Lac operator analogues: bromodeoxyuridine substitution in the lac operator affects the rate of dissociation of the lac repressor

Molecular Mechanisms Regulating Muscle Plasticity in Fish

Growth rates in fish are largely dependent on genetic and environmental factors, of which the latter can be highly variable throughout development. For this reason, muscle growth in fish is particularly dynamic as muscle structure and function can be altered by environmental conditions, a concept referred to as muscle plasticity. Myogenic regulatory factors (MRFs) like Myogenin, MyoD, and Pax7 control the myogenic mechanisms regulating quiescent muscle cell maintenance, proliferation, and differentiation, critical processes central for muscle plasticity. This review focuses on recent advancements in molecular mechanisms involving microRNAs (miRNAs) and DNA methylation that regulate the expression and activity of MRFs in fish. Findings provide overwhelming support that these mechanisms are significant regulators of muscle plasticity, particularly in response to environmental factors like temperature and nutritional challenges. Genetic variation in DNA methylation and miRNA expression also correlate with variation in body weight and growth, suggesting that genetic markers related to these mechanisms may be useful for genomic selection strategies. Collectively, this knowledge improves the understanding of mechanisms regulating muscle plasticity and can contribute to the development of husbandry and breeding strategies that improve growth performance and the ability of the fish to respond to environmental challenges.

In silico studies with substituted adenines to achieve a remarkable stability of mispairs with thymine nucleobase

The modified adenine and thymine mispair achieves a remarkable stability, which can presumably help the DNA lesions to be less cytotoxic.

5-Bromodeoxyuridine Increases Transient Expression of Ectopic Genes in Human Cells

Ectopic genes transferred to cells are temporally expressed, although this phenomenon has not yet been well characterized. We found that 5-bromodeoxyuridine dramatically increased transient expression of ectopic genes in human cells. This effect was elicited by adding 5-bromodeoxyuridine prior to or after transfection. No promoter specificity was observed. Real time PCR analysis showed an approximately 2-fold increase in mRNA levels. Since 5-bromodeoxyuridine decondenses heterochromatin and changes the nuclear envelope, these changes might affect transcriptional and post-transcriptional events in the gene expression of plasmids.

5-Bromo-2'-deoxyuridine induces visible morphological alteration in the DNA puffs of the anterior salivary gland region of Bradysia hygida (Diptera, Sciaridae)

5-Bromo-2'-deoxyuridine (BrdUrd) has long been known to interfere with cell differentiation. We found that treatment of Bradysia hygida larvae with BrdUrd during DNA puff anlage formation in the polytene chromosomes of the salivary gland S1 region noticeably affects anlage morphology. However, it does not affect subsequent metamorphosis to the adult stage. The chromatin of the chromosomal sites that would normally form DNA puffs remains very compact and DNA puff expansion does not occur with administration of 4 to 8 mM BrdUrd. Injection of BrdUrd at different ages provoked a gradient of compaction of the DNA puff chromatin, leading to the formation of very small to almost normal puffs. By immunodetection, we show that the analogue is preferentially incorporated into the DNA puff anlages. When BrdUrd is injected in a mixture with thymidine, it is not incorporated into the DNA, and normal DNA puffs form. Therefore, incorporation of this analogue into the amplified DNA seems to be the cause of this extreme compaction. Autoradiographic experiments and silver grains counting showed that this treatment decreases the efficiency of RNA synthesis at DNA puff anlages.

An amino-terminal fragment of lac repressor binds specifically to lac operator

We have examined the effect of an aminoterminal peptide from the lac repressor (residues 1-59) on the methylation of purines in the lac operator with dimethyl sulfate. The peptide perturbs the methylation of the operator, and the peptide-induced pattern of inhibition and enhancement of methylation, across the operator, closely resembles the pattern induced by intact repressor. This demonstrates that this small amino-terminal peptide binds specifically to the lac operator and that the mechanism of recognition and binding is basically the same as that of intact repressor.

Spontaneous reactivation of a silent telomeric transgene in a human cell line

Subtelomeric reporter genes in human cells are silenced in a telomere length-dependent manner. Here we show that a subtelomeric reporter gene is expressed in only a subpopulation of cells within a clone and that this heterogeneity is generated by switching between expression states. We observed frequent reversion from the silenced state back to active expression. This process was more prominent for subtelomeric transgenes; however, we also observed cases of spontaneous reversion in control clones bearing the reporter at an internal site. We additionally show that treatment of these cells with 5-bromodeoxyuridine results in strong activation of the transgene. Although similar findings have been reported previously in mouse cells, this is, to our knowledge, the first direct observation of ongoing fluctuations in transcription in clonal populations of human cells. Our results suggest that this mechanism, as opposed to progressive silencing or a delayed fixing of expression states, accounts for the variegation in expression observed for subtelomeric transgenes in human cells. These data imply that telomere shortening during human aging could lead to stochastic activation of subtelomeric genes.

