Assembly of transcriptionally active chromatin in Xenopus oocytes requires specific DNA binding factors

Long-term association of a transcription factor with its chromatin binding site can stabilize gene expression and cell fate commitment

Some kinds of transcription factor proteins are very important in initiating and guiding cell fate differentiation. Overexpression of these factors can force many other kinds of cells to become muscle or nerve. Examples are MyoD for muscle and Ascl1 for nerve. It is not known how long such a factor must remain bound to its binding site for it to have its function; this could be seconds, minutes, hours, or days. We have developed a procedure to determine the required residence time for the Ascl1 nerve factor to have its function. This factor remains closely associated with its chromatin binding site for hours or days. This may be a general characteristic of such factors in nondividing (adult) cells.

Some lineage-determining transcription factors are overwhelmingly important in directing embryonic cells to a particular differentiation pathway, such as Ascl1 for nerve. They also have an exceptionally strong ability to force cells to change from an unrelated pathway to one preferred by their action. Transcription factors are believed to have a very short residence time of only a few seconds on their specific DNA or chromatin-binding sites. We have developed a procedure in which DNA containing one copy of the binding site for the neural-inducing factor Ascl1 is injected directly into a Xenopus oocyte nucleus which has been preloaded with a limiting amount of the Ascl1 transcription factor protein. This is followed by a further injection of DNA as a competitor, either in a plasmid or in chromosomal DNA, containing the same binding site but with a different reporter. Importantly, expression of the reporter provides a measure of the function of the transcription factor in addition to its residence time. The same long residence time and resistance to competition are seen with the estrogen receptor and its DNA response elements. We find that in this nondividing oocyte, the nerve-inducing factor Ascl1 can remain bound to a specific chromatin site for hours or days and thereby help to stabilize gene expression. This stability of transcription factor binding to chromatin is a necessary part of its action because removal of this factor causes discontinuation of its effect on gene expression. Stable transcription factor binding may be a characteristic of nondividing cells.

Restricted specificity of Xenopus TFIIIA for transcription of somatic 5S rRNA genes

Xenopus transcription factor IIIA (TFIIIA) is phosphorylated on serine-16 by CK2. Replacements with alanine or glutamic acid were made at this position in order to address the question of whether phosphorylation possibly influences the function of this factor. Neither substitution has an effect on the DNA or RNA binding activity of TFIIIA. The wild-type factor and the alanine variant activate transcription of somatic- and oocyte-type 5S rRNA genes in nuclear extract immunodepleted of endogenous TFIIIA. The glutamic acid variant (S16E) supports the transcription of somatic-type genes at levels comparable to those of wild-type TFIIIA; however, there is no transcription of the oocyte-type genes. This differential behavior of the phosphomimetic mutant protein is also observed in vivo when using early-stage embryos, where this mutant failed to activate transcription of the endogenous oocyte-type genes. Template exclusion assays establish that the S16E mutant binds to the oocyte-type 5S rRNA genes and recruits at least one other polymerase III transcription factor into an inactive complex. Phosphorylation of TFIIIA by CK2 may allow the factor to continue to act as a positive activator of the somatic-type genes and simultaneously as a repressor of the oocyte-type 5S rRNA genes, indicating that there is a mechanism that actively promotes repression of the oocyte-type genes at the end of oogenesis.

Tetracycline-regulated gene expression switch in Xenopus laevis

Xenopus is a well-characterized model system for the investigation of biological processes at the molecular, cellular, and developmental level. The successful application of a rapid and reliable method for transgenic approaches in Xenopus has led to renewed interest in this system. We have explored the applicability of tetracycline-regulated gene expression, first described by Gossen and Bujard in 1992, to the Xenopus system. By optimizing conditions, tetracycline repressor induced expression of a luciferase reporter gene was readily and reproducibly achieved in both the Xenopus oocyte and developing embryo. This high level of expression was effectively abrogated by addition of low levels of tetracycline. The significance of this newly defined system for studies of chromatin dynamics and developmental processes is discussed.

Replication-coupled chromatin assembly is required for the repression of basal transcription in vivo

The chromatin assembly process coupled to DNA synthesis in the Xenopus oocyte nucleus is significantly more repressive toward basal transcription than chromatin assembly on duplex DNA. We show that chromatin assembly concurrent with DNA synthesis over the promoter region itself is causal for repression. However, the trans-activator Gal4-VP16 both relieves repression and activates transcription regardless of the chromatin assembly pathway. This activation is independent of whether Gal4-VP16 addition occurs before or after chromatin assembly. We propose that replication-coupled chromatin assembly represents a general mechanism to direct the efficient repression of basal transcription. However transcription induction by a specific activator, Gal4-VP16, occurs independent of this chromatin-mediated repression.

Transient gene expression of foreign genes in preheated protoplasts: stimulation of expression of transfected genes lacking heat shock elements

Transfection of preheated petunia protoplasts with several biologically active DNA constructs resulted in a significantly higher gene expression than that observed in transfected unheated protoplasts. It was observed with supercoiled, linearized and single-stranded DNA structures that stimulation of transient gene expression in preheated protoplasts was neither dependent on the reporter gene nor on the regulatory elements used. Heat treatment at 42 degrees C also increased expression in protoplasts transfected with a plasmid bearing the tobacco mosaic virus (TMV) translational enhancer, omega. Northern blot analysis revealed that heat treatment of protoplasts before the transfection event greatly increased the amount of the newly synthesized transcripts. Preheating of protoplasts did not affect the transfection efficiency, namely the number of transfected cells in the population, nor the amount of DNA in transfected nuclei, as was inferred from histochemical staining and Southern blot analysis, respectively. The possible mechanism by which heat treatment stimulates transient gene expression of genes lacking obvious heat shock elements is offered. The relevance of the present findings to transient gene expression in plants in general and to viral gene expression in particular is discussed.

Tissue-specific trans-activation of the rabbit beta-globin promoter in Xenopus oocytes

Identification of transcription factors regulating tissue-specific gene expression implies functional tests in transcription systems. In spite of its practical advantages, the Xenopus oocyte has only rarely been used for trans-activation studies, because some critical parameters inherent to the system may cause artefacts. Depending on the amount of DNA injected, even tissue-specific genes may be spontaneously transcribed. To develop a reliable trans-activation assay, we used the erythroid-specific rabbit beta-globin gene and, for comparison, the constitutively transcribed viral thymidine kinase gene. The viral gene is active over a wide range of injected DNA (0.2-10 ng), and addition of nuclear proteins from various cell types does not stimulate but often inhibits this activity. When large amounts of DNA are injected (greater than 10 ng), transcription is inhibited by self competition. Addition of nuclear proteins now re-establishes activity probably through increasing the pool of general transcription factors. By contrast, spontaneous activity of the beta-globin promoter occurs only within a narrow range of injected DNA (0.2-1 ng). At higher DNA concentrations (greater than 5 ng) spontaneous transcription becomes negligible. The addition of nuclear proteins from nonerythroid cells extracts has no or only a weak stimulatory effect on the beta-globin promoter. Only nuclear proteins isolated from erythroid tissues, bone marrow and spleen, bring about a strong transcriptional activation. Co-injection with either the polyoma virus, or the oviduct-specific chicken lysozyme gene shows that the beta-globin promoter is selectively activated by factors present in erythroid cell extracts.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA superhelicity enhances the assembly of transcriptionally active chromatin in vitro

