results in a decrease or complete loss of DNase I hypersensitivity. These data imply the presence of common structural elements within the core of each LCR HS which are required for erythroid-specific chromatin structure reorganization.

Base Sequence↗
PubMed2004

Organophosphorous pesticide exposure alters sperm chromatin structure in Mexican agricultural workers.

Our objective was to evaluate alterations in sperm chromatin structure in men occupationally exposed to a mixture of organophosphorus pesticides (OP) because these alterations have been proposed to compromise male fertility and offspring development. Chromatin susceptibility to in situ acid-induced denaturation structure was assessed by the sperm chromatin structure assay (SCSA). Urinary levels of alkylphosphates (DAP) were used to assess exposure. Diethylthiophosphate (DETP) was the most frequent OP metabolite found in urine samples indicating that compounds derived from thiophosphoric acid were mainly used. Chromatin structure was altered in most samples. About 75% of semen samples were classified as having poor fertility potential (>30% of Percentage of DNA Fragmentation Index [DFI%]), whereas individuals without OP occupational exposure showed average DFI% values of 9.9%. Most parameters of conventional semen analysis were within normality except for the presence of immature cells (IGC) in which 82% of the samples were above reference values. There were significant direct associations between urinary DETP concentrations and mean DFI and SD-DFI but marginally (P = 0.079) with DFI%, after adjustment for potential confounders, including IGC. This suggests that OP exposure alters sperm chromatin condensation, which could be reflected in an increased number of cells with greater susceptibility to DNA denaturation. This study showed that human sperm chromatin is a sensitive target to OP exposure and may contribute to adverse reproductive outcomes. Further studies on the relevance of protein phosphorylation as a possible mechanism by which OP alter sperm chromatin are required.

Adolescent↗
PubMed2002

Chromatin structure and dynamics: state-of-the-art.

A meeting entitled "Chromatin Structure and Dynamics: State-of-the-Art" organized by Jordanka Zlatanova and Sanford Leuba was held at the NIH from May 8-10, 2002. It was a timely meeting and addressed our current understanding of chromatin structure, dynamics, and function.

Animals↗
PubMed1986

Alterations in local chromatin structure accompany thyroid hormone induction of growth hormone gene transcription.

The chromatin structure of the growth hormone gene and flanking DNA was analyzed in GC rat pituitary tumor cells, which appropriately express and regulate the gene. Thyroid hormone induced the DNase I hypersensitivity of a chromatin domain spanning the transcriptional initiation site from approximately -200 to +150. Three inducible hypersensitive sites were discerned in this region. One of these sites was in the first intron of the gene. The second site was within a region of 5' flanking DNA which promotes accurate, thyroid hormone-regulated transcriptional initiation. Centered between these two sites was a third hormone-inducible hypersensitive site mapping at the position of the TATA sequence. The hormone responsiveness of these hypersensitive sites suggests that occupied 3,5,3'-triiodo-L-thyronine receptor interacts with sequences flanking the growth hormone promoter, perhaps facilitating the binding or activation of a transcription factor at the TATA homology. Three hormone-independent hypersensitive sites were identified near or within intron or flanking DNA sequences similar to Chinese hamster ovary type 2 repetitive DNA. Two additional hormone-independent hypersensitive sites were located more than 1000 nucleotides up-stream of the growth hormone promoter. These sites were present in the cloned genomic DNA and were the only distinct sites found in rat spleen and cultured rat liver cells. Thyroid hormone treatment of GC cells appeared to increase the moderate DNase I sensitivity of the growth hormone gene region beyond that found in deinduced or glucocorticoid-treated cells. Dexamethasone had no discernible effect on the chromatin structure of the gene or flanking DNA in these studies.

Animals↗
PubMed2002

Alteration of large-scale chromatin structure by estrogen receptor.