Bromodeoxyuridine induces integrin expression at transcriptional (alpha2 subunit) and post-transcriptional (beta1 subunit) levels, and alters the adhesive properties of two human lung tumour cell lines

Integrins are a family of transmembrane glycoproteins that participate in a wide range of cellular events including proliferation, apoptosis and differentiation. Little is known about the mechanisms that control integrin subunit expression in epithelial cells, especially during lung cell differentiation. We have examined the effect of the differentiation-modulating agent, 5-bromo-2'-deoxyuridine (BrdU), on integrin expression in 2 human lung carcinoma cell lines, DLKP and A549. Treatment of both DLKP and A549 with 10 microM BrdU for 7 days resulted in increased expression of alpha2 and beta1 integrin subunit protein expression. Northern blot and RT-PCR analyses revealed progressively increasing levels of the alpha2 mRNA transcripts following BrdU treatment up to 21 days in both cell lines. However, no increase in beta1 integrin mRNA levels was observed in either cell, suggesting post-transcriptional regulation by BrdU. Treatment of HL-60, a leukaemic cell line, with BrdU up to 21 days resulted in no change in alpha2 or beta1 integrin subunit levels at either protein or mRNA levels suggesting that the change seen in the lung cell lines may be epithelial cell lineage-specific. BrdU has also been found to alter the adhesive properties of A549 and DLKP cells. Treated cells were found to adhere significantly faster to collagen type IV and laminin compared to untreated cells. The results presented here suggest that DLKP (and A549) may be useful cellular models to investigate the role of the alpha2beta1 integrin in lung epithelial cell differentiation.

Bromodeoxyuridine increases keratin 19 protein expression at a posttranscriptional level in two human lung tumor cell lines

Keratins form the largest subfamily of intermediate filament proteins and show strict lineage- and differentiation-associated expression in epithelial cells. Little is known about the mechanisms that control keratin protein synthesis in these cells. We have examined the effect of the differentiation-modulating agent, 5'-bromo-2'-deoxyuridine (BrdU), on keratin 19 (K19) expression in two human lung carcinoma cell lines, DLKP and A549. Treatment of both cell lines with 10 microM BrdU for 7 d induced the expression of K19 protein in keratin-negative DLKP cells, and significantly increased K19 protein expression in A549 cells. K19 messenger ribonucleic acids (mRNAs) were detected by Northern blot and reverse transcriptase-polymerase chain reaction analyses in both cell lines, but no increase in K19 mRNA levels was detected in either cell line, even with treatment with BrdU for up to 21 d. This suggests that K19 protein synthesis is normally blocked at a posttranscriptional level in DLKP cells, and BrdU can somehow reverse this block, resulting in the induction of K19 protein synthesis. Treatment of HL60, a leukemic cell line, with BrdU, resulted in noninduction of K19 protein synthesis, and no K19 mRNA transcripts were detected before and after BrdU treatment, possibly suggesting that BrdU is acting in an epithelial-specific manner to reverse a block in K19 protein synthesis in DLKP keratin-negative lung cancer cells. Therefore, DLKP (and A549) may be useful cellular models to investigate if this represents a regulatory step in early lung development or a mechanism whereby tumor cells possess the ability to down-regulate the expression of a more-differentiated phenotype.

5-Bromodeoxyuridine suppresses position effect variegation of transgenes in HeLa cells

An ectopic gene integrated in the host genome is occasionally silenced due to a position effect of its adjacent chromatin structure. We found that 5-bromodeoxyuridine clearly activated such a transgene in HeLa cells. The transgene was also activated to various degrees by inhibitors of histone deacetylase, DNA topoisomerases, or DNA methyltransferase. The peptide antibiotic distamycin A potentiated markedly the effect of 5-bromodeoxyuridine. Transient expression of an artificial AT-hook protein termed MATH20 also potentiated its effect although significantly activated the transgene alone. Since distamycin A and MATH20 are able to displace histone H1 and other DNA-binding proteins bound to specific AT-rich sequences by a dominant, mutually exclusive fashion, these results suggest that 5-bromodeoxyuridine targets such an AT-rich sequence located adjacent to the silenced transgene, resulting in chromatin accessibility.

