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Large-scale chromatin structural domains within mitotic and interphase chromosomes in vivo and in vitro.

Higher-order chromatin structural domains approximately 130 nm in width are observed as prominent components of both Drosophila melanogaster and human mitotic chromosomes using buffer conditions which preserve chromosome morphology as determined by light microscopic comparison with chromosomes within living cells. Spatially discrete chromatin structural domains of similar size also exist as prominent components within interphase nuclei prepared under equivalent conditions. Examination of chromosomes during the anaphase-telophase transition suggests that chromosomes decondense largely through the progressive straightening or uncoiling of these large-scale chromatin domains. A quantitative analysis of the size distribution of these higher-order domains in telophase nuclei indicated a mean width of 126 +/- 36 nm. Three-dimensional views using stereopairs of chromosomes and interphase nuclei from 0.5 micron thick sections suggest that these large-scale chromatin domains consist of 30 nm fibers packed by tight folding into larger, linear, fiber-like elements. Reduction in vitro of either polyamine or divalent cation concentrations within two different buffer systems results in a loss of these large-scale domains, with no higher-order chromatin organization evident above the 20-30 nm fiber. Under these conditions the DNA distribution within mitotic chromosomes and interphase nuclei appears significantly diffuse relative to the appearance by light microscopy within living cells, or, by electron microscopy, within cells fixed directly without permeabilization in buffer. These results suggest that these large-scale chromatin structural domains are fundamental elements of chromosome architecture in vivo.

Animals↗

DNA replication and chromatin structure of simian virus 40 insertion mutants.

Insertion of DNA segments into the nuclease-sensitive region of simian virus 40 alters both replication efficiency and chromatin structure. Mutants containing large insertions between the simian virus 40 origin of replication (ori site) and the 21-base-pair repeated sequences replicated poorly when assayed by transfection into COS-1 cells. Replication of mutants with shorter insertions was moderately reduced. This effect was cis-acting and independent of the nucleotide sequence of the insert. The nuclease-sensitive chromatin structure was retained in these mutants, but the pattern of cleavage sites was displaced in the late direction from the ori site. New cleavage sites appeared within the inserted sequences, suggesting that information specifying the nuclease-sensitive chromatin structure is located on the late side of the inserts. Accessibility to BglI (which cleaves within the ori site) was reduced in the larger insertion mutants. These results support the conclusion that efficient function of the viral origin of replication is correlated with its proximity to an altered chromatin structure.

Animals↗

Chromatin structure in pre- and postblastula embryos of Drosophila.

Early in embryogenesis of Drosophila melanogaster, DNA synthesis is extremely rapid while RNA synthesis is virtually undetectable. We have examined the chromatin structure of nuclei from preblastula embryos to determine whether these unusual rates of replication and transcription correlate with any alteration in the chromatin. DNase I-hypersensitive sites at the 5' end of genes have been postulated to be necessary but not sufficient for activity of the associated gene and have been shown to be established prior to the onset of transcription. In order to ascertain whether the apparent transcriptional incompetence of the early embryos is the result of the absence of such chromatin structure, we have examined nuclei from cleavage-stage embryos to determine whether the DNase I-hypersensitive sites have been established. A variety of genes, including inducible heat-shock genes, a constitutively expressed ribosomal protein gene, and two developmentally regulated genes, have been examined. In every case the pattern of DNase I-hypersensitive sites in preblastula embryos duplicates that in the later (6-18 hr after oviposition) embryos. In addition, two extra sites are observed in the early embryos, one at the 5' end of the hsp 70 gene and one in a gene at chromosomal locus 67B1. These sites do not correlate with any known function; however, neither can functional significance be ruled out. In a further investigation of the chromatin structure of early embryos, a nucleosomal array was generated. The pattern produced from nuclei of early embryos is extremely similar to that from 6- to 18-hr embryos, but somewhat less distinct. Both nucleosomal arrays and DNase I-hypersensitive sites must therefore be established very rapidly following DNA replication. The chromatin structure of cleavage-stage embryos detected by these tests appears to be essentially the same as that of older embryos, both in general, and at specific loci.

Animals↗

Sperm head morphology and nuclear chromatin structure evaluated by flow cytometry in a diallel cross in mice.