Using an in vitro chromatin assembly system, we analyzed the influence of DNA superhelicity on the development of transcriptionally active minichromosomes. Plasmid DNA molecules containing either a Xenopus borealis 5S RNA gene or an X. laevis methionine tRNA gene were utilized as templates for the assembly of chromatin. Both plasmids were processed into active minichromosomes if introduced as supercoiled molecules into the extract (S-150). The degree of superhelicity is a determining factor in the assembly of active chromatin. Molecules containing varying superhelical densities were processed into minichromosomes with different transcriptional activities. The absence of supercoils leads to the assembly of chromatin with substantially lower transcriptional activity. Assembled minichromosomes are stable enough to be isolated by sucrose gradient centrifugation while retaining their transcriptional phenotype. The formation of nucleosomes with a periodic spacing occurred with the same efficiency and to the same degree regardless of the initial DNA topology. Hence, a determining factor in the development of transcriptionally active chromatin may be the initial superhelicity of the DNA molecule to which activator (trans-acting factors) or repressor (histones) proteins bind. Once the chromatin assembly process has begun, the transcriptional activity of the resulting minichromosome may already have been determined.

Activation and repression of a beta-globin gene in cell hybrids is accompanied by a shift in its temporal replication

To investigate whether a switch in the transcriptional activity of a gene is associated with a change in the timing of replication during the S phase, we examined the replication timing of the beta-globin genes in two different types of somatic cell hybrids. In mouse hepatoma (Hepa 1a) x mouse erythroleukemia (MEL) hybrid cells, the beta-globin gene from the MEL parent is transcriptionally inactivated and is later replicating than in the parental MEL cell line. In human fibroblast (GM3552) x MEL hybrid cells, the human beta-globin gene is transcriptionally activated, and all of the sequences within the human beta-globin domain (200 kilobases) we have examined appear to be earlier replicating than those in the parental fibroblast cell line. The chromatin configuration of the activated human beta-globin domain in the hybrids is relatively more sensitive to nucleases than that in the fibroblasts. Furthermore, major nuclease-hypersensitive sites that were absent in the chromatin flanking the distal 5' region of the human beta-globin gene cluster in the parental fibroblast cell line are present in the transcriptionally activated domain in the hybrid cell line. These results suggest that timing of replication of globin genes has been altered in these hybrid cells and thus is not fixed during the process of differentiation.

The need for enhancers in gene expression first appears during mouse development with formation of the zygotic nucleus

Microinjection of the firefly luciferase gene coupled to a thymidine kinase (tk) promoter provided a quantitative assay to evaluate the requirements for gene expression in individual mouse oocytes and embryos. Polyoma virus (PyV) enhancers had no effect on the level of gene expression or competition for transcription factors as long as the DNA remained either in the oocyte germinal vesicle or the pronuclei of one-cell embryos. Expression of injected genes could be observed in pronuclei because the signal that normally triggers zygotic gene expression in two-cell embryos still occurred in one-cell embryos arrested in S phase. However, when the tk promoter was injected into zygotic nuclei of two-cell embryos, enhancers increased the number of embryos that expressed luciferase as well as the level of luciferase activity per embryo. PyV enhancer mutation F101, selected for growth in mouse embryonal carcinoma F9 cells, stimulated expression in developing two-cell embryos about seven times better than the wild-type PyV enhancer and competed effectively for factors required for transcription. These results were consistent with the fact that enhancers are required to activate the PyV origin of DNA replication in developing two-cell embryos but not in one-cell embryos. The maximum levels of gene expression in oocytes, one-cell embryos, and developing two-cell embryos (1:67:21) were inversely related to the extent of chromatin assembly, but the need for enhancers was independent of chromatin assembly. Therefore, it appears that the need for enhancers to activate promoters or origins of replication results from some negative regulatory factor that first appears as a component of zygotic nuclear structure.

Age-dependent increase of DNA topoisomerase II activity in quail oviduct; modulation of the nuclear matrix-associated enzyme activity by protein phosphorylation and poly(ADP-ribosyl)ation

Nuclear DNA topoisomerase II activity in quail oviduct tissue was found to increase by about 70% with age. This age-dependent increase was observed with both the enzyme in whole nuclear extract and nuclear matrix-associated topoisomerase II. Both purified topoisomerase II and the nuclear matrix-bound enzyme were found to be modifiable by phosphorylation and poly(ADP-ribosyl)ation. Phosphorylation of the purified enzyme by isolated nuclear protein kinase NII or protein kinase C resulted in a 2- to 3-fold increase in specific activity, while poly(ADP-ribosyl)ation by soluble poly(ADP-ribose) synthetase caused a 50% inhibition of the enzyme. Using immunoprecipitation and immunoblotting procedures, phosphorylation and poly(ADP-ribosyl)ation could also be demonstrated to occur with the nuclear matrix-associated enzyme. The nuclear matrix-associated NII-like protein kinase activity, assumed to be involved in post-translational modification of topoisomerase II, displayed a 1.4- to 1.6-fold increase in old animals compared to mature ones, while the matrix-bound poly(ADP-ribose) synthetase activity decreased by about 50%. It is suggested that age-correlated enhancement of DNA topoisomerase II activity, possibly due to age-dependent changes in activities of nuclear protein kinases and poly(ADP-ribose) synthetase, may result in alterations in the topological state of DNA, possibly affecting DNA replication, transcription and repair with age.

Activation and repression of a beta-globin gene in cell hybrids is accompanied by a shift in its temporal replication

To investigate whether a switch in the transcriptional activity of a gene is associated with a change in the timing of replication during the S phase, we examined the replication timing of the beta-globin genes in two different types of somatic cell hybrids. In mouse hepatoma (Hepa 1a) x mouse erythroleukemia (MEL) hybrid cells, the beta-globin gene from the MEL parent is transcriptionally inactivated and is later replicating than in the parental MEL cell line. In human fibroblast (GM3552) x MEL hybrid cells, the human beta-globin gene is transcriptionally activated, and all of the sequences within the human beta-globin domain (200 kilobases) we have examined appear to be earlier replicating than those in the parental fibroblast cell line. The chromatin configuration of the activated human beta-globin domain in the hybrids is relatively more sensitive to nucleases than that in the fibroblasts. Furthermore, major nuclease-hypersensitive sites that were absent in the chromatin flanking the distal 5' region of the human beta-globin gene cluster in the parental fibroblast cell line are present in the transcriptionally activated domain in the hybrid cell line. These results suggest that timing of replication of globin genes has been altered in these hybrid cells and thus is not fixed during the process of differentiation.