Bromodeoxyuridine induces keratin protein synthesis at a posttranscriptional level in human lung tumour cell lines

Keratin intermediate filaments are formed in epithelial cells in a cell- and tissue-specific manner, but much remains unknown regarding the mechanisms which control the synthesis of these proteins. We examined the effect of the differentiation modulation agent, bromodeoxyuridine (BrdU), on two human keratin-negative (by immunocytochemistry) lung cell lines, DLKP and H82, and showed immunohistochemically that treatment with 10 microM BrdU over 7 days induced K8 and K18 protein synthesis in both lines. Immunoprecipitation and Western blot analyses revealed low levels of K8 and K18 proteins in untreated cell homogenates. These levels increased following treatment with BrdU for 7 days. K8 and K18 mRNAs were detected by Northern blot and reverse transcriptase polymerase chain reaction analyses in both lines before BrdU treatment, but no increase in mRNA levels was observed in either cell line over 21 days of treatment. This suggests, firstly, that keratin synthesis is normally blocked at a posttranscriptional level in DLKP and H82 cells, and secondly, that BrdU can reverse this block. A549 is a human lung cell line which contains K8 and K18 proteins. Treatment with BrdU increased K8 and K18 protein levels in these cells. No corresponding increase in K8 mRNA levels occurred, while an apparent increase in K18 mRNA levels was detected. HL-60 is a leukaemic cell-line of haematopoietic rather than epithelial lineage which contains K8 and K18 mRNA transcripts prior to BrdU treatment, but does not contain keratin proteins. Again, K8 and K18 mRNA levels remained unchanged during BrdU treatment. However, neither K8 nor K18 proteins were detected following treatment, although BrdU is known to alter expression of other genes in HL-60 cells. BrdU thus appears to act at a posttranscriptional level and in an epithelial-specific manner to reverse a block in keratin synthesis in keratin-negative lung cancer cells and increase synthesis in keratin-positive lung cancer cells. This may represent a regulatory step in early lung development or a mechanism whereby tumour cells downregulate expression of a differentiated phenotype.

p53 mutations, methylation and genomic instability in the progression of chronic myeloid leukaemia

In chronic myeloid leukaemia (CML), as with other tumour types, mutations of the p53 gene are associated with disease progression. Changes in regional methylation of DNA with CML tumour development have also been demonstrated. Methylation is one mechanism by which gene expression is controlled and the CpG sites, which are the targets of DNA methylation, are also the sites of a number of the mutations found in the p53 gene. Cells harbouring mutant p53 have been shown to accumulate further genomic and genetic aberrations and methylation which alters the conformation of DNA is also believed to play a role in genomic stability. There appears to be an interplay between p53 deregulation and changing methylation patterns with the progression of CML. The cause and effect of changes in both of these critical gene regulating, DNA repair and genomic stability factors and their deviation during the progression of CML will be discussed.

Methylation sensitive protein binding to an intragenic active X-specific methylated region in the M. robustus Hprt gene

An intragenic region of the wallaroo (Macropus robustus) hypoxanthine phosphoribosyltransferase gene which contains three active X-specific methylated cytosines was examined for protein(s) binding. In vitro DNase I footprinting of unmethylated DNA identified three footprints, one of which (footprint I) contained two of the known differentially methylated sites (a HpaII and a HhaI site). Methylation of the footprint I HpaII site only, abolished the formation of several, specific DNA-protein complexes in mobility shift assays. UV cross-linking experiments indicated that polypeptides involved in the methylation sensitive interactions with footprint I had molecular weights ranging from 72 to 48 kDa. Analogous results were obtained with nuclear extracts from both eutherian and metatherian cells, indicating that these proteins are conserved. We suggest that the binding of these proteins to the inactive X may play some role in gene silencing, with the active gene being protected from this effect by methylation of the binding site.