The estrogen receptor (ER), a member of the nuclear hormone receptor superfamily important in human physiology and disease, recruits coactivators which modify local chromatin structure. Here we describe effects of ER on large-scale chromatin structure as visualized in live cells. We targeted ER to gene-amplified chromosome arms containing large numbers of lac operator sites either directly, through a lac repressor-ER fusion protein (lac rep-ER), or indirectly, by fusing lac repressor with the ER interaction domain of the coactivator steroid receptor coactivator 1. Significant decondensation of large-scale chromatin structure, comparable to that produced by the approximately 150-fold-stronger viral protein 16 (VP16) transcriptional activator, was produced by ER in the absence of estradiol using both approaches. Addition of estradiol induced a partial reversal of this unfolding by green fluorescent protein-lac rep-ER but not by wild-type ER recruited by a lac repressor-SRC570-780 fusion protein. The chromatin decondensation activity did not require transcriptional activation by ER nor did it require ligand-induced coactivator interactions, and unfolding did not correlate with histone hyperacetylation. Ligand-induced coactivator interactions with helix 12 of ER were necessary for the partial refolding of chromatin in response to estradiol using the lac rep-ER tethering system. This work demonstrates that when tethered or recruited to DNA, ER possesses a novel large-scale chromatin unfolding activity.

Acetylation↗
PubMed1995

Dioxin induces localized, graded changes in chromatin structure: implications for Cyp1A1 gene transcription.

In mouse hepatoma cells, the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, or dioxin) induces Cyp1A1 gene transcription, a process that requires two basic helix-loop-helix regulatory proteins, the aromatic hydrocarbon receptor (AhR) and the aromatic hydrocarbon receptor nuclear translocator (Arnt). We have used a ligation-mediated PCR technique to analyze dioxin-induced changes in protein-DNA interactions and chromatin structure of the Cyp1A1 enhancer-promoter in its native chromosomal setting. Dioxin-induced binding of the AhR/Arnt heteromer to enhancer chromatin is associated with a localized (about 200 bp) alteration in chromatin structure that is manifested by increased accessibility of the DNA; these changes probably reflect direct disruption of a nucleosome by AhR/Arnt. Dioxin induces analogous AhR/Arnt-dependent changes in chromatin structure and accessibility at the Cyp1A1 promoter. However, the changes at the promoter must occur by a different, more indirect mechanism, because they are induced from a distance and do not reflect a local effect of AhR/Arnt binding. Dose-response experiments indicate that the changes in chromatin structure at the enhancer and promoter are graded and mirror the graded induction of Cyp1A1 transcription by dioxin. We discuss these results in terms of a TCDD-induced shift in an equilibrium between nucleosomal and nonnucleosomal chromatin configurations.

Animals↗
PubMed1977

Variation in chromatin structure in two cell types from the same tissue: a short DNA repeat length in cerebral cortex neurons.

We have used micrococcal nuclease as a probe of the repeating structure of chromatin in four nuclear populations from three tissues of the rabbit. Neuronal nuclei isolated from the cerebral cortex contain about 160 base pairs of DNA in the chromatin repeat unit, as compared with about 200 base pairs for nonastrocytic glial cell nuclei from the same tissue, neuronal nuclei from the cerebellum and liver nuclei. All four types of nuclei show the same features of nucleosomal organization as other eucaryotic nuclei so far studied: nucleosomes liberated by digestion with micrococcal nuclease give a "core particle" containing 140 base pairs as a metastable intermediate on further digestion and a series of single-strand DNA fragments which are mutiples of 10 bases after digestion with DNAase I. Nuclei from cerebral cortex neurons, which have a short repeat, are distinct from the others in being larger, in having a higher proportion of euchromatin (dispersed chromatin) as judged by microscopy and in being more active in RNA synthesis in vitro.

Animals↗
PubMed2004

Anything else but GAGA: a nonhistone protein complex reshapes chromatin structure.

The packaging of DNA in the cell nucleus is a major obstacle, but also a crucial means of control in processes such as DNA replication, recombination and gene transcription. Studies in recent years have revealed that dynamic changes in the basic nucleosome structure of chromatin play a key role, particularly in the activation and silencing of gene expression. It is widely assumed that these changes are often linked to equally important, but as yet poorly understood, modifications of higher-order chromatin architecture. Recent studies in the fruit-fly Drosophila melanogaster show how protein complexes that bind to 'GAGA' DNA elements can replace nucleosomes to create a local chromatin environment that facilitates a variety of site-specific regulatory responses. In this article, I will summarize recent insights into the composition and architecture of GAGA-binding protein complexes, and discuss their multifaceted role in homeotic gene regulation.

