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PubMed1978

Fine-structural changes in the nucleus of primordial oocytes in immature hamsters.

This study reports observations on fine-structural changes in the nucleus of the oocyte in hamsters during the establishment of the primordial (unilaminar) follicle at 7 to 12 days after birth. Following pachytene, the nuclei at early diplotene contain simple chromosomal cores surrounding by a sheath of fibrillo-granular material symmetrically disposed in the form of lateral projections and loops. From 9 days onwards increasing numbers of the oocytes show nuclei lacking such chromosomal threads: instead, they contain randomly disposed, condensed fibrillar clumps with associated dense knots of material, and prominent aggregations of 25--30-nm granules. This second nuclear form is assumed by all oocytes examined at 11 and 12 days and appears to be the definitive diplotene phase. These changes in the appearance of the nuclear chromatin are discussed in the light of those found in oocytes of other species, and it is concluded that the hamster diplotene phase consists of a transitory 'compace' or uniform lampbrush stage, followed by a definitive dictyate condition like that in the rat, but with markedly differential condensation or extreme diffusion of lateral loops. This conclusion is examined in relation to findings which report a marked increase in the sensitivity of hamster oocytes to X-radiation at the time that the observed changes in nuclear configuration are taking place. The combined observations support the hypothesis that the dictyate stage in rodent oocytes represents a modified diplotene phase in which the high degree of spatial diffusion of components of chromosomes of the lampbrush type results in a reduced capacity for repair following exposure to ionizing radiations.

Animals↗
PubMed2006

The regulation of HIV-1 transcription: molecular targets for chemotherapeutic intervention.

The regulation of transcription of the human immunodeficiency virus (HIV) is a complex event that requires the cooperative action of both viral and cellular components. In latently infected resting CD4(+) T cells HIV-1 transcription seems to be repressed by deacetylation events mediated by histone deacetylases (HDACs). Upon reactivation of HIV-1 from latency, HDACs are displaced in response to the recruitment of histone acetyltransferases (HATs) by NF-kappaB or the viral transcriptional activator Tat and result in multiple acetylation events. Following chromatin remodeling of the viral promoter region, transcription is initiated and leads to the formation of the TAR element. The complex of Tat with p-TEFb then binds the loop structures of TAR RNA thereby positioning CDK9 to phosphorylate the cellular RNA polymerase II. The Tat-TAR-dependent phosphorylation of RNA polymerase II plays an important role in transcriptional elongation as well as in other post-transcriptional events. As such, targeting of Tat protein (and/or cellular cofactors) provide an interesting perspective for therapeutic intervention in the HIV replicative cycle and may afford lifetime control of the HIV infection.

Animals↗
PubMed2004

The Epstein-Barr virus transactivator Zta binds to its own promoter and is required for full promoter activity during anti-Ig and TGF-beta1 mediated reactivation.

Transcription of the immediate early gene BZLF1 is mediated initially through the activation of cellular transcription factors. Reporter-based studies have provided evidence that following this initial activation, the BZLF1 gene product Zta may be involved in an autoactivation loop through binding to its promoter Zp. In contrast, other reports have shown that transfection of a Zta expression vector in latently infected cells does not activate endogenous Zp. Using chromatin immunoprecipitation (ChIP) assays, we show here that Zta binds to endogenous Zp following induction of the lytic cycle by anti-Ig and TGF-beta1 and that binding occurs early enough to play a role in the activation of Zp. We have also generated a dominant-negative Zta and shown that it inhibits activation of endogenous Zp. These data support a two-step model for Zp activation during reactivation involving initial activation by cellular factors followed by an autoactivation step.

Antibodies↗
PubMed1996

Visualizing the spatial relationships between defined DNA sequences and the axial region of extracted metaphase chromosomes.

Using fluorescence in situ hybridization to extracted metaphase chromosomes, we present visual evidence that specific human DNA sequences occupy distinctive positions with respect to the axial region of chromosomes and that the DNA is organized into loops emanating from this region. In a stretch of unique DNA on chromosome 11, large loops of DNA can be traced and one specific region associated with the axial region of the chromosome. Within rDNA, nontranscribed spacer sequences are more closely apposed to the chromosome axis than are rRNA genes. Heterochromatic and euchromatic DNAs appear to be organized into loops of similar size. We could not detect loops at centromeres; most alphoid DNA appears to remain close to the axial region.

