Chromatin alteration, transcription and replication: What's the opening line to the story?

Polymerase accessibility to chromatin is a limiting step in both RNA and DNA synthesis. Unwinding DNA and nucleosomes during polymerase complex binding and processing likely requires priming by chromatin restructuring. The initiating step in these processes remains an area of speculation. This review focuses on the physical handling of chromatin during transcription and replication, the fate of nucleosomes assembled on DNA during unwinding and processing the chromatin substrate, and how these alterations in chromatin structure may affect gene expression. Transcription or replication may alter chromatin structure during synthesis, enabling regulatory factor binding and, potentially, future rounds of transcription. As chromatin remodeling and transcription factor binding augment transcription and replication, and are themselves increased by these processes, a temporal model of structural alterations and gene activation is built that may be more circular than linear.

S-Phase progression mediates activation of a silenced gene in synthetic nuclei

Aberrant expression of developmentally silenced genes, characteristic of tumor cells and regenerating tissue, is highly correlated with increased cell proliferation. By modeling this process in vitro in synthetic nuclei, we find that DNA replication leads to deregulation of established developmental expression patterns. Chromatin assembly in the presence of adult mouse liver nuclear extract mediates developmental stage-specific silencing of the tumor marker gene alpha-fetoprotein (AFP). Replication of silenced AFP chromatin in synthetic nuclei depletes sequence-specific transcription repressors, thereby disrupting developmentally regulated repression. Hepatoma-derived factors can target partial derepression of AFP, but full transcription activation requires DNA replication. Thus, unscheduled entry into S phase directly mediates activation of a developmentally silenced gene by (i) depleting developmental stage-specific transcription repressors and (ii) facilitating binding of transactivators.

The seed-specific transactivator, ABI3, induces oleosin gene expression

A microspore-derived cell suspension culture of Brassica napus was used as a host for expression studies involving seed oleosin genes. The suspension culture was previously shown to display biochemistry and gene expression typical of zygotic embryos. Using a biolistic, transient expression approach we demonstrate that the seed-specific activator ABI3 promotes oleosin gene expression in these cultures. Co-bombardment of an oleosin promoter-GUS fusion and a full-length ABI3 gene from Arabidopsis resulted in four to six-fold enhancement of GUS expression. Deletion analysis was performed to identify which oleosin upstream sequences were required for ABI3 regulation. These studies found that a truncated oleosin promoter containing 160 bp of 5' regulatory sequence was sufficient to confer ABI3 responsiveness. Mutation of a canonical abscisic acid response element within this 160 bp region had a dramatic effect on basal expression, reducing levels to 25% of control. However, this mutation had no significant effect on ABI3 transactivation, indicating that the reduction in basal oleosin expression was distinct from the ABI3 response. These results also suggest that ABI3-mediated transactivation occurs through either a less-conserved ABRE element or other abscisic acid-independent sequences within the minimal promoter. Together, these data provide the first direct evidence that ABI3 mediates oleosin transactivation.

Hepatocyte nuclear factor 3 relieves chromatin-mediated repression of the alpha-fetoprotein gene

The alpha-fetoprotein gene (AFP) is tightly regulated at the tissue-specific level, with expression confined to endoderm-derived cells. We have reconstituted AFP transcription on chromatin-assembled DNA templates in vitro. Our studies show that chromatin assembly is essential for hepatic-specific expression of the AFP gene. While nucleosome-free AFP DNA is robustly transcribed in vitro by both cervical (HeLa) and hepatocellular (HepG2) carcinoma extracts, the general transcription factors and transactivators present in HeLa extract cannot relieve chromatin-mediated repression of AFP. In contrast, preincubation with either HepG2 extract or HeLa extract supplemented with recombinant hepatocyte nuclear factor 3 alpha (HNF3alpha), a hepatic-enriched factor expressed very early during liver development, is sufficient to confer transcriptional activation on a chromatin-repressed AFP template. Transient transfection studies illustrate that HNF3alpha can activate AFP expression in a non-liver cellular environment, confirming a pivotal role for HNF3alpha in establishing hepatic-specific gene expression. Restriction enzyme accessibility assays reveal that HNF3alpha promotes the assembly of an open chromatin structure at the AFP promoter. Combined, these functional and structural data suggest that chromatin assembly establishes a barrier to block inappropriate expression of AFP in non-hepatic tissues and that tissue-specific factors, such as HNF3alpha, are required to alleviate the chromatin-mediated repression.