Bromodeoxyuridine- and cyclic AMP-mediated regulation of tyrosinase in Syrian hamster melanoma cells

The thymidine analog 5-bromodeoxyuridine (BrdU) suppresses pigmentation and tyrosinase activity in Syrian hamster melanoma cells W1-1-1. Studies on the molecular mechanism of suppression of pigmentation indicated that BrdU treatment affects the level of tyrosinase gene transcripts. No detectable tyrosinase message was found by Northern blot analysis in cells cultured in the presence of BrdU at concentrations even as low as 0.2 microM. The level of tyrosinase mRNA was found to reflect the level of pigmentation and tyrosinase activity. Studies with dibutyryl cyclic AMP (cAMP) showed that it inhibited pigment synthesis in W1-1-1 cells. With increasing concentrations of cAMP ranging from 10 microM to 300 microM, pigmentation and tyrosinase activity decreased progressively. This inhibition was found to be associated with a corresponding decrease in the level of tyrosinase mRNA. W1-1-1 cells were found not to respond to melanocyte stimulating hormone (MSH). There was no change in pigmentation, tyrosinase activity, or tyrosinase mRNA level in W1-1-1 cells in the presence of MSH. Similarly, theophylline, a phosphodiesterase inhibitor, had no effect on pigmentation or tyrosinase activity in W1-1-1 cells.

Replication of latent Epstein-Barr virus genomes in normal and malignant lymphoid cells

DNA replication of 2 human lymphoid cell lines (U296 and Raji), latently infected with the Epstein-Barr virus, has been compared using a density transfer approach. Typical of non-malignant lymphoblastoid cells, U296 cells divided once in bromodeoxyuridine-supplemented medium to form hybrid but not heavy-density host DNA. Replication of the intracellular Epstein-Barr virus DNA was selectively inhibited in these cells with only 15% of the viral genomes duplicating once to form hybrid-density viral DNA. However, some heavy-density viral DNA was formed in the U296 cells and DNA synthesis can thus initiate again on newly duplicated viral genomes in cells that have traversed only a single S phase. These results contrast strongly with observations concerning the Burkitt-lymphoma-derived cell line. Lymphoma cells are not growth-inhibited and most of the latent Epstein-Barr virus genomes of the Raji line replicated once, and only once, in successive S phases. While the majority of the 50 Epstein-Barr virus genomes of both the Raji and U296 cell lines are maintained as extra-chromosomal DNA plasmids, the control of their duplication is distinctly different in the respective malignant and non-malignant host cells.

5-bromo-2'-deoxyuridine blocks myogenesis by extinguishing expression of MyoD1

The pyrimidine analog 5-bromodeoxyuridine (BUdR) competes with thymidine for incorporation into DNA. Substitution of BUdR for thymidine does not significantly affect cell viability but does block cell differentiation in many different lineages. BUdR substitution in a mouse myoblast line blocked myogenic differentiation and extinguished the expression of the myogenic determination gene MyoD1. Forced expression of MyoD1 from a transfected expression vector in a BUdR-substituted myoblast overcame the block to differentiation imposed by BUdR. Activation of BUdR-substituted muscle structural genes and apparently normal differentiation were observed in transfected myoblasts. This shows that BUdR blocks myogenesis at the level of a myogenic regulatory gene, possibly MyoD1, not by directly inhibiting the activation of muscle structural genes. It is consistent with the idea that BUdR selectively blocks a class of regulatory genes, each member of which is important for the development of a different cell lineage.

Replication of latent Epstein-Barr virus genomes in Raji cells

The replication of the 50 to 60 latent, predominantly extrachromosomal, Epstein-Barr virus genomes maintained by the Burkitt-lymphoma-derived Raji cell line was investigated by using a Meselson-Stahl density transfer approach. Samples of DNA isolated from cells cultivated for different periods in bromodeoxyuridine-supplemented medium were fractionated according to density, and the distribution of viral and cellular DNAs among the heavy-, hybrid-, and light-density species was quantitated. The results indicate that the majority of latent Epstein-Barr virus DNA plasmids each replicate once during the cell cycle.

Variations in duplex DNA conformation detected by the binding of monoclonal autoimmune antibodies

Four monoclonal antibodies (Jel 229, 239, 241, 242) which bound to duplex DNA were prepared from two autoimmune female NZB/NZW mice. Their binding to various nucleic acids was investigated by a competitive solid phase radioimmune assay which allows the estimation of relative binding constants. None of the antibodies showed any consistent variation of binding constant with base composition and thus they must recognize features of the DNA backbone. Jel 241 binds across the major groove but the interaction with poly(pyrimidine) X poly(purine) DNAs was barely detectable. This antibody appears to recognize the "alternating-B" conformation which is promoted by methylation of pyrimidines in alternating sequences. The other three antibodies bind in the minor groove. In particular, for Jel 229 the preferred antigen was poly(dG) X poly(dC) with only weak binding to poly(dA) X poly(dT). This suggests a requirement for a wide minor groove. Thus autoimmune antibodies provide examples of "analogue" recognition and can be used to detect structural variations in the grooves of duplex DNA.