Centromere↗
PubMed1996

Sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in human cells: the role of transcription units.

DNA sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in HeLa cells have been cloned and 106 representative clones sequenced; 10 clones containing random genomic fragments served as controls. As chromatin is prone to rearrangement, care was taken to isolate sequences using 'physiological' conditions that did not create additional attachments. Comparison (by Southern blotting) of the concentration of each cloned sequence in 'total' and 'attached' fractions of DNA showed that most clones did contain attached sequences, but even highly-attached sequences were not attached in all cells in the population. Results demonstrated that 28% of clones were derived from three specific parts of the mitochondrial genome and 22% from different parts of the alu repeat. In addition, 41% of clones contained unique nuclear sequences; these contained no more of the motifs found attached to nuclear scaffolds or matrices (ie SARs or MARs) than would be expected from their base composition. No other attachment motif(s) could be identified by sequence analysis. However, Northern blotting showed that all the mitochondrial clones and 76% of clones containing unique sequences were transcribed; the degree of attachment correlated with transcriptional activity. These results are consistent with transcription being responsible for ever-changing attachments in both nuclei and mitochondria.

Base Sequence↗
PubMed1980

The presence of RNA in a double helix inhibits its interaction with histone protein.

The binding of core histones (H2A, H2B, H3, H4) to a circular plasmid DNA and to a circular DNA-RNA hybrid molecule of similar size has been compared. Circular hybrid molecules were formed from single stranded fd DNA by synthesis of the complimentary strand with ribonucleotides using wheat germ RNA polymerase II. Upon reconstitution of plasmid DNA circles with histone, the sedimentation profiles of the DNA remained sharp by increased several fold in rate. Material from the peak fractions of these sedimentations appeared to be condensed circular loops of nucleosomes when examined by electron microscopy (EM), and the mass ratio of DNA to histone (at the histone concentrations which produced the fastest sedimentations) was typical of native chromatin. In contrast, the sedimentation behavior of DNA-RNA hybrid circles after addition of histone remained unchanged except for a minor fraction which exhibited a broad and faster sedimentation rate. Examination by EM revealed that most of the molecules appeared identical to protein free hybrid circles while the minor, faster sedimenting fraction appeared to be two or more circles bound together by protein aggregates. Finally, a linear molecule consisting of about 3000 base pairs of duplex DNA covalently joined on both ends to 1500 base pairs of RNA-DNA hybrid helix was constructed. Reconstitution of this molecule with core histone showed nucleosome formation only on the central DNA duplex region. Isopycnic banding of fixed hybrid-histone mixtures showed that little or no histone had bound to the bulk of the full hybrid molecules. We suggest that the presence of RNA in a nucleic acid duplex inhibits the condensation of the duplex into a nucleosomal structure by histone.

Chromosome Banding↗
PubMedDate not supplied

Exfoliative cytology of lymphoepitheliomalike carcinoma of the uterine cervix. A report of two cases.

