Intrinsic sites of transcription termination and pausing in the c-myc gene

Transcription Regulation in Archaea

The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription.

BET bromodomain inhibitors synergize with ATR inhibitors to induce DNA damage, apoptosis, senescence-associated secretory pathway and ER stress in Myc-induced lymphoma cells

Inhibiting the bromodomain and extra-terminal (BET) domain family of epigenetic reader proteins has been shown to have potent anti-tumoral activity, which is commonly attributed to suppression of transcription. In this study, we show that two structurally distinct BET inhibitors (BETi) interfere with replication and cell cycle progression of murine Myc-induced lymphoma cells at sub-lethal concentrations when the transcriptome remains largely unaltered. This inhibition of replication coincides with a DNA-damage response and enhanced sensitivity to inhibitors of the upstream replication stress sensor ATR in vitro and in mouse models of B-cell lymphoma. Mechanistically, ATR and BETi combination therapy cause robust transcriptional changes of genes involved in cell death, senescence-associated secretory pathway, NFkB signaling and ER stress. Our data reveal that BETi can potentiate the cell stress and death caused by ATR inhibitors. This suggests that ATRi can be used in combination therapies of lymphomas without the use of genotoxic drugs.

Ubiquitylation and degradation of elongating RNA polymerase II: the last resort

During its journey across a gene, RNA polymerase II has to contend with a number of obstacles to its progression, including nucleosomes, DNA-binding proteins, DNA damage, and sequences that are intrinsically difficult to transcribe. Not surprisingly, a large number of elongation factors have evolved to ensure that transcription stalling or arrest does not occur. If, however, the polymerase cannot be restarted, it becomes poly-ubiquitylated and degraded by the proteasome. This process is highly regulated, ensuring that only RNAPII molecules that cannot otherwise be salvaged are degraded. In this review, we describe the mechanisms and factors responsible for the last resort mechanism of transcriptional elongation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.

Isolation and functional analysis of RNA polymerase II elongation complexes

The elongation phase of transcription by RNA polymerase II (RNAP II) is tightly controlled by a large number of transcription elongation factors. Here we describe experimental approaches for the isolation of RNAPII elongation complexes in vitro and the use of these complexes in the examination of the function of a variety of factors. The methods start with formation of elongation complexes on DNA templates immobilized to paramagnetic beads. Elongation is halted by removing the nucleotides and the ternary elongation complexes are then stripped of factors by a high salt wash. The effect of any factor or mixture of factors on elongation is determined by adding the factor(s) along with nucleotides and observing the change in the pattern of RNAs generated. Association of a factor with elongation complexes can be examined using an elongation complex-electrophoretic mobility shift assay (EC-EMSA) in which elongation complexes that have been liberated from the beads are analyzed on a native gel. Besides being used to dissect the mechanisms of elongation control, these experimental systems are useful for analyzing the function of termination factors and mRNA processing factors. Together these experimental systems permit detailed characterization of the molecular mechanisms of elongation, termination, and mRNA processing factors by providing information concerning both physical interactions with and functional consequences of the factors on RNAPII elongation complexes.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1)

Glucocorticoid (GC) effects are mediated by the glucocorticoid receptor (GR). Several studies have demonstrated that a lower number of receptors per cell were associated with poor GC response. The regulation of GR expression is complex; the levels of GR can be autologously regulated by its ligand and also by transcriptional, post-transcriptional and post-translational mechanisms. Using three human myeloma cell lines that parallel the development of GC resistance, this work describes the mechanism involved in the downregulation of GR expression. The decreased expression was neither due to mutations in the gene encoding GR, NR3C1, nor due to methylation of the promoters. A gradual decrease in NR3C1 transcripts was seen during the development of resistance, the level of expression of exon 1 to 2 RNA fragments remained the same in sensitive and resistant cell lines but a chromatin immunoprecipitation assay demonstrated that RNA polymerase II, detectable throughout exon 2 to 3 in the sensitive cells, was undetectable on exon 3 in the resistant variant, suggesting lower or no transcription at this site. These studies demonstrated that downregulation of NR3C1 mRNA in a resistant cell line involves a block to transcriptional elongation within intron B of NR3C1. This block may represent an important element in the regulation of GR expression.