A monoclonal antibody specific for the duplex DNA poly[d(TC)].poly[d(GA)]

Although most duplex DNAs are not immunogenic some synthetic DNAs such as poly[d(Tm5C)].poly[d(GA)] are weakly immunogenic allowing the production of monoclonal antibodies. The specificity of one of these antibodies, Jel 172, was investigated in detail by a competitive solid-phase radioimmune assay. Jel 172 bound well to poly[d(TC)].poly[d(GA)] but not to other duplex DNAs such as poly[d(TTC)].poly[d(GAA)] and poly[d(TCC)].poly[d(GGA)]. The binding to poly[d(Br5UC)].poly[d(GA)] was enhanced while that to poly[d(TC)].poly[d(IA)] was decreased compared to poly[d(TC)].poly[D(GA)]. Thus, not only is the antibody very specific for a sequence of duplex DNA but it also appears to recognize functional groups in both grooves of the helix.

Sister chromatid differential staining and NOR activity of BrdU-resistant sublines

Two 30 μg/ml BrdU-resistant sublines and two 60 μg/ml BrdU-resistant sublines are induced from a Chinese hamster cell line Wg3h (HGPRT(-)) by one-step and two-step selections, respectively. By inoculating the cells into BrdU-free medium or by adding more BrdU into the culture medium for 26-27 h, it was found that the two BrdU-resistant sublines analysed have very clear sister chromatid differential (SCD) staining patterns. This indicates that some of the nuclear DNA of the BrdU-resistant cells incorporate with BrdU to reach a kinetic balance. Frequencies of sister chromatid exchange (SCE) of the resistant cells are twice to four times as high as those of the Wg3h cells, depending on which BrdU-resistant subline is analysed. The SCE frequencies of the resistant cells also increase with the BrdU concentration in the medium. Analysis of silver-stained nucleolar organizer regions (NORs) indicates that the NOR activity of three out of the four BrdU-resistant sublines is significantly suppressed, i.e., averages of the Ag-NOR number and number of the chromosomes bearing Ag-NORs per cell decrease significantly. The degree of suppression for different BrdU-resistant sublines may be quite different. The suppressed NOR activity of the resistant cells can gradually be restored when the cells are inoculated into BrdU-free medium, but the recovery speed is far lower than that of the Wg3h cells. The suppression of the NOR activity of the BrdU-resistant sublines should be due to BrdU toxicity.

Deoxycytidine reverses the suppression of nucleolar organizer regions' activity caused by BrdU

In this article we report that 5'-bromodeoxyuridine (BrdU) significantly suppresses the nucleolar organizer regions (NORs) activity of Chinese hamster cells (both dipliod cells and cell line Wg3-h) (P<0.001). One of the most obvious characteristics of the suppression is a significant decrease in the total number of the Ag-NORs per cell rather than in a frequency variation of the associated Ag-NORs. The decrease in the Ag-NORs number is mainly because of the decrease in number of chromosomes bearing 2 Ag-NORs. The degree of the suppression increases with increase in BrdU concentration in the culture medium. There is a close relationship between the suppression and the BrdU-treatment time, i.e. for a given concentration of the BrdU, the longer the BrdU-treatment time, the stronger the suppression. When the BrdU-treated cells are transferred into BrdU-free medium and allowed to grow in it for another 30 h, NORs activity can be restored. Therefore, the suppression of NORs activity may be due to BrdU toxicity. When deoxycytidine (dC) is added into medium containing 30 μg/ml of BrdU, the total number of both the Ag-NORs and the chromosomes bearing Ag-NORs per cell increases to the level of untreated cells. Our results thus indicate that the addition of dC reverses the suppression of the NORs activity caused by BrdU.

Functional groups on 'Z' DNA recognized by monoclonal antibodies

Both brominated poly[d(GC)] and poly[d( Gm5C )] form stable left-handed Z-DNA structures at physiological ionic strengths. These two antigens were used to prepare monoclonal antibodies from immunized mice. The specificity of the antibodies was studied in detail with a solid-phase radioimmune assay as well as by means of competition experiments. Both immunogens produced several relatively non-specific antibodies but two types of very specific antibody were also distinguished. The first binds poly[d( Gm5C )] but not brominated poly[d(GC)] while the other has the opposite specificity and will only bind the brominated polymer.