A 3' exonuclease activity degrades the pseudogene 5S RNA transcript and processes the major oocyte 5S RNA transcript in Xenopus oocytes

Transcription of the major oocyte 5S RNA gene (o) and pseudogene (psi) of Xenopus laevis yields different RNAs with three different homologous systems: oocyte microinjection, whole oocyte extract, and fractionated TFIIIA + TFIIIB + TFIIIC components. Those peculiar results are caused by a 3' RNA exonuclease activity, which is inhibited in the oocyte extract, that rapidly degrades the pseudogene 5S RNA but does not degrade as readily the chimeric RNA transcripts generated by HindIII-truncated 5S RNA pseudogenes. The same, or a similar, RNase activity processes the 130- and the 142-base-long transcripts of the major oocyte 5S RNA gene into mature 120-base-long 5S RNA. We performed site-specific mutagenesis on the somatic 5S RNA gene and changed specific nucleotides on the somatic 5S RNA. These studies indicated that the structure that confers stability to the 5S RNA in vivo and in vitro is the 9-bp helix formed in 5S RNA, but not in psi 5S RNA, by the complementary 5' and 3' ends of the molecule.

The C-terminal domain of transcription factor IIIA interacts differently with different 5S RNA genes

DNase I footprints and affinity measurements showed that the C-terminal arm of Xenopus transcription factor IIIA interacts differently with different Xenopus 5S DNAs, forming three distinct types of transcription factor IIIA-5S DNA complexes: a somatic type, a major-oocyte (and pseudogene) type, and a trace-oocyte type. Site-directed mutagenesis on the major-oocyte 5S gene revealed that somatic-type changes at positions 53, 55, and 56 changed the structure of the transcription factor IIIA-5S DNA complex from major-oocyte to somatic, and a single trace-oocyte change at position 56 caused the change from major-oocyte to trace-oocyte complex. We further show that the somatic-type changes are accompanied by a marked enhancement in the rate of 5S RNA transcription, and we discuss the possible biological relevance of these findings.

Changes in DNA topology can modulate in vitro transcription of certain RNA polymerase III genes

The role of DNA supercoiling in eukaryotic gene expression is not fully understood. The objective of this study was to examine the regulation of in vitro chromatin assembly by topological alterations in the DNA template using a cell-free extract from Xenopus laevis oocytes (S-150). The results suggest that input DNA topology may be a determining factor in controlling the transcriptional activity of the Xenopus tRNA and one particular 5S gene. When the input topology is supercoiled, high levels of transcription are observed, whereas input relaxed DNA is transcribed to a much lower extent. Transcription from an input relaxed template is stimulated by the addition of supercoiled nonspecific, vector DNA. Furthermore, in direct competition experiments, supercoiled DNA molecules were shown to be transcriptionally dominant over relaxed DNA molecules. Taken together, these data suggest that the efficiency with which a repressor or activator binding protein interacts with DNA may be significantly influenced by the topological status of its target. We demonstrate that modulation of reaction parameters which alter the normal topological processing events catalyzed by the S-150 can dramatically influence the level of gene expression.

The C-terminal domain of transcription factor IIIA interacts differently with different 5S RNA genes

DNase I footprints and affinity measurements showed that the C-terminal arm of Xenopus transcription factor IIIA interacts differently with different Xenopus 5S DNAs, forming three distinct types of transcription factor IIIA-5S DNA complexes: a somatic type, a major-oocyte (and pseudogene) type, and a trace-oocyte type. Site-directed mutagenesis on the major-oocyte 5S gene revealed that somatic-type changes at positions 53, 55, and 56 changed the structure of the transcription factor IIIA-5S DNA complex from major-oocyte to somatic, and a single trace-oocyte change at position 56 caused the change from major-oocyte to trace-oocyte complex. We further show that the somatic-type changes are accompanied by a marked enhancement in the rate of 5S RNA transcription, and we discuss the possible biological relevance of these findings.

Characterization of the repressed 5S DNA minichromosomes assembled in vitro with a high-speed supernatant of Xenopus laevis oocytes

We describe an in vitro system, based on the Xenopus laevis oocyte supernatant of Glikin et al. (G. Glikin, I. Ruberti, and A. Worcel, Cell 37:33-41, 1984), that packages DNA into minichromosomes with regularly spaced nucleosomes containing histones H3, H4, H2A, and H2B but no histone H1. The same supernatant also assembles the 5S RNA transcription complex; however, under the conditions that favor chromatin assembly, transcription is inhibited and a phased nucleosome forms over the 5S RNA gene. The minichromosomes that are fully loaded with nucleosomes remain refractory to transcriptional activation by 5S RNA transcription factors. Our data suggest that this repression is caused by a nucleosome covering the 5S RNA gene and that histone H1 is not required for regular nucleosome spacing or for gene repression in this system.

Developmental regulation of two 5S ribosomal RNA genes

The developmental regulation of two kinds of Xenopus 5S RNA genes (oocyte and somatic types) can be explained by differences in the stability of protein-protein and protein-DNA interactions in a transcription complex that directs transcription initiation by RNA polymerase III. Dissociation of transcription factors from oocyte 5S RNA genes during development allows them to be repressed by chromatin assembly. In the same cells, somatic 5S RNA genes remain active because their transcription complexes are stable.

Competition between DNA templates injected into Xenopus laevis oocytes

We have examined the competition between microinjected DNA templates for endogenous Xenopus oocyte transcription factors. The results suggest that (a) coinjected templates compete with one another for transcription factors, (b) the competitive ability of a template is not necessarily a function of the rate of transcription of the gene, (c) competition is due to the presence of specific DNA sequences, and (d) preincubation of the test gene affects competition.

Characterization of the repressed 5S DNA minichromosomes assembled in vitro with a high-speed supernatant of Xenopus laevis oocytes

We describe an in vitro system, based on the Xenopus laevis oocyte supernatant of Glikin et al. (G. Glikin, I. Ruberti, and A. Worcel, Cell 37:33-41, 1984), that packages DNA into minichromosomes with regularly spaced nucleosomes containing histones H3, H4, H2A, and H2B but no histone H1. The same supernatant also assembles the 5S RNA transcription complex; however, under the conditions that favor chromatin assembly, transcription is inhibited and a phased nucleosome forms over the 5S RNA gene. The minichromosomes that are fully loaded with nucleosomes remain refractory to transcriptional activation by 5S RNA transcription factors. Our data suggest that this repression is caused by a nucleosome covering the 5S RNA gene and that histone H1 is not required for regular nucleosome spacing or for gene repression in this system.

Developmental regulation of two 5S ribosomal RNA genes

The developmental regulation of two kinds of Xenopus 5S RNA genes (oocyte and somatic types) can be explained by differences in the stability of protein-protein and protein-DNA interactions in a transcription complex that directs transcription initiation by RNA polymerase III. Dissociation of transcription factors from oocyte 5S RNA genes during development allows them to be repressed by chromatin assembly. In the same cells, somatic 5S RNA genes remain active because their transcription complexes are stable.