Knockdown of TFIIS by RNA silencing inhibits cancer cell proliferation and induces apoptosis

Background

A common element among cancer cells is the presence of improperly controlled transcription. In these cells, the degree of specific activation of some genes is abnormal, and altering the aberrant transcription may therefore directly target cancer. TFIIS is a transcription elongation factor, which directly binds the transcription motor, RNA Polymerase II and allows it to read through various transcription arrest sites. We report on RNA interference of TFIIS, a transcription elongation factor, and its affect on proliferation of cancer cells in culture.

Methods

RNA interference was performed by transfecting siRNA to specifically knock down TFIIS expression in MCF7, MCF10A, PL45 and A549 cells. Levels of TFIIS expression were determined by the Quantigene method, and relative protein levels of TFIIS, c-myc and p53 were determined by C-ELISA. Induction of apoptosis was determined by an enzymatic Caspase 3/7 assay, as well as a non-enzymatic assay detecting cytoplasmic mono- and oligonucleosomes. A gene array analysis was conducted for effects of TFIIS siRNA on MCF7 and MCF10A cell lines.

Results

Knockdown of TFIIS reduced cancer cell proliferation in breast, lung and pancreatic cancer cell lines. More specifically, TFIIS knockdown in the MCF7 breast cancer cell line induced cancer cell death and increased c-myc and p53 expression whereas TFIIS knockdown in the non-cancerous breast cell line MCF10A was less affected. Differential effects of TFIIS knockdown in MCF7 and MCF10A cells included the estrogenic, c-myc and p53 pathways, as observed by C-ELISA and gene array, and were likely involved in MCF7 cell-death.

Conclusion

Although transcription is a fundamental process, targeting select core transcription factors may provide for a new and potent avenue for cancer therapeutics. In the present study, knockdown of TFIIS inhibited cancer cell proliferation, suggesting that TFIIS could be studied as a potential cancer target within the transcription machinery.

Effect of length variations at nucleotide positions 303-315 in human mitochondrial DNA on transcription termination

In addition to stabilizing the RNA-DNA hybrid, conserved sequence block (CSB) II, which is located at nucleotides 299-315 on mitochondrial DNA, relates with the transcription termination for initiation of heavy strand synthesis in human mitochondrial replication. Due to length polymorphisms at nucleotides 303-315, individuals contain homo- or heteroplasmic profiles with length variants from C(5)TC(6) to C(15)TC(6) or from C(9) to C(13). Using in vitro transcription with templates containing these variations, we demonstrated that the production of prematurely terminated (PT) transcripts depends on the 303-315 sequences, and that longer templates result in relatively higher levels of PT transcripts. The 3' ends of PT transcripts were observed within or downstream of CSB II. Termination positions downstream of nucleotide 303 were shifted upstream by longer variations, but not shifted by shorter variations. We found that length variations between 303 and 315 generate quantitative and qualitative differences in PT transcripts.

Downstream DNA selectively affects a paused conformation of human RNA polymerase II

Transcriptional pausing by human RNA polymerase II (RNAPII) in the HIV-1 LTR is caused principally by a weak RNA:DNA hybrid that allows rearrangement of reactive or catalytic groups in the enzyme's active site. This rearrangement creates a transiently paused state called the unactivated intermediate that can backtrack into a more long-lived paused species. We report that three different regions of the not-yet-transcribed DNA just downstream of the pause site affect the duration of the HIV-1 pause, and also can influence pause formation. Downstream DNA in at least one region, a T-tract from +5 to +8, increases pause duration by specifically affecting the unactivated intermediate, without corresponding effects on the active or backtracked states. We suggest this effect depends on RNAPII-modulated DNA plasticity and speculate it is mediated by the "trigger loop" thought to participate in RNAP's catalytic cycle. These findings provide a new framework for understanding downstream DNA effects on RNAP.