Genetic factors affecting spermatogenesis, sperm morphology, and chromatin structure in mice were estimated using a diallel cross of the inbred lines C3H/HeJ, C57BL/6J, DBA/2J, and BALB/cByJ. Flow cytometry of acridine orange stained cells was used to evaluate proportions of testicular tetraploid, diploid, and haploid cells and nuclear chromatin structure of sperm, measured by resistance of chromatin to in situ acid denaturation, and quantified by the ratio of double- to single-stranded DNA (alpha t). Percent morphologically abnormal sperm was scored by light microscopy. Heterosis, line, maternal, and reciprocal effects, and general and specific combining abilities were estimated for body and testis weights, testicular cell proportions, sperm alpha t values, and percent abnormal sperm. Heterosis was important for testis weight, alpha t values, and percent abnormal sperm. Inbreds varied in body and testicular weights, alpha t values, and percent abnormal sperm. Significant maternal effects were noted for several traits but could be due to sex-linked (X or Y) factors, since maternal and sex-linked effects were confounded. Although a high positive correlation existed between alpha t values and percent abnormal sperm, the proportion of sperm with altered chromatin structure, measured by FCM, was generally much lower than proportion of morphologically abnormal cells.

Animals↗

The relationship between higher-order chromatin structure and transcription.

It has generally been assumed that transcriptionally active genes are in an 'open' chromatin structure and that silent genes have a 'closed' chromatin structure. Here we re-assess this axiom in the light of genome-wide studies of chromatin fibre structure. Using a combination of sucrose gradient sedimentation and genomic microarrays of the human genome, we argue that open chromatin fibres originate from regions of high gene density, whether or not those genes are transcriptionally active.

Chromatin↗

Correlation between sperm motility and sperm chromatin structure assay parameters.

OBJECTIVE: To evaluate the association between chromatin structure and sperm motility. DESIGN: Cross-sectional prospective study. SETTING: Scanian Andrology Centre, Malmö, Sweden; ENEA Casaccia, Rome, Italy; and Department of Occupational Medicine, Aarhus University, Aarhus, Denmark. PATIENT(S): One hundred seventy-one males from Danish first pregnancy planner couples (group 1) and 278 Swedish military conscripts (group 2). MAIN OUTCOME MEASURE(S): Sperm chromatin structure assay (SCSA) parameters, DNA fragmentation index (DFI), high DNA stainable (HDS), and sperm motility, which was evaluated manually and by use of computer-aided sperm analysis (CASA). RESULT(S): A statistically significant negative correlation between DFI and the CASA percentage of motile sperms (group 1: r = -0.53; group 2: r = -0.38) was found. For the manual motility assessment, the correlation coefficients were slightly lower. Furthermore, HDS correlated negatively with CASA sperm motility (group 1: r = -0.39; group 2: r = -0.36) and percentage of World Health Organization category A motile sperm. In multiple linear regression analysis, concentration and SCSA parameters, but not the time of abstinence, were statistically significant predictors of sperm motility. CONCLUSION(S): There is a moderate correlation between sperm motility and SCSA parameters. The study supports the assumption that both SCSA and motility can be relatively independent predictors of male fertility.

Chromatin↗

Analysis of chromatin structure by in vivo formaldehyde cross-linking.

Recent advances leave no doubt that higher order chromatin structures play a fundamental role in many developmentally important mechanisms of gene regulation. In particular analyses in genetic model systems like yeast and Drosophila uncovered novel proteins that are involved in the regulation of chromatin structures. Many of these proteins do not bind directly to DNA but interact in large multimeric complexes. To identify the DNA elements regulated by these multiprotein complexes, alternative approaches to the standard methods of DNA-protein analysis had to be devised. Here we present a method that preserves the architecture of the higher order chromatin structures by cross-linking cells in vivo with formaldehyde. An immunoprecipitation strategy is then used to identify the DNA targets of chromosomal proteins of interest. This method can be applied to study the distribution of proteins at high resolution over extended chromosomal regions.

Animals↗

Parathymosin affects the binding of linker histone H1 to nucleosomes and remodels chromatin structure.

Linker histone H1 is the major factor that stabilizes higher order chromatin structure and modulates the action of chromatin-remodeling enzymes. We have previously shown that parathymosin, an acidic, nuclear protein binds to histone H1 in vitro and in vivo. Confocal laser scanning microscopy reveals a nuclear punctuate staining of the endogenous protein in interphase cells, which is excluded from dense heterochromatic regions. Using an in vitro chromatin reconstitution system under physiological conditions, we show here that parathymosin (ParaT) inhibits the binding of H1 to chromatin in a dose-dependent manner. Consistent with these findings, H1-containing chromatin assembled in the presence of ParaT has reduced nucleosome spacing. These observations suggest that interaction of the two proteins might result in a conformational change of H1. Fluorescence spectroscopy and circular dichroism-based measurements on mixtures of H1 and ParaT confirm this hypothesis. Human sperm nuclei challenged with ParaT become highly decondensed, whereas overexpression of green fluorescent protein- or FLAG-tagged protein in HeLa cells induces global chromatin decondensation and increases the accessibility of chromatin to micrococcal nuclease digestion. Our data suggest a role of parathymosin in the remodeling of higher order chromatin structure through modulation of H1 interaction with nucleosomes and point to its involvement in chromatin-dependent functions.