BACKGROUND: Lymphoepitheliomalike carcinomas (LECs) are morphologically similar to undifferentiated nasopharyngeal carcinoma but occur at sites other than the nasopharynx. They rarely occur in the uterine cervix. Sixty-five cases of LEC of the cervix have been published to date, and the pitfalls of histopathologic interpretation have been discussed. This undifferentiated carcinoma with a prominent lymphocytic infiltrate represents a challenge for the pathologist examining a scant cervical biopsy or Pap smear. Distinguishing LEC as a separate entity is important. Despite the fact that the epithelial component is poorly differentiated, this neoplasm is associated with a lower frequency of lymph node metastases, is potentially radiosensitive and has a better prognosis. Although mentioned in passing in several papers, the exfoliative cytology of this cervical neoplasm has not been adequately discussed. We report the cytologic features of LEC in cervical smears obtained from two patients. CASES: The first patient presented with menometrorrhagia and postcoital bleeding. The cervical smear taken at the time of presentation was reported as unsatisfactory for evaluation. ASCUS was diagnosed on a vaginal smear obtained one year earlier. The second patient presented with a complaint of postcoital bleeding. A cervical smear and the cervical biopsy taken at the time of presentation were reported as ASCUS and high grade dysplasia versus carcinoma, respectively. A retrospective review of the cervical smears revealed rare malignant cells occurring singly or in small groups. The tumor cells had a high nuclear/cytoplasmic ratio, irregular nuclear membrane and hyperchromatic nuclei with coarse chromatin and were obscured by heavy inflammation and blood. The background resembled that of a menstrual smear. CONCLUSION: The diagnosis of LEC of the cervix is often made on a loop electrical excision procedure or on a hysterectomy specimen. The presence of heavy inflammation and blood, which can obscure the malignant nature of the cells, presents the cytopathologist with a challenging diagnosis of LEC in cervical smears. In view of the prognostic implications, it is desirable for the pathologist to classify LEC as a distinct entity.

Adult↗
PubMed1997

Relative distribution of rDNA and proteins of the RNA polymerase I transcription machinery at chromosomal NORs.

Using confocal and immunofluorescence microscopy the relative distribution of the ribosomal chromatin and some proteins of the RNA polymerase I transcription machinery such as upstream binding factor (UBF), RNA polymerase I and DNA topoisomerase I was analyzed on chromosomal nucleolus organizer regions (NORs) of PtK1 cells. Staining with various DNA fluorochromes revealed that the ribosomal chromatin may be found at the axial region of the NOR and also at lateral expansions around the axis that can also be detected by in situ hybridization. It was observed that the transcription machinery shows a crescent-shaped distribution around the axial ribosomal chromatin at the NOR of metaphase and anaphase chromatids. An ultrastructural analysis of serially sectioned NORs supports this crescent-shape organization. Taking into account previous and present results and the loop/scaffold model of chromosome structure, we propose a model of NOR organization. The model proposes that ribosomal genes that were inactive in the preceding interphase would be present as condensed short Q-loops occupying the axial region of the NOR. Ribosomal genes previously active during interphase would be undercondensed as large R-loops associated with the transcription machinery, which is distributed in a crescent-shaped fashion around the previously active ribosomal DNA.

Anaphase↗
PubMed1996

Autoregulatory loop in the regulation of the mammalian ftz-f1 gene.

The mammalian ftz-f1 (mftz-f1) gene encoding Ad4BP/SF-1 has been demonstrated to be essential for the development of adrenal and gonadal glands. In a previous study, we identified an E box as the transcriptional element in the 5'-upstream region of the rat mftz-f1 gene. In the present study, we found a steroidogenic cell-specific transcriptional element in the first intron of the gene. Gel mobility shift and DNase I footprint analyses clearly revealed that Ad4BP itself binds to the element (Ad4 site). This finding was further supported by the positive effect of an Ad4BP expression vector on the transcription and by the significant decrease in the transcription caused by nucleotide substitutions within the Ad4 site. Similar loss was also caused by substitutions in the E box, indicating that the two elements are essential for the full transcriptional activity of the gene. DNase I hypersensitivity assays revealed that the chromatin structure around the Ad4 site and the E box was "open up" in the adrenal glands and Y-1 cells, whereas "closed down" in the liver. These observations indicated that the mftz-f1 gene is controlled by the autoregulatory loop in the steroidogenic tissues. The autoregulatory mechanism seems to be necessary to keep the mftz-f1 gene activated and thus maintain the tissues differentiated.

Animals↗
PubMed1975

Release of discrete subunits after nuclease and trypsin digestion of chromatin.