Transcription attenuation

In this review, we describe a variety of mechanisms that bacteria use to regulate transcription elongation in order to control gene expression in response to changes in their environment. Together, these mechanisms are known as attenuation and antitermination, and both involve controlling the formation of a transcription terminator structure in the RNA transcript prior to a structural gene or operon. We examine attenuation and antitermination from the point of view of the different biomolecules that are used to influence the RNA structure. Attenuation of many amino acid biosynthetic operons, particularly in enteric bacteria, is controlled by ribosomes translating leader peptides. RNA-binding proteins regulate attenuation, particularly in gram-positive bacteria such as Bacillus subtilis. Transfer RNA is also used to bind to leader RNAs and influence transcription antitermination in a large number of amino acyl tRNA synthetase genes and several biosynthetic genes in gram-positive bacteria. Finally, antisense RNA is involved in mediating transcription attenuation to control copy number of several plasmids.

In vivo and in vitro studies of immunoglobulin gene somatic hypermutation

Following antigen encounter, two distinct processes modify immunoglobulin genes. The variable region is diversified by somatic hypermutation while the constant region may be changed by class-switch recombination. Although both genetic events can occur concurrently within germinal centre B cells, there are examples of each occurring independently of the other. Here we compare the contributions of class-switch recombination and somatic hypermutation to the diversification of the serum immunoglobulin repertoire and review evidence that suggests that, despite clear differences, the two processes may share some aspects of their mechanism in common.

The c-MYC allele that is translocated into the IgH locus undergoes constitutive hypermutation in a Burkitt's lymphoma line

Burkitt's lymphomas harbour chromosomal translocations bringing c-MYC into the vicinity of one of the immunoglobulin gene loci. Point mutations have been described within c-MYC in several Burkitt's lymphomas and it has been proposed that translocation into the Ig loci might have transformed c-MYC into a substrate for the antibody hypermutation mechanism. Here we test this hypothesis by exploiting a Burkitt's lymphoma line (Ramos) that we have previously shown to hypermutate its immunoglobulin genes constitutively. We find that, during in vitro culture, Ramos mutates the c-MYC allele that is translocated into the IgH locus whilst leaving the untranslocated c-MYC and other control genes essentially unaffected. The mutations are introduced downstream of the c-MYC transcription start with the pattern of substitutions being characteristic of the antibody hypermutation mechanism; the mutation frequency is 2-3-fold lower than for the endogenous functional IgH allele. Thus chromosomal translocations involving the Ig loci may not only contribute to transformation by deregulating oncogene expression but could also act by potentiating subsequent oncogene hypermutation.

Transcriptional pause, arrest and termination sites for RNA polymerase II in mammalian N- and c-myc genes

Using either highly purified RNA polymerase II (pol II) elongation complexes assembled on oligo(dC)-tailed templates or promoter-initiated (extract-generated) pol II elongation complexes, the precise 3" ends of transcripts produced during transcription in vitro at several human c- and N- myc pause, arrest and termination sites were determined. Despite a low overall similarity between the entire c- and N- myc first exon sequences, many positions of pol II pausing, arrest or termination occurred within short regions of related sequence shared between the c- and N- myc templates. The c- and N- myc genes showed three general classes of sequence conservation near intrinsic pause, arrest or termination sites: (i) sites where arrest or termination occurred after the synthesis of runs of uridines (Us) preceding the transcript 3" end, (ii) sites downstream of potential RNA hairpins and (iii) sites after nucleotide addition following either a U or a C or following a combination of several pyrimidines near the transcript 3" end. The finding that regions of similarity occur near the sites of pol II pausing, arrest or termination suggests that the mechanism of c- and N- myc regulation at the level of transcript elongation may be similar and not divergent as previously proposed.

Protein kinase C inhibits transcription from the RNA polymerase III promoter of the human c-myc gene

The c-myc promoter has a unique characteristic showing both RNA polymerase II (pol II) and RNA polymerase III (pol III) activities. Previous studies demonstrated that activating PKC results in upregulation of c-myc expression from its pol II promoter. However, how PKC activation affects expression from the pol III promoter of the c-myc gene is not well understood. This study examines the effect of PKC on the pol III transcription from the c-myc gene by using an in vitro system. We report the inhibition of the c-myc pol III transcript by activating PKC. Further, either a phosphocellulose fraction of HeLa whole cell extract (WCE) enriched for transcription factor TF IIIB, or recombinant TATA-box binding protein could restore the inhibited c-myc pol III transcription under conditions that activate PKC. A role has been proposed for the c-myc pol III transcript in the regulation of c-myc gene expression. Therefore, this report discusses the significance of the downregulation of c-myc expression from its pol III promoter and the possible interplay between the pol II and pol III promoters of this gene.