Differential stimulation of sea urchin early and late H2B histone gene expression by a gastrula nuclear extract after injection into Xenopus laevis oocytes

Sea urchin early histone genes are active in preblastula embryos; late histone genes are maximally expressed during subsequent stages of embryogenesis. We used the Xenopus laevis oocyte to assay for trans-acting factors involved in this differential regulation. Sea urchin nuclear proteins were prepared by extracting gastrula-stage chromatin successively with 0.45, 1, and 2 M NaCl. We injected three fractions into oocytes along with plasmids bearing sea urchin early and late H2b histone genes. While neither the 0 to 0.45 M nor the 1 to 2 M salt fraction affected H2b gene expression, the 0.45 to 1 M salt fraction stimulated early and late H2b mRNA levels significantly. Late H2b gene expression was stimulated preferentially when the early and late genes were coinjected into the same oocytes. This extract did not stimulate the accumulation of transcripts of injected herpesvirus thymidine kinase genes or of the sea urchin Spec 1 gene, suggesting that the stimulatory activity is not a general transcription factor. We localized the DNA sequence required for the stimulatory effect to a region of the late H2b gene located between -43 and +62 relative to the transcription start site. A component of the 0.45 to 1 M salt wash fraction specifically bound to the 105-base-pair late gene DNA sequence and to the corresponding early gene fragment. The abundance of this binding activity decreased on a per genome basis during early development of the sea urchin.

Methylation of single CpG dinucleotides within a promoter element of the Herpes simplex virus tk gene reduces its transcription in vivo

The binding of the transcription factors Sp1 and CTF immediately upstream from the TATA box of the Herpes simplex virus (type 1) thymidine kinase-coding gene (tk) facilitates efficient transcription of this gene in microinjected Xenopus laevis oocytes. To establish whether the presence of methylated CpG dinucleotides within the binding sites of these two factors affects transcription of the tk gene in vivo, we replaced a 33-bp promoter segment, consisting solely of the Sp1 and CTF binding sites, with synthetic oligodeoxynucleotide duplexes containing 5-methylcytosine residues at selected positions. We show that symmetrical methylation (modification of both strands) of any of the four CpGs within this promoter segment resulted in an approximately 20-fold reduction in the specific transcription of the tk gene in Xenopus oocytes, as shown by primer extension analysis of the isolated mRNA. As no other methylated CpG dinucleotides were present within the entire 9.2-kb vector, our results demonstrate that the presence of a single mCpG dinucleotide within the promoter region is sufficient for transcriptional inactivation of the tk gene. The possible mechanisms of this downregulation are discussed.

Multiple functional motifs in the chicken U1 RNA gene enhancer

The DNA sequence requirements of chicken U1 RNA gene expression have been examined in an oocyte transcription system. An enhancer region, which was required for efficient U1 RNA gene expression, is contained within a region of conserved DNA sequences spanning nucleotide positions -230 to -183, upstream of the transcriptional initiation site. These DNA sequences can be divided into at least two distinct subregions or domains that acted synergistically to provide a greater than 20-fold stimulation of U1 RNA synthesis. The first domain contains the octamer sequence ATGCAAAT and was recognized by a DNA-binding factor present in HeLa cell extracts. The second domain (the SPH domain) consists of conserved sequences immediately downstream of the octamer and is an essential component of the enhancer. In the oocyte, the DNA sequences of the SPH domain were able to enhance gene expression at least 10-fold in the absence of the octamer domain. In contrast, the octamer domain, although required for full U1 RNA gene activity, was unable to stimulate expression in the absence of the adjacent downstream DNA sequences. These findings imply that sequences 3' of the octamer play a major role in the function of the chicken U1 RNA gene enhancer. This concept was supported by transcriptional competition studies in which a cloned chicken U4B RNA gene was used to compete for limiting transcription factors in oocytes. Multiple sequence motifs that can function in a variety of cis-linked configurations may be a general feature of vertebrate small nuclear RNA gene enhancers.

Differential stimulation of sea urchin early and late H2B histone gene expression by a gastrula nuclear extract after injection into Xenopus laevis oocytes

Sea urchin early histone genes are active in preblastula embryos; late histone genes are maximally expressed during subsequent stages of embryogenesis. We used the Xenopus laevis oocyte to assay for trans-acting factors involved in this differential regulation. Sea urchin nuclear proteins were prepared by extracting gastrula-stage chromatin successively with 0.45, 1, and 2 M NaCl. We injected three fractions into oocytes along with plasmids bearing sea urchin early and late H2b histone genes. While neither the 0 to 0.45 M nor the 1 to 2 M salt fraction affected H2b gene expression, the 0.45 to 1 M salt fraction stimulated early and late H2b mRNA levels significantly. Late H2b gene expression was stimulated preferentially when the early and late genes were coinjected into the same oocytes. This extract did not stimulate the accumulation of transcripts of injected herpesvirus thymidine kinase genes or of the sea urchin Spec 1 gene, suggesting that the stimulatory activity is not a general transcription factor. We localized the DNA sequence required for the stimulatory effect to a region of the late H2b gene located between -43 and +62 relative to the transcription start site. A component of the 0.45 to 1 M salt wash fraction specifically bound to the 105-base-pair late gene DNA sequence and to the corresponding early gene fragment. The abundance of this binding activity decreased on a per genome basis during early development of the sea urchin.

Transcriptionally inactive oocyte-type 5S RNA genes of Xenopus laevis are complexed with TFIIIA in vitro

An extract from whole oocytes of Xenopus laevis was shown to transcribe somatic-type 5S RNA genes approximately 100-fold more efficiently than oocyte-type 5S RNA genes. This preference was at least 10-fold greater than the preference seen upon microinjection of 5S RNA genes into oocyte nuclei or upon in vitro transcription in an oocyte nuclear extract. The approximately 100-fold transcriptional bias in favor of the somatic-type 5S RNA genes observed in vitro in the whole oocyte extract was similar to the transcriptional bias observed in developing Xenopus embryos. We also showed that in the whole oocyte extract, a promoter-binding protein required for 5S RNA gene transcription, TFIIIA, was bound both to the actively transcribed somatic-type 5S RNA gene and to the largely inactive oocyte-type 5S RNA genes. These findings suggest that the mechanism for the differential expression of 5S RNA genes during Xenopus development does not involve differential binding of TFIIIA to 5S RNA genes.

Differential 5S RNA gene expression in vitro

In extracts derived from activated eggs of Xenopus, oocyte 5S RNA gene transcription complexes are destabilized under conditions where somatic 5S RNA gene transcription complexes are stable. Trans-acting factors in destabilized complexes are in equilibrium with free factors in the extract, and thus transcription becomes dependent upon the concentration of the limiting factor in the extract. By reducing TFIIIA, a limiting factor in the egg extract, a cloned somatic 5S RNA gene is transcribed as much as 400-fold more efficiently than a cloned oocyte 5S RNA gene.