Digestion of chromatin with DNase (nucleate 3'-oligonucleotidohydrolase, EC 3.1.4.7) releases 11-12S nucleoprotein particles. After extensive nuclease digestion, the DNA in these particles consists of a collection of eight discrete DNA fragments. When these nuclease-particles are treated with trypsin (EC 3.4.21.4), only 20 to 30 amino-acid residues are cleaved from histone N-terminals, the histone C-terminal segments being resistant. The resulting 5S nucleoprotein particles have now been shown on acrylamide gels to consist of a series of eight discrete DNA-containing bands. Four of these bands contain C-terminal cleavage fragments from four histones (III, IV, IIb2, and IIb1) tightly bound to them; a fifth contains fragments from only histones III and IV. The remaining three bands contain only DNA. Since these protein-free DNA bands were resistant to nuclease prior to trypsin treatment, they were presumably associated with histone N-terminal segments in the native structure. Trypsin, therefore, appears to split nuclease-particles, releasing two subfractions of DNA--one associated with protein, the other not. The data is compatible with a model in which the majority of DNA in the eukaryotic nucleus is folded into hairpin loops of double-stranded helix, each created by the concerted cross-linking action of 6 to 10 histones which interact to form a trypsin-resistant complex composed, for the most part, of all four major histones. These loops may further fold upon themselves to form the "nu" bodies that have been visualized by electron microscopy.

Amino Acids↗
PubMed2006

Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis.

Fertilization in flowering plants initiates the development of the embryo and endosperm, which nurtures the embryo. A few genes subjected to imprinting are expressed in endosperm from their maternal allele, while their paternal allele remains silenced. Imprinting of the FWA gene involves DNA methylation. Mechanisms controlling imprinting of the Polycomb group (Pc-G) gene MEDEA (MEA) are not yet fully understood. Here we report that MEA imprinting is regulated by histone methylation. This epigenetic chromatin modification is mediated by several Pc-G activities during the entire plant life cycle. We show that Pc-G complexes maintain MEA transcription silenced throughout vegetative life and male gametogenesis. In endosperm, the maternal allele of MEA encodes an essential component of a Pc-G complex, which maintains silencing of the paternal MEA allele. Hence, we conclude that a feedback loop controls MEA imprinting. This feedback loop ensures a complete maternal control of MEA expression from both parental alleles and might have provided a template for evolution of imprinting in plants.

Arabidopsis↗
PubMed2006

Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4.

The innate immune system is absolutely required for host defence, but, uncontrolled, it leads to inflammatory disease. This control is mediated, in part, by cytokines that are secreted by macrophages. Immune regulation is extraordinarily complex, and can be best investigated with systems approaches (that is, using computational tools to predict regulatory networks arising from global, high-throughput data sets). Here we use cluster analysis of a comprehensive set of transcriptomic data derived from Toll-like receptor (TLR)-activated macrophages to identify a prominent group of genes that appear to be regulated by activating transcription factor 3 (ATF3), a member of the CREB/ATF family of transcription factors. Network analysis predicted that ATF3 is part of a transcriptional complex that also contains members of the nuclear factor (NF)-kappaB family of transcription factors. Promoter analysis of the putative ATF3-regulated gene cluster demonstrated an over-representation of closely apposed ATF3 and NF-kappaB binding sites, which was verified by chromatin immunoprecipitation and hybridization to a DNA microarray. This cluster included important cytokines such as interleukin (IL)-6 and IL-12b. ATF3 and Rel (a component of NF-kappaB) were shown to bind to the regulatory regions of these genes upon macrophage activation. A kinetic model of Il6 and Il12b messenger RNA expression as a function of ATF3 and NF-kappaB promoter binding predicted that ATF3 is a negative regulator of Il6 and Il12b transcription, and this hypothesis was validated using Atf3-null mice. ATF3 seems to inhibit Il6 and Il12b transcription by altering chromatin structure, thereby restricting access to transcription factors. Because ATF3 is itself induced by lipopolysaccharide, it seems to regulate TLR-stimulated inflammatory responses as part of a negative-feedback loop.

Activating Transcription Factor 3↗
PubMed1999

p53-induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting.