Animals↗

Trichostatin A reduces hormone-induced transcription of the MMTV promoter and has pleiotropic effects on its chromatin structure.

The deacetylase inhibitor trichostatin A (TSA) has long been used to study the relationship between gene transcription and the acetylation status of chromatin. We have used Xenopus laevis oocytes to study the effects of TSA on glucocorticoid receptor (GR)-dependent transcription and we have related these effects to changes in the chromatin structure of a reporter mouse mammary tumor virus (MMTV) promoter. We show that TSA induces a low level of constitutive transcription. This correlates with a change of acetylation pattern and a more open chromatin structure over the MMTV chromatin, and with specific acetylation and remodeling events in the promoter region. Specifically, a repositioning of initially randomly positioned nucleosomes along the distal MMTV long terminal repeat is seen. This nucleosome rearrangement is similar to the translational nucleosome positioning that occurs upon hormone activation. We also note a reduced hormone response in the presence of TSA. TSA effects have for a long time been associated with transcriptional activation and chromatin opening through inhibition of the deacetylation of histones. However, our results and those of others show that TSA-induced changes in expression and chromatin structure can be quite different in different promoter contexts and, thus, the effects of TSA are more complex than previously believed.

Acetylation↗

[Study of the effect of different concentrations of a detergent on the chromatin structure of Physarum polycephalum during the mitotic cycle].

The influence of different concentrations of detergent Joy on the chromatin structure of Physarum polycephalum in the process of mitotic cycle was studied electronmicroscopically. The investigations showed that at Joy concentrations less than 0,01% a small part of nuclei disrupt and, as a rule, chromatin is insufficiently dispersed; at concentrations more than 0,1% the detergent may influence the chromatin structure of Physarum polycephalum. Based on the data obtained we consider that the optimal detergent concentrations that practically do not influence the chromatin structure and lead to disruption of the majority of nuclei and to the proper dispersion of chromatin is 0,1-0,01%.

Cell Division↗

Long-term effects of triethylenemelamine exposure on mouse testis cells and sperm chromatin structure assayed by flow cytometry.

The toxic and potentially mutagenic actions of triethylenemelamine (TEM) on mouse body and testis weights, testicular cell kinetics, sperm production, sperm head morphology, and sperm chromatin structure were assessed in two experiments. The first experiment examined effects of four dose levels of TEM, assayed 1, 4, and 10 wk after toxic exposure. In the second study, effects from five dosage levels were measured at 1, 4, and 10 wk, and the highest dosage level was evaluated over 44 wk. TEM produced an expected dose related loss of spermatogenic activity and subsequent recovery as determined by dual-parameter (DNA, RNA) flow cytometry (FCM) measurements of testicular cells. Both testicular weights and caudal sperm reserves remained generally below controls after 44 wk recovery following exposure to the highest (1.0 mg/kg daily x 5) dosage. Chromatin structure alterations, defined as increased susceptibility to DNA denaturation in situ, and sperm head morphology were highly correlated (.87-.93, P less than .001) with dose and with each other. Data obtained from the sperm chromatin structure essay (SCSA) on fresh sperm was highly correlated with measurements of aliquots of the same sample collected over 44 wk, frozen, and then measured on the same day. Sperm head morphology and sperm chromatin structure remained abnormal at 44 wk for the 1.0 mg/kg TEM dosage, suggesting that the abnormalities, present long after the initial toxic response, may be a result of mutation. This study demonstrates that flow cytometry provides a unique, rapid, and efficient means to measure effects of reproductive toxins and potential mutagens.

Animals↗

Fine mapping of the chromatin structure of a cell cycle-regulated human H4 histone gene.

We have observed changes in the chromatin structure of a human histone gene promoter that may be functionally related to variations in transcription during the cell cycle. A detailed analysis of the chromatin structure of a cell cycle-dependent human H4 histone gene and its flanking sequences was performed using DNase I, S1 nuclease, and restriction endonucleases. This gene was previously shown to have a DNase I- and S1-sensitive site for which the boundaries varied with the cell cycle, and we have now precisely mapped these modifications. During S phase, the entire coding region of this gene and the 5'-flanking region up to approximately -600 base pairs are sensitive to both DNase I and S1, while during mitosis/G1, accessibility to these enzymes is greatly decreased in regions from -250 to -600 base pairs and downstream of +100 base pairs. DNase I- and S1-hypersensitive sites in the proximal promoter region (which contains two sites of protein-DNA interaction as well as sequence elements necessary for the correct initiation of transcription) are present throughout the cell cycle, as is an additional site sensitive to both DNase I and S1, located at -700 to -800 base pairs. Restriction enzyme analysis confirmed the general openness of the promoter region and relative insensitivity of the 3'-flanking region, while salt wash experiments indicated several discrete sites in the promoter that are candidates for regulatory interactions. The chromatin structure of the proximal promoter region of this H4 gene is different during early S phase when it is maximally transcribed, as indicated by the ability of a high salt wash to render this region inaccessible to the restriction enzyme MspI only at this time of the cell cycle.