Sequence-specific responses of restriction endonucleases to bromodeoxyuridine substitution in mammalian DNA

Substitution of BrdU for dT in mammalian DNA alters the rates of DNA cleavage by restriction endonucleases in a manner that can be related to the specificity of cleavage. A formula is proposed that describes inhibitory and stimulatory contributions arising from the substitution of a Br atom for the CH3 group on T. The larger Br atom is postulated to sterically hinder the nuclease from binding to adjacent groups in the DNA cleavage site, while allowing a tighter binding to itself. The inhibition caused by steric hindrance is predicted to vary inversely with distance from the point of cleavage, whereas the stimulation caused by tighter binding is predicted to be independent of distance. The resultant formula gives a good fit to the data obtained for thirteen different restriction nucleases of known specificity. The parameters in the formula appear to be simple functions of ionic strength. This formula can be used to predict the effect of BrdU substitution on any endonuclease whose specificity of cleavage is known.

Isolation of mutants of CHO cells resistant to 6(p-hydroxyphenylazo)-uracil I. A novel BrdU cross-resistant phenotype

Three classes of mutants resistant to the drug 6(p-hydroxyphenylazo)-uracil have been isolated from mutagenized cultures of CHO cells. One class of these mutants designated HPURA exhibits a unique form of cross-resistance to bromodeoxyuridine in that it is resistant to this drug only in the presence of thymidine. The molecular basis of the BrdU resistance is unknown but does not appear to involve the known targets of the drug. An interesting feature of these mutants is that they give rise, at a high frequency, to a subpopulation of cells which are much more resistant to BrdU.

Specificity of autoimmune monoclonal Fab fragments binding to single-stranded deoxyribonucleic acid

Fab fragments from hybridoma HEd 10 [Lee, J. S., Lewis, J.R., Morgan, A.R., Mosmann, T.R., & Singh, B. (1981) Nucleic Acids Res. 9, 1707-1721] were prepared in large amounts by papain digestion of the immunoglobulin G (IgG) fraction from ascites fluid. Binding data were generated by a fluorescence quenching technique, and binding constants [K(0)] were estimated from Scatchard plots. The Fab fragments bound tightly to poly(dT) [K(0) = 12.7 X 10(6) M-1], and analysis of binding constants for the series p(dT)2 to p(dT)17 showed that the recognition sequence consisted of four consecutive residues. The effect of ionic strength on the interaction suggested that only two phosphates were involved. Binding constants for poly(dU), poly[d(brU)], poly[d(brC)], and poly(rU) were 1.0 X 10(6) M-1, 18.8 X 10(6) M-1, 0.5 X 10(6) M-1, and less than 0.5 X 10(6) M-1, respectively, implicating the involvement of the 3, 4, and 5 positions of the pyrimidine ring as well as the deoxyribose sugar in the recognition process. At high ionic strength (0.5 M) K(0) for whole IgG binding to poly(dT) was 75 X 10(6) M-1 compared to a value of 1.1 X 10(6) M-1 for the Fab fragment. These results may have implications for the tissue damage caused by DNA-containing immune complexes in systemic lupus erythematosus.

5-Bromodeoxyuridine specifically inhibits the synthesis of estrogen-induced proteins in MCF7 cells

In the MCF7 human breast cancer cell line, estrogens induce a secreted glycoprotein with an Mr of 46 000 (46 000-Mr protein) and the progesterone receptor; they also increase to a lesser extent the secretion of [35S]-methionine-labelled proteins. When the cells are grown in the presence of 5-bromo-2'-deoxyuridine (BrdUrd, 5 microgram/ml for 4 days) these estrogen-induced responses are substantially inhibited while other proteins not regulated by estrogens and cell growth are not affected by BrdUrd. This effect of BrdUrd is not secondary to a decrease in estrogen receptor levels and appears to require incorporation of BrdUrd into DNA for the following reasons. First, there is a lag before any effect of BrdUrd is seen which is similar to the doubling time of the cells. Second, the effect of BrdUrd is not seen when cells are cultured in medium containing BrdUrd and 1-beta-D-arabinofuranosylcytosine, a DNA synthesis inhibitor, or excess thymidine, which blocks the incorporation of BrdUrd into DNA. Finally 2'-deoxycytidine, which reverses the effects of non-incorporated BrdUrd, is without effect on the inhibition of the estrogen-induced 46 000-Mr protein. We conclude that BrdUrd selectively prevents the effects of estrogens in MCF7 cells and that the mechanism of this anti-estrogenic effect of BrdUrd probably requires its incorporation into DNA and occurs beyond the nuclear translocation step of the estrogen receptor. Alterations in the recognition of chromatin effector sites by the estrogen-receptor complex could be involved in preventing hormone action.