Basic mechanisms of transcript elongation and its regulation

Ternary complexes of DNA-dependent RNA polymerase with its DNA template and nascent transcript are central intermediates in transcription. In recent years, several unusual biochemical reactions have been discovered that affect the progression of RNA polymerase in ternary complexes through various transcription units. These reactions can be signaled intrinsically, by nucleic acid sequences and the RNA polymerase, or extrinsically, by protein or other regulatory factors. These factors can affect any of these processes, including promoter proximal and promoter distal pausing in both prokaryotes and eukaryotes, and therefore play a central role in regulation of gene expression. In eukaryotic systems, at least two of these factors appear to be related to cellular transformation and human cancers. New models for the structure of ternary complexes, and for the mechanism by which they move along DNA, provide plausible explanations for novel biochemical reactions that have been observed. These models predict that RNA polymerase moves along DNA without the constant possibility of dissociation and consequent termination. A further prediction of these models is that the polymerase can move in a discontinuous or inchworm-like manner. Many direct predictions of these models have been confirmed. However, one feature of RNA chain elongation not predicted by the model is that the DNA sequence can determine whether the enzyme moves discontinuously or monotonically. In at least two cases, the encounter between the RNA polymerase and a DNA block to elongation appears to specifically induce a discontinuous mode of synthesis. These findings provide important new insights into the RNA chain elongation process and offer the prospect of understanding many significant biological regulatory systems at the molecular level.

Intrinsic termination of T7 RNA polymerase mediated by either RNA or DNA

Intrinsic termination of T7 RNA polymerase transcription occurs at different signals in vitro. One type of signal is similar to that mediating factor-independent termination of Escherichia coli RNA polymerase, whereas the other type does not involve RNA hairpin formation. By examining the termination behaviour of T7 RNA polymerase at the E.coli rrnB operon t1 terminator, at the T7-t(phi) terminator, at the human preproparathyroid hormone gene terminator on both single- and double-stranded templates, and in the presence of GTP or ITP during transcription, we show that the termination event can be mediated by either RNA or DNA structural features. Moreover, by using co-transcriptional probing with potassium permanganate, we present evidence for the presence of transcription-induced hyperreactive thymidines on the non-template strand in the DNA-mediated event, and a putative sequence motif is identified. We conclude that intrinsic termination of T7 RNA polymerase transcription in vitro can be mediated either by a hairpin in the nascent RNA or by a sequence motif including hyperreactive thymidines in the non-template DNA strand.

Amanitin greatly reduces the rate of transcription by RNA polymerase II ternary complexes but fails to inhibit some transcript cleavage modes

The toxin alpha-amanitin is frequently employed to completely block RNA synthesis by RNA polymerase II. However, we find that polymerase II ternary transcription complexes stalled by the absence of NTPs resume RNA synthesis when NTPs and amanitin are added. Chain elongation with amanitin can continue for hours at approximately 1% of the normal rate. Amanitin also greatly slows pyrophosphorolysis by elongation-competent complexes. Complexes which are arrested (that is, which have paused in transcription for long periods in the presence of excess NTPs) are essentially incapable of resuming transcription in the presence of alpha-amanitin. Complexes traversing sequences that can provoke arrest are much more likely to stop transcription in the presence of the toxin. The substitution of IMP for GMP at the 3' end of the nascent RNA greatly increases the sensitivity of stalled transcription complexes to amanitin. Neither arrested nor stalled complexes display detectable SII-mediated transcript cleavage following amanitin treatment. However, arrested complexes possess a low level, intrinsic transcript cleavage activity which is completely amanitin-resistant; furthermore, pyrophosphorolytic transcript cleavage in arrested complexes is not affected by amanitin.