Functional analysis of chromatin assembled in synthetic nuclei

Numerous regulatory mechanisms contribute to the control of eukaryotic transcription. These controls are manifested through higher-order protein-DNA structure within the nucleus. In vitro assays have proven extremely useful in deciphering the potential regulatory roles of chromatin and nuclear structure in transcription. Embryonic egg extracts of Xenopus with their vast maternal stores and rapid cell-cycle oscillations can be exploited to recapitulate multiple layers of nuclear regulation. Incubation of cloned DNA templates in Xenopus egg extracts promotes a self-ordered assembly of physiologically spaced nucleosomes and synthetic nuclei structure formation. Interaction of membrane vesicles with chromatin leads to formation of a bilayer nuclear envelope encapsulating the DNA. These synthetic nuclei are functional organelles capable of active protein transport and a single round of semiconservative DNA synthesis. This system can be used to directly test the mechanisms by which trans-acting factors promote transcription on nucleosomal DNA, either during chromatin assembly or postassembly or in conjunction with remodeling machinery and/or DNA replication. The functional consequences of trans-acting factor interaction within synthetic nuclei are determined by a coupled in vitro transcription analysis. Immobilizing biotin end-labeled DNA templates on paramagnetic streptavidin beads greatly improves the flexibility of the system. The ease of chromatin-assembled template recovery allows the introduction of wash steps, buffer changes, and specific reaction optimization. These methods for reconstituting gene regulatory mechanisms in vitro are an attempt to strike a balance between biochemical accessibility and physiological relevance.

p53-mediated repression of alpha-fetoprotein gene expression by specific DNA binding

Aberrant expression of the alpha-fetoprotein (AFP) gene is characteristic of a majority of hepatocellular carcinoma cases and serves as a diagnostic tumor-specific marker. By dissecting regulatory mechanisms through electromobility gel shift, transient-transfection, Western blot, and in vitro transcription analyses, we find that AFP gene expression is controlled in part by mutually exclusive binding of two trans-acting factors, p53 and hepatic nuclear factor 3 (HNF-3). HNF-3 protein activates while p53 represses AFP transcription through sequence-specific binding within the previously identified AFP developmental repressor domain. A single mutation within the DNA binding domain of p53 protein or a mutation of the p53 DNA binding element within the AFP developmental repressor eliminates p53-repressive effects in both transient-transfection and cell-free expression systems. Coexpression of p300 histone acetyltransferase, which has been shown to acetylate p53 and increase specific DNA binding, amplifies the p53-mediated repression. Western blot analysis of proteins present in developmentally staged, liver nuclear extracts reveal a one-to-one correlation between activation of p53 protein and repression of AFP during hepatic development. Induction of p53 in response to actinomycin D or hypoxic stress decreases AFP expression. Studies in fibroblast cells lacking HNF-3 further support a model for p53-mediated repression that is both passive through displacement of a tissue-specific activating factor and active in the presence of tissue-specific corepressors. This mechanism for p53-mediated repression of AFP gene expression may be active during hepatic differentiation and lost in the process of tumorigenesis.

Predicting functional capacity during treadmill testing independent of exercise protocol

Clinically useful estimates of VO2max from treadmill tests (GXT) may be made using protocol-specific equations. In many cases, GXT may proceed more effectively if the clinician is free to adjust speed and grade independent of a specific protocol. We sought to determine whether VO2max could be predicted from the estimated steady-state VO2 of the terminal exercise stage. Seventy clinically stable individuals performed GXT with direct measurement of VO2. Exercise was incremented each minute to optimize clinical examination. Measured VO2max was compared to the estimated steady-state VO2 of the terminal stage based on ACSM equations. Equations for walking or running were used based on the patient's observed method of ambulation. The measured VO2max was always less than the ACSM estimate, with a regular relationship between measured and estimated VO2max. No handrail support: VO2max = 0.869.ACSM -0.07; R2 = 0.955, SEE = 4.8 ml.min-1.kg-1 (N = 30). With handrail support: VO2max = 0.694.ACSM + 3.33; R2 = 0.833, SEE = 4.4 ml.min-1.kg-1 (N = 40). The equations were cross-validated with 20 patients. The correlation between predicted and observed values was r = 0.98 and 0.97 without and with handrail support, respectively. The mean absolute prediction error (3.1 and 4.1 ml.min-1.kg-1) were similar to protocol-specific equations. We conclude that VO2max can be predicted independent of treadmill protocol with approximately the same error as protocol-specific equations.