On the influence of thymidine analogues on the activity of phage fd promoters in vitro

RF I DNA of phage fd containing 5-bromo-deoxyuridine (br5Ud) or deoxyuridine (Ud) instead of deoxythymidine (Td) inthe codogenic strand was synthesized in vitro. The modified genomes could be cleaved by restriction endonuclease Hpa II. Although the recognition site of Hpa II is CCGG, the cleavage rate was significantly reduced with Ud-containing DNA. Both base substitutions altered the mobilities of several DNA fragments under the conditions of polyacrylamide gel electrophoresis. The fragments containing binding sites for RNA polymerase were assayed for the rates of stable complex formation. The substitution of Td for both, Ud and br5Ud, strongly influenced this parameter. Thus the methyl group of Td has to be regarded as one of the sites in DNA which determine the rate of stable RNA polymerase binding and thereby possibly mediate promoter activity in vitro (24,25,26). In most cases the rate of complex formation was decreased by Ud, but increased by br5Ud.

DNA methylation and gene function

In most higher organisms, DNA is modified after synthesis by the enzymatic conversion of many cytosine residues to 5-methylcytosine. For several years, control of gene activity by DNA methylation has been recognized as a logically attractive possibility, but experimental support has proved elusive. However, there is now reason to believe, from recent studies, that DNA methylation is a key element in the hierarchy of control mechanisms that govern vertebrate gene function and differentiation.

Conformational transitions in closed circular DNA molecules. II. Biological implications

A model of regulation of gene action based on the theory of conformational transitions in closed circular DNA molecules is proposed and discussed in connection with the mechanisms of cellular differentiation. The model predicts two main types of regulation of gene action (1) the change in the topological linking number of the DNA loops leading to the change in the amount of the DNA segments present in the transcriptionally active A-form and (2) the change of some nucleotide sequences in closed superhelical DNA loops resulting in conformational transitions of some of the other sequences in the same loop. The first type of regulation may explain the mechanism of terminal differentiation of the stem cells and the changes accompanying the malignant transformation. The second one may explain the variegated position effect of the gene and determination of the stem cells during ontogenesis.

Interaction of the cAMP receptor protein with the lac promoter

The cyclic AMP receptor protein (CRP) stimulates transcription of the lactose operon by binding to the lac promoter. I have identified those 5-positions of thymines in the promoter that lie close to bound CRP. Although ultraviolet irradiation of DNA with 5-bromouracil substituted in place of thymine normally cleaves the DNA at the bromouracils, a protein bound to the DNA can perturb these cleavages at those locations at which the protein lies close to the bromine. The contacts inferred from this photochemical probe and the results of nucleolytic attack of this complex by exonuclease III support a model where the cyclic AMP receptor protein binds to the promoter making symmetrical contacts with one face of the double helix and then stimulates transcription through contacts with RNA polymerase.

Inhibition of Friend erythroleukemic cell differentiation by bromodeoxyuridine: correlation with the amount of bromodeoxyuridine in DNA

These studies were undertaken to examine the relationship between the inhibition by 5-bromodeoxyuridine (BrdU) of erythroid differentiation in Friend erythroleukemia cells and the incorporation of BrdU into DNA. Experiments were carried out in which the incorporation of BrdU into DNA and the concentration of BrdU to which the cells were exposed were varied independently of each other. In addition, the ability of deoxycytidine (dC) to reverse the effects of BrdU on hemoglobin production and to reduce the amount of BrdU in DNA was analyzed. Under all the conditions tested, the effects of BrdU were correlated with the amount of BrdU incorporated into nuclear DNA. These results differ from those of recent studies on the inhibition of pigmentation and the induction of mutations by BrdU in Syrian hamster melanoma cells. The results suggest that BrdU may be producing its biological effects by a variety of different mechanisms.