Multiple functional motifs in the chicken U1 RNA gene enhancer

The DNA sequence requirements of chicken U1 RNA gene expression have been examined in an oocyte transcription system. An enhancer region, which was required for efficient U1 RNA gene expression, is contained within a region of conserved DNA sequences spanning nucleotide positions -230 to -183, upstream of the transcriptional initiation site. These DNA sequences can be divided into at least two distinct subregions or domains that acted synergistically to provide a greater than 20-fold stimulation of U1 RNA synthesis. The first domain contains the octamer sequence ATGCAAAT and was recognized by a DNA-binding factor present in HeLa cell extracts. The second domain (the SPH domain) consists of conserved sequences immediately downstream of the octamer and is an essential component of the enhancer. In the oocyte, the DNA sequences of the SPH domain were able to enhance gene expression at least 10-fold in the absence of the octamer domain. In contrast, the octamer domain, although required for full U1 RNA gene activity, was unable to stimulate expression in the absence of the adjacent downstream DNA sequences. These findings imply that sequences 3' of the octamer play a major role in the function of the chicken U1 RNA gene enhancer. This concept was supported by transcriptional competition studies in which a cloned chicken U4B RNA gene was used to compete for limiting transcription factors in oocytes. Multiple sequence motifs that can function in a variety of cis-linked configurations may be a general feature of vertebrate small nuclear RNA gene enhancers.

Transcriptionally inactive oocyte-type 5S RNA genes of Xenopus laevis are complexed with TFIIIA in vitro

An extract from whole oocytes of Xenopus laevis was shown to transcribe somatic-type 5S RNA genes approximately 100-fold more efficiently than oocyte-type 5S RNA genes. This preference was at least 10-fold greater than the preference seen upon microinjection of 5S RNA genes into oocyte nuclei or upon in vitro transcription in an oocyte nuclear extract. The approximately 100-fold transcriptional bias in favor of the somatic-type 5S RNA genes observed in vitro in the whole oocyte extract was similar to the transcriptional bias observed in developing Xenopus embryos. We also showed that in the whole oocyte extract, a promoter-binding protein required for 5S RNA gene transcription, TFIIIA, was bound both to the actively transcribed somatic-type 5S RNA gene and to the largely inactive oocyte-type 5S RNA genes. These findings suggest that the mechanism for the differential expression of 5S RNA genes during Xenopus development does not involve differential binding of TFIIIA to 5S RNA genes.

Characterization of ribosomal RNA synthesis in a gene dosage mutant: the relationship of topoisomerase I and chromatin structure to transcriptional activity

The genes encoding 18S, 5.8S, and 28S ribosomal RNA (rRNA) are tandemly repeated at the nucleolus organizer region (NOR). The NORs in the chicken map to one pair of microchromosomes. A line of chickens that contains individuals that are either disomic, trisomic, or tetrasomic for this chromosome, and have two, three, or four nucleoli and NORs, per cell, respectively, has been described previously. Aneuploid animals display a proportional increase in the rRNA gene copy number per cell. But, despite an increase in rDNA dosage, the levels of mature rRNA are regulated to normal levels in cells from aneuploid chickens (Muscarella, D.E., V.M. Vogt, and S.E. Bloom, 1985, J. Cell Biol., 101:1749-1756). This paper addresses the question of how regulation of mature rRNA synthesis occurs in cells with elevated levels of rDNA. An analysis of rRNA transcription in chicken embryo fibroblasts (CEFs) revealed that the relative rates of rRNA synthesis and processing and the amounts of precursor rRNA per cell are similar for all three genotypes. A comparison of chromatin structure, as determined by sensitivity of rDNA in nuclei from CEFs to digestion by DNase I, revealed that some of the rRNA genes from aneuploid cells are more resistant to digestion than corresponding sequences in the disomic cells. A determination of the distribution of topoisomerase I on rDNA has also been performed using the compound camptothecin, which introduces single- and double-strand breaks in topoisomerase-DNA complexes. Quantitation of camptothecin-induced cleavages revealed that a larger proportion of the rRNA genes in aneuploid cells was resistant to cleavage than in disomic cells, and therefore have no detectable amounts of topoisomerase I. These results suggest that the regulation of rRNA synthesis in CEFs with elevated levels of rDNA is achieved by the use of a subset of the rRNA genes.

Transcription of adenovirus 2 major late and peptide IX genes under conditions of in vitro nucleosome assembly

Plasmid DNA containing adenovirus 2 major late and peptide IX genes was assembled into nucleosomes in vitro, and the assembled nucleosomes were used as a template to study the regulatory mechanism of transcription initiation under these conditions. Neither the major late nor peptide IX genes was transcribed on the already-assembled nucleosomes. However, the major late gene, but not the peptide IX gene, was transcribed efficiently when the DNA was incubated with HeLa cell extracts prior to assembly into nucleosomes. These results indicate that prebinding of some component in the cell extracts to DNA is essential to activate transcription of the major late gene on nucleosomes assembled under the conditions used here. Since gene IX on the nucleosomes was not transcriptionally active regardless of preincubation of DNA with the extracts, some other component or another, different template structure which is not able to be identified in an in vitro system with deproteinized DNA template might be required for activation of peptide IX gene transcription. To know the function of the upstream sequences of the major late gene, effects of the deletion on transcription of nucleosomes were compared with that of deproteinized DNA. The result showed that depression of transcription by deleting the upstream sequences had more effect on nucleosomes than on deproteinized DNA.

Non-histone chromatin proteins that recognize specific sequences of DNA

Numerous chromatographic procedures have recently been developed to purify to near homogeneity various eukaryotic non-histone chromatin proteins that recognize and bind to specific sequences of DNA. In this brief review we have discussed a number of these different methods that we feel are important and probably represent the starting points for much of the future research work in this area. We view this coverage as being only an introduction, however, and strongly recommend that the reader consult the original papers for details of methods and protocols. We, nevertheless, hope that the information presented here will be of some assistance to those researchers and students who wish to become acquainted with the latest developments in this rapidly advancing field of chromatography. Although it is evident from what has been presented that the purification of each DNA sequence-specific non-histone chromatin protein initially starts with common or classical isolation and fractionation procedures, the final (and often crucial) steps of enrichment and purification often involve distinctive or unique procedures for each individual protein of interest. In many cases these final steps involve new techniques such as DNA sequence-specific bioaffinity and photoaffinity chromatography which not only ensure the isolation of specific protein species from complex mixtures but also result in a tremendous enrichment for nuclear proteins that are often present in the nucleus in extremely low concentrations. Furthermore, the entire process of protein purification has been remarkedly facilitated with the advent of high-performance liquid chromatographic and fast protein liquid chromatographic techniques which now allow for the very rapid separation and purification of proteins in a matter of minutes from mixtures that in the recent past would have required hours or days to purify. Thus, separation and purification techniques are now available that set the stage for the rapid isolation of rare, DNA sequence-specific, NHC nuclear proteins from almost any cellular source. It is therefore reasonable to anticipate that in the near future there will be major advances made in our understanding of the specific nuclear proteins that regulate gene expression in eukaryotic cells.