DNA binding activity of p53 is crucial for its tumor suppressor function. Our recent studies have shown that four molecules of the DNA binding domain of human p53 (p53DBD) bind the response elements with high cooperativity and bend the DNA. By using A-tract phasing experiments, we find significant differences between the bending and twisting of DNA by p53DBD and by full-length human wild-type (wt) p53. Our data show that four subunits of p53DBD bend the DNA by 32-36 degrees, whereas wt p53 bends it by 51-57 degrees. The directionality of bending is consistent with major groove bends at the two pentamer junctions in the consensus DNA response element. More sophisticated phasing analyses also demonstrate that p53DBD and wt p53 overtwist the DNA response element by approximately 35 degrees and approximately 70 degrees, respectively. These results are in accord with molecular modeling studies of the tetrameric complex. Within the constraints imposed by the protein subunits, the DNA can assume a range of conformations resulting from correlated changes in bend and twist angles such that the p53-DNA tetrameric complex is stabilized by DNA overtwisting and bending toward the major groove at the CATG tetramers. This bending is consistent with the inherent sequence-dependent anisotropy of the duplex. Overall, the four p53 moieties are placed laterally in a staggered array on the external side of the DNA loop and have numerous interprotein interactions that increase the stability and cooperativity of binding. The novel architecture of the p53 tetrameric complex has important functional implications including possible p53 interactions with chromatin.

Base Sequence↗
PubMed1993

Mechanism of dioxin action: receptor-enhancer interactions in intact cells.

We have used a ligation-mediated polymerase chain reaction technique to analyze protein-DNA interactions at a dioxin-responsive enhancer upstream of the CYP1A1 gene in intact mouse hepatoma cells. In its inactive state, the enhancer binds few, if any, proteins within the major DNA groove in vivo. Thus, the inactive enhancer is relatively inaccessible to DNA-binding proteins. Exposure of cells to 2,3,7,8-tetrachlorodibenzo-p-dioxin leads to the binding of the liganded Ah receptor at six sites within the major DNA groove of the enhancer. The receptor-enhancer interactions occur rapidly and do not require ongoing transcription, consistent with their role in regulating CYP1A1 gene expression. The liganded receptor, which is a heteromer composed of at least two basic helix-loop-helix proteins, is probably the only DNA-binding transcription factor necessary to activate the enhancer in vivo. The small size and irregular distribution of receptor binding sites suggest that chromatin structure imposes substantial steric constraints upon the function of the receptor-enhancer system in intact cells.

Animals↗
PubMed2004

Cooperative interaction between the basic helix-loop-helix transcription factor dHAND and myocyte enhancer factor 2C regulates myocardial gene expression.

Cardiac-restricted transcription factors dHAND and myocyte enhancer factor 2C are expressed in the developing heart and activate several cardiac promoters. However, their regulatory mechanisms are still to be understood. To elucidate their exact regulatory functions, we have developed an RNA interference strategy to specifically inhibit dHAND and myocyte enhancer factor 2C protein production in H9c2 cells, which are derived from rat embryonic heart. Expression of endogenous cardiac genes atrial natriuretic peptide and alpha-myosin heavy chain was down-regulated in H9c2 cells lacking both dHAND and myocyte enhancer factor 2C, indicating that these factors are required for the maintenance of the cardiac genetic program. Consistent with these, expression of atrial natriuretic peptide and alpha-myosin heavy chain was up-regulated in H9c2 cells, which overexpressed dHAND and myocyte enhancer factor 2C. In addition, dHAND and myocyte enhancer factor 2C interact to synergistically activate atrial natriuretic peptide and alpha-myosin heavy chain transcription. Furthermore, chromatin immunoprecipitation analysis in H9c2 cells treated with phenylephrine showed that dHAND and myocyte enhancer factor 2C protein complex bind to the A/T sequence on atrial natriuretic peptide promoter. Taken together, these results not only suggest that the complex cis-trans interaction of dHAND, myocyte enhancer factor 2C, and the target gene may fine-tune gene expression in cardiac myocytes but also provide a molecular paradigm to elucidate the mechanisms of action of dHAND and myocyte enhancer factor 2C in the developing heart.

Animals↗
PubMed2004

The SWI/SNF chromatin remodeling protein Brg1 is required for vertebrate neurogenesis and mediates transactivation of Ngn and NeuroD.