c-Myc expression is controlled by the mitogenic cAMP-cascade in thyrocytes

In dog thyroid epithelial cells in primary culture, thyrotropin (TSH), acting through cAMP, induces proliferation and differentiation expression, whereas epidermal growth factor (EGF) and phorbol esters induce proliferation and dedifferentiation. In these cells, we have detailed the regulation by cAMP of the c-myc protooncogene mRNA and protein. The cAMP signaling pathway induces a biphasic increase of c-myc mRNA and protein. c-Myc protein accumulation follows the abundance and kinetics of its mRNA expression. Using in vitro elongation of nascent transcripts to measure transcription and actinomycin D (AcD) chase experiments to study mRNA stability, we have shown that in the first phase cAMP releases a transcriptional elongation block. No modification of transcriptional initiation was observed. After 30 min of treatment with TSH, c-myc mRNA was also stabilized. During the second phase, cAMP stabilization of the mRNA disappears and transcription is again shut off. Thus, in a tissue in which it stimulates proliferation and specific gene expression, cAMP regulates biphasically c-myc expression by mechanisms operating at the transcriptional and posttranscriptional levels.

Galectin-3: differential accumulation of distinct mRNAs in serum-stimulated mouse 3T3 fibroblasts

The murine Galectin-3 gene spans approximately 12 kb of DNA and contains six exons, with the translation initiation codon located in exon II. On the basis of restriction mapping and sequence analysis of the DNA upstream of exon II, primer extension assays, rapid amplification of cDNA ends, and ribonuclease protection assays were designed and carried out to determine the initiation site of transcription and the sequence of exon I. The results revealed at least two transcription initiation sites (alpha and delta), each of which appears to be specifically associated with the use of alternative donor splice sites, resulting in distinct mRNA species. Type I message initiates at transcription start site delta, uses splice donor site No. 2, retaining a 27 bp sequence, whereas type II message initiates at transcription start site alpha, uses splice donor site No. 1, resulting in the loss of the 27 bp sequence. Primer extension assays carried out with mRNA isolated from 3T3 fibroblasts at various times after serum stimulation indicate that while the type II message varies in level only a little over the first 20 h, there is dramatic accumulation of the type I message, which peaks at 16 h post mitogen addition.

Hypermutation of the MYC gene in diffuse large cell lymphomas with translocations involving band 8q24

The sequence of the exon 1/intron 1 boundary region of the MYC gene was determined in two diffuse large cell lymphomas (DLCL), one with t(8;14) (q24;q32) and the other with t(8;22) (q24;q11). Both tumors had multiple mutations in this region. Also, both tumors had mutations in the protein binding site in intron 1, which is a frequent target for mutational inactivation in endemic Burkitt's lymphoma (eBL). The translocations at 8q24, and multiple mutations in the exon 1/intron 1 boundary region, are reminiscent of similar findings in eBL. The same underlying oncogenic event that occurs in most eBLs is thus found in some DLCLs.

Transcription termination

Chromosomes are organized into units of expression that are bounded by sites where transcription of DNA sequences into RNA is initiated and terminated. To allow for efficient stepwise assembly of complete transcripts, the transcribing enzyme (RNA polymerase) makes a stable complex with the DNA template until it reaches the terminator. Three general mechanisms of transcription termination have been recognized: one is by a spontaneous dissociation of the RNA at a sequence segment where RNA polymerase does not maintain its usual stable interaction with the nascent chain; another involves the action of a protein (rho factor in bacteria) on the nascent RNA to mediate its dissociation; and a third involves an action triggered by a protein that binds to the DNA at a sequence that is just downstream of the termination stop point. Transcription termination is important in the regulation of gene expression both by modulating the relative levels of various genes within a single unit of expression and by controlling continuation of transcription in response to a metabolic or regulatory signal.

Stimulation of transcript elongation requires both the zinc finger and RNA polymerase II binding domains of human TFIIS

The eukaryotic transcriptional factor TFIIS enhances transcript elongation by RNA polymerase II. Here we describe two functional domains in the 280 amino acid human TFIIS protein: residues within positions 100-230 are required for binding to polymerase, and residues 230-280, which form a zinc finger, are required in conjunction with the polymerase binding region for transcriptional stimulation. Interestingly, a mutant TFIIS with only the polymerase binding domain actually inhibits transcription, whereas a mutant in which the polymerase binding and zinc finger domains are separated by an octapeptide is only weakly active. The zinc finger itself has no effect on transcription, but in contrast to the wild-type protein, it binds to oligonucleotides. These findings suggest that TFIIS may interact with RNA polymerase II such that the normally masked zinc finger can specifically contact nucleotides in the transcription elongation zone at a position juxtaposed to the polymerization site.