Transcription of adenovirus 2 major late and peptide IX genes under conditions of in vitro nucleosome assembly

Plasmid DNA containing adenovirus 2 major late and peptide IX genes was assembled into nucleosomes in vitro, and the assembled nucleosomes were used as a template to study the regulatory mechanism of transcription initiation under these conditions. Neither the major late nor peptide IX genes was transcribed on the already-assembled nucleosomes. However, the major late gene, but not the peptide IX gene, was transcribed efficiently when the DNA was incubated with HeLa cell extracts prior to assembly into nucleosomes. These results indicate that prebinding of some component in the cell extracts to DNA is essential to activate transcription of the major late gene on nucleosomes assembled under the conditions used here. Since gene IX on the nucleosomes was not transcriptionally active regardless of preincubation of DNA with the extracts, some other component or another, different template structure which is not able to be identified in an in vitro system with deproteinized DNA template might be required for activation of peptide IX gene transcription. To know the function of the upstream sequences of the major late gene, effects of the deletion on transcription of nucleosomes were compared with that of deproteinized DNA. The result showed that depression of transcription by deleting the upstream sequences had more effect on nucleosomes than on deproteinized DNA.

Transcription of eucaryotic tRNA1met and 5SRNA genes by RNA polymerase III is blocked by base mismatches in the intragenic control regions

We have constructed duplex DNAs containing single G-T or A-C mismatches in the X. laevis tRNA1met gene. Mismatches within regions of this gene which are bound by transcription factor TFIIIC prevent transcription by RNA polymerase III. Homoduplexes with G-C----A-T mutations at some of the same sites, however, are transcribed efficiently in oocytes. Mismatches outside of the tRNA1met gene have no effect upon transcription. A survey of several point mutants in the Syrian hamster 5SRNA gene indicates that mismatches outside the internal control region somewhat reduce transcription, but a mismatch within the internal control region blocks transcription. Thus, the presence of mismatched bases in the region of DNA which interacts with RNA polymerase III transcription factors blocks transcription, perhaps by interfering with DNA renaturation following transit of the RNA polymerase.

pBR322 DNA inhibits simian virus 40 gene expression in Xenopus laevis oocytes

SV40 DNA form I is expressed efficiently after its injection into the nuclei of Xenopus laevis oocytes, resulting in the synthesis of RNA and protein products of both viral late and early transcription units. However it was observed that injection of SV40 genes cloned into pBR322 or related plasmids yielded vastly reduced quantities of viral DNA and proteins. If SV40 DNA was cleaved from the plasmid, and then recircularized prior to microinjection, viral expression was regained. The inhibition by plasmid DNA was not confined to an effect in cis because coinjection of circular pBR322 DNA along with SV40 DNA, as separate entities, also blocked viral RNA and protein synthesis. As circular but not linear pBR322 DNA was actively transcribed by polymerase II in oocytes, even in the presence of SV40 DNA, it is likely that pBR322 competes for transcription factors required for viral gene expression. Injection of pBR322 as early as two hours after injection of SV40 DNA into the oocyte nucleus did not inhibit SV40 RNA synthesis, indicating that once initiated, SV40 transcription is stable and insensitive to the competition by plasmid DNA. A plasmid vector was developed that allows expression of SV40 DNA in Xenopus laevis oocytes.

Structural and functional analysis of chicken U4 small nuclear RNA genes

Two distinct chicken U4 RNA genes have been cloned and characterized. They are closely linked within 465 base pairs of each other and have the same transcriptional orientation. The downstream U4 homology is a true gene, based on the criteria that it is colinear with chicken U4B RNA and is expressed when injected into Xenopus laevis oocytes. The upstream U4 homology, however, contains seven base substitutions relative to U4B RNA. This sequence may be a nonexpressed pseudogene, but the pattern of base substitutions suggests that it more probably encodes a variant yet functional U4 RNA product not yet characterized at the RNA level. In support of this, the two U4 genes have regions of homology with each other in their 5'-flanking DNA at two positions known to be essential for the efficient expression of vertebrate U1 and U2 small nuclear RNA genes. In the case of U1 and U2 RNA genes, the more distal region (located near position-200 with respect to the RNA cap site) is known to function as a transcriptional enhancer. Although this region is highly conserved in overall structure and sequence among U1 and U2 RNA genes, it is much less conserved in the chicken U4 RNA genes reported here. Interestingly, short sequence elements present in the -200 region of the U4 RNA genes are inverted (i.e., on the complementary strand) relative to their usual orientation upstream of U1 and U2 RNA genes. Thus, the -200 region of the U4 RNA genes may represent a natural evolutionary occurrence of an enhancer sequence inversion.

Topological characterization of the simian virus 40 transcription complex

We have used sedimentation analysis as well as agarose gel electrophoresis to characterize the topological state of the DNA of the Simian Virus 40 (SV40) transcription complex. We found that the complex DNA contained constrained topological tension, presumably resulting from nucleosome-like structures, but no detectable unconstrained (i.e., relaxable) topological tension. These results contradict previous conclusions that the SV40 transcription complex contains only unconstrained topological tension. Our findings are also the opposite of what has been proposed to be the case for the 5S gene analyzed in Xenopus oocytes. Thus the proposal that expression from the 5S gene is associated with substantial topological tension is not valid for expression from the SV40 late gene.

Peptides regulate the activity of RNA polymerases in Tetrahymena

An exponentially multiplying population of the protozoa Tetrahymena has a highly variable transcription rate when cultivated in a complex broth medium. It is shown that peptides in the medium specifically stimulate transcription and that the cells in response synthesize a peptide with a molecular weight of 3000-4000. This peptide inhibits transcription in vivo in cells with high rates of transcription and in in vitro transcription systems. We have partially purified radioactively labelled inhibitor peptide and found that cells stimulated to high transcription rate selectively accumulate inhibitor peptide in the nuclei. In vitro experiments have shown that the inhibitor peptide can reduce the RNA polymerase activity in the nuclei. The presence of inhibitor seems to lower the affinity of RNA-polymerases towards DNA and to increase their release during incubation of isolated nuclei. On the other hand, stimulatory peptides will compete with the inhibitor, and the polymerase activity in isolated nuclei is determined--at least partially--by the ratio between stimulatory and inhibitory peptide factors. It is suggested that regulatory peptides also are involved in regulation of transcription in vivo.

Upstream domains of the Xenopus laevis rDNA promoter are revealed in microinjected oocytes

The DNA sequences involved in promoting transcription of the Xenopus laevis rRNA genes were determined by microinjecting a series of deletion mutants into oocyte nuclei. A very small promoter region is sufficient to direct efficient transcription when templates are microinjected at high rDNA concentration, since 5'delta- 9 and 3'delta +6 templates are fully active. However, as the concentration of injected template is decreased, an increasing requirement for upstream domains, extending to nucleotide approximately -170, is observed. The major downstream border of the required region does not change. This apparently expanding 5' promoter border results from the fact that, as the rDNA concentration is decreased, transcription from templates lacking the upstream promoter domain falls off much more sharply than does transcription from a complete promoter. In fact, the deleted promoters are virtually inactive below a threshold rDNA concentration. It is indeed the rDNA concentration that is important, for coinjected vector DNA does not increase the level of transcription obtained from low concentrations of the 5' deletions. From these data we conclude that polymerase I transcription factors can recognize and initiate transcription from a small core promoter domain, but that sequences extending upstream to nucleotide approximately -170 increase the efficiency of initiation. A model is presented that could account for these results.