Phosphorylation of the SHC proteins on tyrosine correlates with the transformation of fibroblasts and erythroblasts by the v-sea tyrosine kinase

The S13 avian erythroblastosis viral genome encodes an oncogenic tyrosine kinase, termed env-sea, that is capable of transforming fibroblasts and erythroblasts. Although the tyrosine kinase activity of the env-sea protein has been shown to be necessary for transformation, no substrates for this enzyme have been detected in vivo. Here we demonstrate that the recently described shc proteins are phosphorylated on tyrosine residues in both S13 transformed fibroblasts and erythroblasts. Furthermore, using an S13 temperature sensitive mutant, we show that the phosphorylation of the shc proteins occurs concomitantly with the activation of the tyrosine kinase activity of the env-sea protein. These observations make the phosphorylation of the shc proteins a good candidate for being involved in oncogenic signaling by the env-sea oncoprotein.

Altered glycosylation of the env-sea oncoprotein inhibits intracellular transport and transformation

The transforming gene product of the S13 avian erythroblastosis virus, env-sea, is a member of the growth factor receptor class of tyrosine kinases. The env-sea precursor protein gp155env-sea is proteolytically processed into the mature cleavage products gp85env and gp70env-sea, which are subsequently terminally glycosylated and transported to the cell surface. Previous studies have shown that the abnormal glycosylation of gp155env-sea induced by the carbohydrate processing inhibitor castanospermine blocks the proteolytic cleavage of gp155env-sea and impairs its transforming ability. We have shown recently that an uncleaved but fully glycosylated sea-encoded protein retains the ability to transform chicken embryo fibroblasts, indicating that proteolytic processing is not essential for transformation by the env-sea tyrosine kinase. To address the question of how castanospermine blocks transformation by env-sea, differential sucrose gradient centrifugation was performed on env-sea-transformed cells treated with the inhibitor. This report shows that no surface forms of env-sea could be detected in inhibitor-treated cells, suggesting that castanospermine acts by blocking the transport of sea-encoded proteins to the cell surface.

Post-translational modifications of the env-sea oncogene product: the role of proteolytic processing in transformation

The transforming gene product of the S13 avian erythroblastosis virus, env-sea, is a member of the growth factor receptor class of tyrosine kinases. The env-sea precursor protein gp155env-sea is proteolytically processed into the mature cleavage products gp85env-sea and gp70env-sea which are subsequently terminally glycosylated. Previous studies have shown that the abnormal glycosylation of gp155env-sea which takes place in the presence of the inhibitor castanospermine inhibits the proteolytic cleavage of gp155env-sea and blocks its transforming ability. To define a role for proteolytic processing of env-sea in transformation, we have introduced mutations at the protease recognition site which efficiently block cleavage without affecting the biosynthesis or transport of the resulting uncleaved protein. We show here that an uncleaved but fully glycosylated sea-encoded protein retains the ability to transform chicken embryo fibroblasts, indicating that proteolytic processing is not essential for transformation by the env-sea tyrosine kinase.

A myristylated form of the sea oncoprotein can transform chicken embryo fibroblasts

The transforming gene product of the S13 avian erythroblastosis virus, v-sea, is a member of the growth factor receptor class of tyrosine kinases. In the virus genome, the sea sequences are fused in frame to the virus env gene, thereby generating an abnormally large envelope protein because of the presence of a cytoplasmic tyrosine kinase domain. To determine what role these envelope sequences play in v-sea transformation, we generated a myristylated form of v-sea which contains no envelope sequences. In this report, we show that this myristylated sea-encoded protein retained the ability to transform chicken embryo fibroblasts, indicating that envelope sequences are not essential for transformation by the v-sea tyrosine kinase.

Possible pre-dissociation of diorganotin dihalide complexes: relationship between antitumour activity and structure

An examination of crystallographic data has indicated that the structure/activity relationship for diorganotin dihalide complexes is different from that of other metal dihalides, in that the Sn-N bond lengths appear to determine the antitumour activity.

Investigations into the antitumour activity of organotin compounds. I. Diorganotin dihalide and di-pseudohalide complexes

The antitumor activity of a series of diorganotin dihalide and di-pseudohalide complexes, R2SnX2, L2, where R = Methyl (Me), Ethyl (Et), n-Propyl (Pr), n-Butyl (Bu) or Phenyl (Ph); X = F, Cl, Br, I or NCS; and L = O- or N- donor organic ligand, which were modelled on the active platinum complexes, has been investigated. A number of these derivatives exhibit reproducible therapeutic activity in vivo towards P-388 lymphocytic leukaemia in mice, particularly the diethyltin dihalide and dipseudohalide complexes. The possible factors influencing activity are discussed, both in terms of the stereochemistry of the dialkyltin compounds and their structural similarity to the platinum antitumour drugs.