An apparent pause site in the transcription unit of the rabbit alpha-globin gene

Transcription of the rabbit alpha-globin gene begins primarily at the cap site, although some upstream start sites are also observed. Analysis by RNA polymerase run-on assays in nuclei shows that transcription continues at a high level past the polyadenylation site, after which the polymerase density actually increases in a region of about 400 nucleotides, followed by a gradual decline over the 700 nucleotides. These features are also observed in the transcription unit of the rabbit beta-globin gene. The region with the unexpectedly high nascent RNA hybridization signal in the 3' flank contains a conserved sequence, KGCAGCWGGR (K = G or T, W = A or T, R = A or G), followed by an inverted repeat. The inverted repeat (perhaps with the conserved sequence) may be a pause site for RNA polymerase II, thus accounting for the increase in polymerase density. This sequence and inverted repeat are found in the 3' flank of several globin genes and the simian virus 40 (SV40) early genes, as well as in the regions implicated in pausing or termination of transcription of eight different genes. Deletion of the conserved sequence and inverted repeat from the 3' flank of the SV40 early region causes a small increase in the levels of transcription downstream from this site. Replacement with the conserved sequence and inverted repeat from the rabbit alpha-globin gene causes an accumulation of polymerases, supporting the hypothesis that polymerases pause at this site. This proposed pause site may affect the efficiency of termination at some sites further downstream, perhaps by loss of a processivity factor.

RNA polymerase II pauses in vitro, but does not terminate, at discrete sites in promoter-proximal regions on polyomavirus transcription complexes

Many RNA polymerases stall and/or prematurely terminate transcription nearby the early and late promoters of polyomavirus in vivo during the late phase of productive infection. In this paper we analyzed the RNAs made when these promoter-proximal RNA polymerases were allowed to elongate their nascent chains in vitro on viral transcription complexes isolated from infected cells. RNA was labeled in the presence of a high specific activity of one [alpha-32P]-ribonucleoside triphosphate (rNTP) (less than 1 microM final concentration) and saturating concentrations of the other three rNTPs. Under these conditions, promoter-proximal RNAs of discrete sizes were produced. We show that these discrete RNA species are produced by pausing of RNA polymerase II due to limiting concentrations of one of the rNTPs, and that the positions of the pause sites depend on which rNTP is limiting. This pausing does not result in release of the RNA polymerase or the nascent RNA chain from the transcription complex, as these chains can be further extended when high concentrations of all four rNTPs are supplied. Our results conflict with the interpretations of other investigators who suggest that formation of discrete RNA products, under similar in vitro conditions, reflects authentic termination by RNA polymerase II.

Molecular genetic evidence for a differentiation-proliferation coupling during DMSO-induced myeloid maturation of HL-60 cells: role of the transcription elongation block in the c-myc gene

Proliferation-differentiation coupling was studied during dimethyl sulfoxide (DMSO)-induced myeloid maturation of HL-60 cells using transcription of the myeloperoxidase (MPO) and c-myc genes as indicators of differentiation and proliferation, respectively. Concomitant cell cycle kinetic analysis correlated the proliferation and transcription patterns. Transcription, cell cycle phases and rate of DNA synthesis were examined for up to 5 days of induction and, at 1-day intervals, analyzed during a 24-h reculture without the inducer. DMSO suppressed transcription of the c-myc and MPO genes with a t1/2 of 16 min and 7 h, respectively. The ability to recover transcription following reculture diminished with the progression of the induction and ultimately was lost; concomitantly, the cells irreversibly lost the capacity to divide. This indicated that the differentiation and proliferation processes are inseparable and that terminal differentiation accompanies irreversible proliferation arrest in HL-60 cells. We also studied the kinetics of the block to transcription elongation at the exon 1-intron 1 boundary of the c-myc gene. This block produces a 0.38 kb truncated transcript that is constitutively expressed in somatic cells (Re et al., Oncogene 5, 1247, 1990). During induction the level of the 0.38 kb RNA increased, while that of the complete c-myc mRNA decreased, indicating that this truncated RNA is generated instead of message through a monotonously initiated transcriptional process. Transcription initiation and synthesis of the 0.3 kb RNA persisted in terminally differentiated cells, suggesting a role for this RNA in non-proliferating cells.