Myeloma mutant with a novel 3' flanking region: loss of normal sequence and insertion of repetitive elements leads to decreased transcription but normal processing of the alpha heavy-chain gene products

We isolated and characterized LP1.2, a mouse myeloma mutant with a deletion of at least 4 kilobases (kb) immediately 3' of the alpha gene and introduction of at least 5 kb of novel (nonimmunoglobulin) sequence in its place. A 6.2-kb genomic EcoRI fragment from the mutated allele was cloned, and a subfragment was sequenced. The deletion begins 11 base pairs (bp) beyond the normal site of cleavage and polyadenylation for the secreted form of alpha mRNA. A short direct repeat, eight copies of the 17-mer GCCT ATAGAAGTAAGGA, is located at the junction of the alpha and novel sequences. The first 4 bp of the 17-mer are identical to the last 4 bp of the alpha sequence. Novel sequences downstream of the direct repeats in LP1.2 include a low-copy-number sequence flanked by two distinct, highly repetitive elements. The low-copy-number portion of the novel sequence appears on a single 30-kb EcoRI fragment in several myelomas and in liver DNA; one copy of this fragment has rearranged in cell line W3129, and this allele has rearranged a second time in LP1.2. LP1.2 contains low levels of apparently normal alpha protein and mRNA. The S1 nuclease protection of nuclear and cytoplasmic RNAs shows that cleavage and polyadenylation are efficient and accurate and that they occur without the accumulation of aberrant transcripts. Alpha transcription in isolated nuclei is decreased sevenfold in LP1.2 relative to its parent, which accounts for the low steady-state levels of cytoplasmic alpha mRNA and protein in LP1.2. Decreased alpha transcription could result either from the deletion of a positive regulator in the 3' flanking region or from the introduction of novel sequences which exert a negative effect.

Rapid enrichment of HeLa transcription factors IIIB and IIIC by using affinity chromatography based on avidin-biotin interactions

Plasmid DNA containing the adenovirus type 2 genes for VA RNA was linearized at a site distal to the gene, end labeled with a biotin-nucleotide analog of TTP, and incubated with avidin to form an avidin-biotinylated DNA complex. HeLa cell S100 extracts containing crude RNA polymerase III and transcription factors (TFs) IIIB and IIIC were programmed with the avidin-biotin-VA DNA to allow stable complex formation (A.B. Lassar, P.L. Martin, and R.G. Roeder, Science 222:740-748, 1983). Chromatography of the programmed extract over a biotin-cellulose affinity resin resulted in the selective, and virtually quantitative, retention of one of two stable preinitiation complexes, either VA-IIIC or VA-IIIC-IIIB, depending on the length of template incubation in the S100 extract. After washing the resin with 0.10 M and 0.25 M KCl to remove RNA polymerase III and nonspecifically bound proteins, respectively, TFIIIC was eluted from the VA-IIIC complex by the addition of 1.5 M KCl. The VA-IIIC-IIIB complex exhibited a higher salt stability. Most of TFIIIB and some TFIIIC were released by the addition of 1.5 M KCl; however, the majority of TFIIIC activity was recovered only after a subsequent 3.0 M KCl elution. The specific activity of the TFIIIC in the 3.0 M KCl fraction was 770-fold higher than that in the S100 extract, while the protein content of the 1.5 and 3.0 M KCl fractions was reduced 7,500- and 100,000-fold, respectively.

Structural and functional analysis of chicken U4 small nuclear RNA genes

Two distinct chicken U4 RNA genes have been cloned and characterized. They are closely linked within 465 base pairs of each other and have the same transcriptional orientation. The downstream U4 homology is a true gene, based on the criteria that it is colinear with chicken U4B RNA and is expressed when injected into Xenopus laevis oocytes. The upstream U4 homology, however, contains seven base substitutions relative to U4B RNA. This sequence may be a nonexpressed pseudogene, but the pattern of base substitutions suggests that it more probably encodes a variant yet functional U4 RNA product not yet characterized at the RNA level. In support of this, the two U4 genes have regions of homology with each other in their 5'-flanking DNA at two positions known to be essential for the efficient expression of vertebrate U1 and U2 small nuclear RNA genes. In the case of U1 and U2 RNA genes, the more distal region (located near position-200 with respect to the RNA cap site) is known to function as a transcriptional enhancer. Although this region is highly conserved in overall structure and sequence among U1 and U2 RNA genes, it is much less conserved in the chicken U4 RNA genes reported here. Interestingly, short sequence elements present in the -200 region of the U4 RNA genes are inverted (i.e., on the complementary strand) relative to their usual orientation upstream of U1 and U2 RNA genes. Thus, the -200 region of the U4 RNA genes may represent a natural evolutionary occurrence of an enhancer sequence inversion.

Sequence-dependent DNA replication in preimplantation mouse embryos

Circular, double-stranded DNA molecules were injected into nuclei of mouse oocytes and one- or two-cell embryos to determine whether specific sequences were required to replicate DNA during mouse development. Although all of the injected DNAs were stable, replication of plasmid pML-1 DNA was not detected unless it contained either polyomavirus (PyV) or simian virus 40 (SV40) DNA sequences. Replication occurred in embryos, but not in oocytes. PyV DNA, either alone or recombined with pML-1, underwent multiple rounds of replication to produce superhelical and relaxed circular monomers after injection into one- or two-cell embryos. SV40 DNA also replicated, but only 3% as well as PyV DNA. Coinjection of PyV DNA with either pML-1 or SV40 had no effect on the replicating properties of the three DNAs. These results are consistent with a requirement for specific cis-acting sequences to replicate DNA in mammalian embryos, in contrast to sequence-independent replication of DNA injected into Xenopus eggs. Furthermore, PyV DNA replication in mouse embryos required PyV large T-antigen and either the alpha-beta-core or beta-core configuration of the PyV origin of replication. Although the alpha-core configuration replicated in differentiated mouse cells, it failed to replicate in mouse embryos, demonstrating cell-specific activation of an origin of replication. Replication or expression of PyV DNA interfered with normal embryonic development. These results reveal that mouse embryos are permissive for PyV DNA replication, in contrast to the absence of PyV DNA replication and gene expression in mouse embryonal carcinoma cells.