Methylation of DNA in mouse early embryos, teratocarcinoma cells and adult tissues of mouse and rabbit

The distribution and amount of 5-methylcytosine (5-MeCyt) in DNA was measured for early embryos of mouse strain CF1 (2 to 4 cell stage to blastocyst) and mouse teratocarcinoma cells. In each case, the pattern of methylation was examined by use of the restriction enzymes Hha I and HPA II HPA II, which cut DNA at the sites 5'GCGC and 5'CCGG respectively, when the cytosines at these sites are not methylated. Mouse embryo DNA was found to have the same level of methylation as adult mouse tissues, and no changes in methylation were seen during differentiation of the teratocarcinoma cells. The ratio of 5-MeCyt/Cyt in DNA was measured by high performance liquid chromatography for the differentiating teratocarcinoma cells and for several adult mouse and rabbit tissues. The variation between tissues or between teratocarcinoma cells at different stages of differentiation was less than 10 percent. These results are discussed in view of proposals that 5-MeCyt plays a role in differentiation.

Structures and mechanisms of DNA restriction and modification enzymes

DNA restriction and modification enzymes are responsible for the hostspecific barriers to interstrain and interspecies transfer of genetic information that have been observed in a variety of bacterial cell types. Although the phenomenon of host specificity was initially observed in the early 1950s (Luria & Human, 1952; Bertani & Weigle, 1953), it was nearly a decade later that Arber and his colleagues accurately predicted the molecular basis of the phenomenon. Their experiments with bacteriophage λ demonstrated that a given host-specificity system imparts a specific modification to the viral DNA, and further, that restriction of DNA lacking the appropriate modification is s consquence of nucleolytic hydrolysis upon entry into the host cell (Arber & Dussoix, 1962; Dussoix & Arber, 1962; Arber, Hattman & Dussoix, 1963).

Contacts between Escherichia coli RNA polymerase and thymines in the lac UV5 promoter

I have identified those 5 positions of thymines in the lac UV5 promoter that lie close to bound Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). Although ultraviolet irradiation of DNA with 5-bromouracil substituted in place of thymine normally cleaves the DNA at the bromouracils, a protein bound to the DNA can perturb these cleavages at those locations at which the protein lies close to the bromine. In the lac promoter most of these contacts lie in three regions. Four contacts lie in the region where transcription initiates; four lie in the "Pribnow box," which is located about 10 base pairs upstream from the initiation site; and three more lie in the "-35 region," located about 35 base pairs upstream from the initiation site. The "Pribnow box" and the "-35 region" are regions whose sequences are partially conserved between promoters and in which most promoter mutations are located; thus, contacts in these two regions probably represent sites of sequence-specific recognition by RNA polymerase.

Effect of 5-bromodeoxyuridine on heterogeneous nuclear RNA in rat hepatoma cells

Heterogeneous nuclear RNA HnRNA) was isolated from untreated and 5-bromodeoxyuridine (BrdUrd) treated hepatoma tissue culture (HTC) cells. analysis of this RNA by either electrophoresis on polyacrylamide-agarose gels or centrifugation in sucrose gradients demonstrated that BrdUrd caused a shift in the labeled HnRNA population toward a smaller size distribution. This effect was produced by concentrations of BrdUrd which specifically lower the level of the differentiated enzyme tyrosine aminotransferase, but do not greatly affect cell growth. Differential binding to oligo(dT) cellulose was used to fractionate HnRNA further into classes containing poly(A) (alpha), oligo(A) (beta) or neither category of A-rich sequences (gamma). BrdUrd did not alter the relative rates of uridine incorporation into the three classes. The shift in the labeled HnRNA population due to BrdUrd was observed in all three subclasses of HnRNA.

Proteins of BrdU-dependent hamster cell lines as characterized by two-dimensional gel electrophoresis

Cell lines which exhibit the BrdU-dependent phenotype (B4 and HAB) were studied with respect to BrdU-induced alterations in genetic expression by two-dimensional gel electrophoresis. A comparison of the proteins from the HAB cells, in which the DNA is 100% substituted by BrdU, to those of the unsubstituted parent line (3460) showed 55 protein alterations; the synthesis of 15 increased while that of the other 40 decreased. When 3460 cells were grown in BrdU such that their DNA was greater than 50% substituted, 27 protein changes could be detected; of these, the synthesis of 10 increased while that of 17 decreased. A comparison of all these changes in the various cell lines showed six which were common to the BrdU-substituted cell lines. The proteins from another Syrian hamster cell line, BHK-21 (C-13) and those of HAB cells grown in thymidine or BrdC were also examined on two-dimensional gels. Although BrdU has a dramatic effect on many cellular functions, relatively few changes in the pattern of protein synthesis could be detected in these cell lines, perhaps reflecting the specialized action of this analogue on particular cellular functions.