Animals↗
PubMed1997

Human Supt5h protein, a putative modulator of chromatin structure, is reversibly phosphorylated in mitosis.

The Saccharomyces cerevisiae proteins Spt4p, Spt5p and Spt6p are involved in transcriptional repression by modulating the structure of chromatin. From HeLa cells we have purified a human homologue of Spt5p, Supt5hp, and show here that the protein is reversibly phosphorylated in mitosis. The cloned cDNA predicts a protein of 1087 residues with 31% identity to yeast Spt5p. It includes an acidic N-terminus, a putative nuclear localization signal and a C-terminal region containing two different repeated motifs. One of them, with the consensus sequence P-T/S-P-S-P-Q/A-S/G-Y, is similar to the C-terminal domain in the largest subunit of RNA polymerase II.

Amino Acid Sequence↗
PubMed1972

Chromatin structure and the cell cycle.

Pancreatic DNase I is used to probe the structure of chromatin isolated from synchronized HeLa cells. The degree to which DNA in chromatin is protected from DNase attack varies during the G(1), S, and G(2) phases of the cell cycle. In addition, the DNase sensitivity of chromatin from contact-inhibited African green monkey kidney cells differs from that of actively dividing, subconfluent cultures. These cell cycle-dependent chromatin changes were observed consistently at all enzyme concentrations (5000-fold range) and incubation times (15 min-2 hr) tested. The results indicate that the degree of complexing between DNA and chromosomal proteins changes during interphase, and they suggest that the chromosome coiling cycle of visible mitosis may extend in more subtle form over the entire cell cycle.

Animals↗
PubMed1976

[Changes in the chromatin structure of hepatocyte nuclei of rats trained to hypoxia].

Structure of chromatin in the nuclei of the isolated surviving hepatocytes and in the isolated nuclei of hepatocytes were studied by fluorochroming with acridine orange and by microfluorimetry of fluorescenc connected with the stain chromatin at 530 and 590 nm in intact rats and in the animals trained to hypoxia in a pressure chamber for 60 days. The nuclei of hepatocytes of intact rats were distributed by fluorescence at 530 nm into three classes with the intensity ratio of 1:2:4; as to the nuclei of hepatocytes of the rats trained to hypoxia - they formed a single class corresponding to the second class of control. In intact rats the ratio of the fluorescence intensity at 590 nm to such at 530 nm (alpha coefficient) formed normal distribution; in trained rats - a bimodal distribution with a shift of the maximum in the direction of reduction and increase of alpha in comparison with control. It is supposed that in hypoxia there is a repression of one and depression of other genes in the chromatine of the nuclei of the liver.

Acridines↗
PubMed2002

Fundamental features of chromatin structure.

Which mechanisms regulate nuclear plasticity? Part of the answer to that question lies in understanding how genes are expressed and regulated in the context of chromatin structure. It is now clear that the genes are regulated in discrete and controlled stages, from packaging into chromatin to their localization within the nucleus. Whereas the genetic information provides the framework for the manufacture of all proteins necessary to create a living cell, chromatin structure controls how, where, and when the genetic information should be used. In this minireview, I summarize the main characteristics of chromatin structure and highlight some of the modifications usually associated with the regulation of gene expression.

Acetylation↗
PubMed2002

Globozoospermia is associated with chromatin structure abnormalities: case report.

A recent study has shown normal sperm chromatin structure in a patient with globozoospermia. However, the poor success rate following intracytoplasmic sperm injection (ICSI) with the use of this sperm suggests that sperm nuclear abnormalities may be present. We report here a study of the sperm DNA integrity and chromosome aneuploidy and diploidy rates of a patient with 100% round-headed sperm. The sperm chromatin packaging quality was assessed by using flow cytometry after staining the DNA with propidium iodide. DNA fragmentation, possibly indicative of apoptosis, was evaluated by flow cytometry using the terminal deoxynucleotidyl transferase-mediated fluorescein-dUTP nick-end labelling (TUNEL) assay. The sperm chromosome aneuploidy and diploidy rates were evaluated by fluorescence in-situ hybridization using alpha-centromeric probes for chromosomes 8, 12, 18, X and Y. The patient with globozoospermia had a significantly higher number of sperm with chromatin decondensation (35 +/- 1.1%) and positive for the TUNEL assay (37 +/- 1.7%) compared with that found in four normal controls (4.7 +/- 0.4 and 22.5 +/- 1.2% respectively). In contrast, the total sperm aneuploidy (0.16%) and diploidy (0.05%) rates for the chromosomes studied were within the range found in 14 normozoospermic men. To the best of our knowledge, this is the first case report of round-headed sperm that has shown an elevated number of sperm with abnormal chromatin structure and DNA strand breaks.