Chromatin remodeling complexes play crucial roles in transcription and are implicated in processes including cell proliferation, differentiation and embryonic patterning. Brg1 is the catalytic subunit of the SWI/SNF chromatin remodeling complex and shows neural-enriched expression. Although early lethality of Brg1-null mice reflects its importance in embryogenesis, this phenotype precluded further study of specific Brg1-dependent developmental processes. Here, we have identified a requirement of Brg1 for both Xenopus primary neurogenesis and neuronal differentiation of mammalian P19 embryonic carcinoma cells. In Xenopus, loss of Brg1 function did not affect neural induction or neural cell fate determination. However, the Sox2-positive, proliferating neural progenitor cell population was expanded, and expression of a terminally differentiated neuronal marker, N-tubulin, was diminished upon loss of Brg1 activity, suggesting that Brg1 is required for neuronal differentiation. The ability of the bHLH transcription factors Ngnr1 and NeuroD to drive neuronal differentiation was also abolished by loss of Brg1 function, indicating that Brg1 is essential for the proneural activities of Ngnr1 and NeuroD. Consistent with this, dominant-negative interference with Brg1 function in P19 cells suppressed neuronal differentiation promoted by NeuroD2, showing the requirement of Brg1 for neuronal differentiation is conserved in mammalian cells. Finally, we discovered that Brg1 physically associates with both Ngnr1 and NeuroD and that interference with Brg1 function blocks Neurogenin3- and NeuroD2-mediated reporter gene transactivation. Together, our results demonstrate that Brg1 (and by inference the SWI/SNF complex) is required for neuronal differentiation by mediating the transcriptional activities of proneural bHLH proteins.

Animals↗
PubMed1986

Evidence for a particular mode of transcription in globular loops of lampbrush chromosomes of the newt Pleurodeles waltlii.

In amphibian lampbrush chromosomes, many loops have a specific morphology; this is the case for globular loops in the newt Pleurodeles. We have previously shown that the specific morphology of these loops is linked to an extreme compactness of the transcription products which make up their matrix. We investigated RNA synthesis in this type of loop by carrying out autoradiographic and transcription inhibition studies. We also analysed the organization of transcriptional complexes in these loops in the electron microscope using spread preparations. These studies revealed the presence of several transcription units in the same loop and asynchronous variations in RNA synthesis in these transcription units. We propose and discuss several hypotheses in order to explain this asynchronous RNA synthesis. We also discuss these results in the context of loop morphology and transcription mode.

Amanitins↗
PubMed1958

An electron microscope study of lampbrush chromosomes.

Lampbrush chromosomes were isolated from germinal vesicles of oocytes from Necturus maculatus, Triturus viridescens, Pseudotriton montanus and Rana pipiens. After treatment of isolated nuclei with 10 per cent sucrose, chromosomes free of nuclear sap are obtained for examination in either the light microscope or in the electron microscope. For electron microscopy the chromosomes were prepared either by Anderson's critical-point procedure or were embedded in methacrylate and sectioned. The evidence presented in favor of the view that the loops, axis, and the chromomeres of lampbrush chromosomes are formed by two chromonemata is based on the following observations: 1. Treatment of isolated chromosomes with 0.002 M KCN loosens the structure of the loops, and a more or less coiled organization is then observed in most of them with the light microscope. At the electron microscope level, each loop consists of a bundle of microfibrils. The latter are 500 A in diameter, and their complex arrangement within the loops is best studied in stereoscopic preparations. 2. Treatment of chromosomes with 0.002 M KCN also unravels the "chromomeric" regions of the axis. A fibrillar organization then becomes visible in the light microscope. In the electron microscope, wide strands are seen within some chromomeres; their diameter corresponds closely to that of the chromonemata forming the loops associated with the same chromomeres. In thin transverse sections of isolated chromosomes, no special structure is visible in the axial region except random profiles of fibrils similar to those seen in the loops of the same preparations. 3. Two strands sometimes connect adjacent chromomeres. Where gaps exist along the axis, after stretching of the chromosomes, a loop occasionally straddles the break and returns to a chromomere on each side.

Animals↗