Analysis of the signals for transcription termination by purified RNA polymerase II

Eukaryotic RNA polymerase II recognizes certain DNA sequences as effective signals for transcription termination in vitro. Previously, we have shown that such termination occurs within T-rich sequences; however, not all T runs stop the enzyme nor is the efficiency of termination correlated with the length of the T run. Here we have investigated the sequence elements that signal transcription termination by purified RNA polymerase II. We have examined terminators located within introns of the human histone H3.3 gene and the human c-myc gene. Deletion analysis of the H3.3 termination region indicates that the sequences between -6 and +24 relative to the strongest termination site are sufficient to cause transcription termination. The minimal termination signal at this site has been localized to the sequence TTTTTTTC-CCTTTTTT in the nontranscribed strand. A similar but nonidentical sequence has been defined for the c-myc termination site. Since RNA polymerase II terminates transcription only within the first run of T residues in these sequences, at least part of the termination signal lies in downstream nontranscribed DNA sequences. Restriction fragment mobility analysis indicates that the H3.3 termination region contains a bend in the DNA helix. Oligonucleotides containing the minimal termination signals also cause restriction fragments to migrate with anomalous mobility. A region of the SV40 genome containing a previously characterized bend also causes RNA polymerase II to terminate transcription. We suggest that a structural element causing a bend in the DNA helix may be part of the signal for transcription termination by purified RNA polymerase II.

Does NF-kappa B relieve the transcription block in c-myc?

In this report, it is shown that the mRNA of the c-myc oncogene is capable of forming an extensive stem-and-loop structure, with a free energy of delta G (25 degrees C) = -34 kcal. This secondary structure is situated at the 3' end of the first exon, immediately upstream of an elongation block. It is shown that this region contains potential binding sites for 3 different activator proteins, namely AP-1, AP-2, and nuclear factor-kappa B (NF-kappa B). From an analysis of the properties of these proteins, NF-kappa B could be identified as a candidate for the trans-acting factor involved in relieving the block to transcription.

A plasmid to visualize and assay termination and antitermination of transcription in Escherichia coli

To facilitate the analysis of termination and antitermination of transcription in prokaryotes, a complex operon has been assembled into the pBR322 replicon, drawing upon natural and synthetic DNA elements. This operon is initiated from a strongly inducible promoter without temperature restraints. It includes a severe transcription terminator and therefore requires antitermination of transcription to express a downstream lacZ reporter gene. Antitermination can be provided by an upstream N-utilization site from phage lambda, working in conjunction with N protein supplied in trans from a compatible plasmid. In this situation, the nusA gene of Salmonella, substituted into the Escherichia coli host, prevents lacZ function, confirming that a good facsimile of lambda's specific antitermination mechanism has been recreated. The nonessential, easily assayed product of this operon, beta-galactosidase, is also screenable by colony color on chromogenic substrate. The plasmid described will therefore serve as a tester for mutations affecting the various aspects of transcription regulation by termination.

The myc family of nuclear proto-oncogenes

Several members of the myc family of proto-oncogenes have been described, and some (c-, N-, and L-myc) have been characterized in considerable detail. They are united by a common gene structure and nucleotide homologies that were used to identify some of them initially. Their protein products also have scattered regions of amino acid identity or homology. Although the cellular activities of the various proteins are unknown, some members may play a role in regulating cell growth and differentiation. They share the ability to cooperate with an activated ras gene and cotransform embryonic rodent cells. In naturally occurring tumors, the members of the myc family of oncogenes appear to be activated by genetic changes (proviral insertion, chromosomal translocation, and gene amplification) that augment or otherwise disrupt normally regulated expression. The members of this family of genes differ markedly in their tissue specificity and developmental regulation of expression. This may account in part for the frequent appearance of activated c-myc genes in a wide variety of neoplasms and the limited appearance of activated N- and L-myc genes in tumors of embryonic or neural origin. The c-myc gene may be activated in tumors by a variety of mechanisms, whereas N- and L-myc appear to be activated only by gene amplification. Regulation of expression of the different myc genes also appears to occur by different mechanisms. Finally, the products of the different genes differ in may regions of the protein, and this divergence probably reflects their specific and individual functions.