Adult↗
PubMed1982

Chromatin structure of the chicken beta-globin gene region. Sensitivity to DNase I, micrococcal nuclease, and DNase II.

We have examined in some detail the chromatin structure of a 6.2 kilobase pair (kbp) chromosomal region containing the chicken beta-globin gene. The chromatin structure was probed with three nucleases, DNase I, micrococcal nuclease, and DNase II, and the rate of digestion of specific subfragments of the region was compared with the rate of bulk DNA digestion. We have characterized the rate of digestion of each fragment in terms of a sensitivity factor which measures the sensitivity of a fragment to a particular nuclease relative to bulk DNA. The sensitivity factors were determined by a least squares curve fitting method based on target analysis. In nuclei isolated from 14-day-old chicken embryo red blood cells, the entire 6.2-kbp region shows approximately a 10- to 20-fold increase in sensitivity to DNase I, a 3-fold increased sensitivity to micrococcal nuclease, and a 6-fold increased sensitivity to DNase II. In addition to the adult beta-globin gene, this region contains 5' and 3' flanking sequences, the 5' half of the inactive, embryonic globin gene, epsilon, and some repeated sequences. There is no obvious correlation between these genetic elements and the overall chromatin structure as measured by the nuclease sensitivity. This same region shows little or no special sensitivity in nuclei isolated from 14-day-old chicken embryo brain. Furthermore, fragments of the inactive ovalbumin gene show little or no sensitivity in either red blood cells or brain. These results support the conclusion that the entire 6.2-kbp region is largely packaged as active chromatin in 14-day-old chicken embryo red blood cells.

Animals↗
PubMed1999

Characterization of a kidney-specific pattern of chromatin structure in the rat phosphoenolpyruvate carboxykinase gene.

The kidney-specific chromatin structure of the phosphoenolpyruvate carboxykinase (PEPCK) gene was examined and compared to that of the liver. Kidney nuclear extracts were found to lack a liver-enriched factor, pepA, that binds to HSS A, a distal enhancer of the PEPCK gene that may be involved in opening the chromatin domain of the PEPCK gene in the liver. To begin the characterization of the kidney-specific chromatin structure of the PEPCK gene, nuclease hypersensitive sites (HSS) were mapped by indirect end-labeling analysis in proximal tubules from control rats, proximal tubules from acidotic rats which express induced levels of PEPCK, and NRK52E cells, a rat kidney epithelial cell line which does not express the PEPCK gene. A subset of HSS, at -400/+1 over the proximal promoter and at +1900 within the coding region, correlate with kidney-specific PEPCK expression. Two other HSS, at -3.1 kb and +6.2 kb, are detected in kidney cells regardless of PEPCK expression. The HSS at -4800, -1240, and +4650, previously identified in PEPCK-expressing liver cells, were not observed in the kidney. As in the liver, the pattern of hypersensitivity in the kidney does not change by altering the rate of transcription.

Acidosis↗
PubMed1980

Application of the Barr and Stround GN5 densitometer for description of the chromatin structure.

Nuclei isolated from rat liver can be separated in non-parenchymal diploid, parenchymal diploid and tetraploid nuclei. These nuclei are studied in their chromatin structure using a Barr and Stroud GN5 integrating densitometer. The measuring instrument has the possibility to read an integrated absorbance and as a second value the area of an absorbing object at different levels of extinction. The projection area of Feulgen-stained nuclei were measured at 557 nm at different extinction levels. From the results the conclusion can be drawn that the chromatin structure of parenchymal diploid and tetraploid nuclei is quite the same, however, the chromatin structure of non-parenchymal nuclei is more condensed. This method can be applied for an objective description of the pattern of chromatin density.

Animals↗