The positive transcription factor of the 5S RNA gene proteolyses during direct exchange between 5S DNA sites

We have examined the association, dissociation, and exchange of the 5S specific transcription factor (TFIIIA) with somatic- and oocyte-type 5S DNA. The factor associates faster with somatic than with oocyte 5S DNA, and the rate of complex formation is accelerated by vector DNA. Once formed, the TFIIIA-5S DNA complex is stable for greater than 4 h in the absence of free 5S DNA, and its dissociation is identical for somatic and for oocyte 5S DNA. In the presence of free 5S DNA, the factor transfers promptly from the complex to the free 5S DNA site. Unexpectedly, the direct exchange of factor between 5S DNA sites leads to proteolysis at the C-terminal arm of TFIIIA.

Expression of simian virus 40 early and late genes in mouse oocytes and embryos

Simian virus 40 (SV40) large- and small-tumor antigens (T-Ag, t-Ag) are normally synthesized early after infection of either permissive (monkey) or nonpermissive (mouse) fibroblasts, whereas an equivalent amount of viral coat protein (V-Ag) is observed late after infection of permissive cells and only after viral DNA replication has occurred. To determine whether or not expression of these genes is regulated in the same manner during early mammalian development, SV40 DNA was injected into the nuclei of mouse oocytes and one- and two-cell embryos. In oocytes, about three times more V-Ag was produced than T-Ag, and both were synthesized concomitantly in the same cells. Viral mRNA and proteins synthesized in oocytes comigrated during gel electrophoresis with the same products synthesized in SV40-infected monkey cells. Viral gene expression required circular DNA molecules injected into the nuclei of transcriptionally and translationally active cells. Injected DNA was stable and underwent conformational changes consistent with chromatin assembly. Oocytes did not replicate either polyomavirus or SV40 DNA. Thus, the temporal order of viral gene expression is circumvented in mouse germ cells, allowing these proteins to be expressed concurrently and in equivalent amounts with no requirement for DNA replication. However, in preimplantation embryos, neither T-Ag nor V-Ag was detected by immunoprecipitation although T-Ag synthesis was demonstrated as a specific requirement for SV40 DNA replication. Thus, viral gene expression in mouse embryos as early as the one-cell stage was reduced at least 500-fold relative to that in oocytes. Similarities between SV40 gene expression in mouse oocytes and that in Xenopus oocytes suggest that germ cells in higher animals share common regulatory mechanisms.

Rapid enrichment of HeLa transcription factors IIIB and IIIC by using affinity chromatography based on avidin-biotin interactions

Plasmid DNA containing the adenovirus type 2 genes for VA RNA was linearized at a site distal to the gene, end labeled with a biotin-nucleotide analog of TTP, and incubated with avidin to form an avidin-biotinylated DNA complex. HeLa cell S100 extracts containing crude RNA polymerase III and transcription factors (TFs) IIIB and IIIC were programmed with the avidin-biotin-VA DNA to allow stable complex formation (A.B. Lassar, P.L. Martin, and R.G. Roeder, Science 222:740-748, 1983). Chromatography of the programmed extract over a biotin-cellulose affinity resin resulted in the selective, and virtually quantitative, retention of one of two stable preinitiation complexes, either VA-IIIC or VA-IIIC-IIIB, depending on the length of template incubation in the S100 extract. After washing the resin with 0.10 M and 0.25 M KCl to remove RNA polymerase III and nonspecifically bound proteins, respectively, TFIIIC was eluted from the VA-IIIC complex by the addition of 1.5 M KCl. The VA-IIIC-IIIB complex exhibited a higher salt stability. Most of TFIIIB and some TFIIIC were released by the addition of 1.5 M KCl; however, the majority of TFIIIC activity was recovered only after a subsequent 3.0 M KCl elution. The specific activity of the TFIIIC in the 3.0 M KCl fraction was 770-fold higher than that in the S100 extract, while the protein content of the 1.5 and 3.0 M KCl fractions was reduced 7,500- and 100,000-fold, respectively.

Expression of transfected DNA depends on DNA topology

Supercoiled DNAs, especially those containing enhancers, yield markedly higher levels of expression than linearized DNA when transfected into CV-1 cells or L cells. Different templates, linear or supercoiled, enhancer-containing or not, saturate for expression at 2 micrograms DNA per dish, suggesting that one role for enhancers and supercoiling is to increase the efficiency with which the same limiting component is used. Plasmids containing only enhancers or only promoters do not compete for expression with an enhancer-driven gene. However, plasmids that contain both enhancers and promoters do complete, suggesting that a second role for enhancers is to increase the binding of a limiting transcription factor. Linear and supercoiled enhancer-promoter plasmids compete equivalently. This suggests that supercoiling affects the ability of transcription factors to activate a given promoter, once bound.

Mechanism of chromatin assembly in Xenopus oocytes

We have analyzed the chromatin assembly reaction catalyzed by the Xenopus oocyte extract (S-150). A 50 S complex is formed upon mixing the 17 S pUC DNA and the S-150. Mature histones are not detected in this complex, which contains relaxed DNA and protein, and generates subnucleosomal 7 S particles upon digestion with micrococcal nuclease. The relaxed nucleoprotein is gradually supercoiled into nucleosomal chromatin in the S-150, via a pathway that requires ATP and is blocked by novobiocin, and this process is accompanied by the appearance of mature histones H3 and H4. Isolated complexes also supercoil in vitro, which implies the complex is a kit that contains histone precursors, as well as topoisomerases and other enzymes required for assembly. We discuss the biological implications of these findings.

Myeloma mutant with a novel 3' flanking region: loss of normal sequence and insertion of repetitive elements leads to decreased transcription but normal processing of the alpha heavy-chain gene products

We isolated and characterized LP1.2, a mouse myeloma mutant with a deletion of at least 4 kilobases (kb) immediately 3' of the alpha gene and introduction of at least 5 kb of novel (nonimmunoglobulin) sequence in its place. A 6.2-kb genomic EcoRI fragment from the mutated allele was cloned, and a subfragment was sequenced. The deletion begins 11 base pairs (bp) beyond the normal site of cleavage and polyadenylation for the secreted form of alpha mRNA. A short direct repeat, eight copies of the 17-mer GCCT ATAGAAGTAAGGA, is located at the junction of the alpha and novel sequences. The first 4 bp of the 17-mer are identical to the last 4 bp of the alpha sequence. Novel sequences downstream of the direct repeats in LP1.2 include a low-copy-number sequence flanked by two distinct, highly repetitive elements. The low-copy-number portion of the novel sequence appears on a single 30-kb EcoRI fragment in several myelomas and in liver DNA; one copy of this fragment has rearranged in cell line W3129, and this allele has rearranged a second time in LP1.2. LP1.2 contains low levels of apparently normal alpha protein and mRNA. The S1 nuclease protection of nuclear and cytoplasmic RNAs shows that cleavage and polyadenylation are efficient and accurate and that they occur without the accumulation of aberrant transcripts. Alpha transcription in isolated nuclei is decreased sevenfold in LP1.2 relative to its parent, which accounts for the low steady-state levels of cytoplasmic alpha mRNA and protein in LP1.2. Decreased alpha transcription could result either from the deletion of a positive regulator in the 3' flanking region or from the introduction of novel sequences which exert a negative effect.