Cell Cycle↗

Chromatin structure and transcriptional regulation of the beta-globin locus.

Chromatin structure plays a critical role in eukaryotic gene transcriptional regulation. The beta-globin locus provides an ideal system within which to study the interplay between chromatin structure and transcriptional regulation. The process of beta-globin locus activation is remarkably intricate and involves at least two distinct events: chromatin opening and gene activation. Great progress has been made in recent years in understanding how locus control regions confer high-level expression to linked genes. Current interest focuses on some special events, including formation of locus control region hypersensitivity sites, ATP-dependent chromatin remodeling, localized H3 hyperacetylation, and intergenic transcription, which link chromatin and beta-globin locus regulation. These events, and their possible molecular bases, are summarized together with speculations concerning their connections.

Acetylation↗

Assembly of oligonucleosomes into a limit series of multimeric higher-order chromatin structures.

Chicken erythrocyte chromatin, obtained after fragmentation with micrococcal nuclease, appears to remain folded in a stable distribution of supranucleosomal structures in buffers containing 80 mM NaCl. These supranucleosomal particles are composed of on average 25 nucleosomes. However, the integrity of the linker DNA within these particles is not required. The supranucleosomal particles have been interpreted by others as superbeads cut out of a preexisting granular nominal 30-nm chromatin fibre. We show that the same distribution of supranucleosomal structures (even those containing internal DNA scissions) can be reconstituted from unfolded nuclear chromatin extracts as present in 10 mM or 600 mM NaCl. Moreover, fractions of oligonucleosomes with mean lengths between 6 and 15 nucleosomes reassemble or aggregate into a limit series of multimeric species. The existence of an assembly barrier could be inferred as we were unable to observe a stable and soluble assembly product containing more than about 25 nucleosomes. We propose an alternative explanation for the generation and observation of a constant distribution of supranucleosomal structures in nuclear extracts, based on the assembly or aggregation property of oligonucleosomes and on the existence of an assembly barrier.

Animals↗

Perturbations of chromatin structure in human genetic disease: recent advances.

Gene expression studies in mammals and simpler eukaryotes have highlighted the central role that chromatin structure and modifications play in both the activation and repression of transcription. Aberrant chromatin structure can cause human genetic disease. Here we discuss recent progress in understanding the molecular mechanisms that underlie three human genetic diseases linked to perturbations of chromatin structure: ICF syndrome, facioscapulohumeral muscular dystrophy and a case of alpha-thalassaemia.

Chromatin↗

A new glucose-repressible gene identified from the analysis of chromatin structure in deletion mutants of yeast SUC2 locus.

We have previously shown that some changes occur in the chromatin structure of the 3' flank of the yeast SUC2 gene in going from a repressed to an active state. In an attempt to find out the causes of these changes, we have carried out experiments in which mutant copies of SUC2 locus lacking either 5' or 3' flanks have been analysed for their transcriptional activity and chromatin structure. These experiments allowed us to discard any relationship between SUC2 transcription and chromatin changes within its 3'flank. Sequencing of this flank and mRNA analysis, however, resulted in the location of a putative peroxisomal 3-oxoacyl-CoA thiolase gene (POT1), which is repressible by glucose. The disruption of the gene produced a yeast strain unable to use oleic acid as a carbon source. This is the first time that chromatin structure analysis has permitted the identification of a new gene.

Acetyl-CoA C-Acyltransferase↗

Chromatin structure at the replication origins and transcription-initiation regions of the ribosomal RNA genes of Tetrahymena.

The chromatin structure of regulatory regions of the extrachromosomal rRNA genes of Tetrahymena thermophila was probed by nuclease treatment of isolated nuclei. The chromatin near the origins of replication contains hypersensitive sites for micrococcal nuclease, DNAase I, and DNAase II. These sites persist in starved cells, consistent with the origins' being maintained in an altered chromatin structure independent of DNA replication. The region between the two origins of replication is organized into a phased array of seven nucleosomes, the fourth of which is centered at the axis of symmetry of the palindromic rDNA. The entire transcribed region and 150 bp upstream from the initiation site are generally accessible to nucleases; any histone proteins associated with these regions are clearly not in a highly organized nucleosomal array as seen in the central region. Comparison of the chromatin structures of the central spacer of T. thermophila and T. pyriformis rDNA reveals that deletion or insertion of DNA has occurred in increments of 200 bp. This is taken to imply that there are constraints on the evolution of spacer DNA sequences at the level of the nucleosome.

Animals↗