Saccharomyces cerevisiae transcription elongation mutants are defective in PUR5 induction in response to nucleotide depletion

IMP dehydrogenase (IMPDH) is the rate-limiting enzyme in the de novo synthesis of guanine nucleotides. It is a target of therapeutically useful drugs and is implicated in the regulation of cell growth rate. In the yeast Saccharomyces cerevisiae, mutations in components of the RNA polymerase II (Pol II) transcription elongation machinery confer increased sensitivity to a drug that inhibits IMPDH, 6-azauracil (6AU), by a mechanism that is poorly understood. This phenotype is thought to reflect the need for an optimally functioning transcription machinery under conditions of lowered intracellular GTP levels. Here we show that in response to the application of IMPDH inhibitors such as 6AU, wild-type yeast strains induce transcription of PUR5, one of four genes encoding IMPDH-related enzymes. Yeast elongation mutants sensitive to 6AU, such as those with a disrupted gene encoding elongation factor SII or those containing amino acid substitutions in Pol II subunits, are defective in PUR5 induction. The inability to fully induce PUR5 correlates with mutations that effect transcription elongation since 6AU-sensitive strains deleted for genes not related to transcription elongation are competent to induce PUR5. DNA encompassing the PUR5 promoter and 5' untranslated region supports 6AU induction of a luciferase reporter gene in wild-type cells. Thus, yeast sense and respond to nucleotide depletion via a mechanism of transcriptional induction that restores nucleotides to levels required for normal growth. An optimally functioning elongation machinery is critical for this response.

Mechanism and regulation of transcriptional elongation by RNA polymerase II

Over the past few years, biochemical and genetic studies have shed considerable light on the structure and function of the RNA polymerase II (pol II) elongation complex and the transcription factors that control it. Novel elongation factors have been identified and their mechanisms of action characterized in increasing detail; new insights into the biological roles of elongation factors have been gained from genetic studies of the regulation of mRNA synthesis in yeast; and intriguing links between the pol II elongation machinery and the pathways of DNA repair and recombination have emerged.

Acetylated histones are associated with FMR1 in normal but not fragile X-syndrome cells

Mutation of FMR1 results in fragile X mental retardation. The most common FMR1 mutation is expansion of a CGG repeat tract at the 5' end of FMR1, which leads to cytosine methylation and transcriptional silencing. Both DNA methylation and histone deacetylation have been associated with transcriptional inactivity. The finding that the methyl cytosine-binding protein MeCP2 binds to histone deacetylases and represses transcription in vivo supports a model in which MeCP2 recruits histone deacetylases to methylated DNA, resulting in histone deacetylation, chromatin condensation and transcriptional silencing. Here we demonstrate that the 5' end of FMR1 is associated with acetylated histones H3 and H4 in cells from normal individuals, but acetylation is reduced in cells from fragile X patients. Treatment of fragile X cells with 5-aza-2'-deoxycytidine (5-aza-dC) resulted in reassociation of acetylated histones H3 and H4 with FMR1 and transcriptional reactivation, whereas treatment with trichostatin A (TSA) led to almost complete acetylated histone H4 and little acetylated histone H3 reassociation with FMR1, as well as no detectable transcription. Our results represent the first description of loss of histone acetylation at a specific locus in human disease, and advance understanding of the mechanism of FMR1 transcriptional silencing.

Mutations in RNA polymerase II and elongation factor SII severely reduce mRNA levels in Saccharomyces cerevisiae

Elongation factor SII interacts with RNA polymerase II and enables it to transcribe through arrest sites in vitro. The set of genes dependent upon SII function in vivo and the effects on RNA levels of mutations in different components of the elongation machinery are poorly understood. Using yeast lacking SII and bearing a conditional allele of RPB2, the gene encoding the second largest subunit of RNA polymerase II, we describe a genetic interaction between SII and RPB2. An SII gene disruption or the rpb2-10 mutation, which yields an arrest-prone enzyme in vitro, confers sensitivity to 6-azauracil (6AU), a drug that depresses cellular nucleoside triphosphates. Cells with both mutations had reduced levels of total poly(A)+ RNA and specific mRNAs and displayed a synergistic level of drug hypersensitivity. In cells in which the SII gene was inactivated, rpb2-10 became dominant, as if template-associated mutant RNA polymerase II hindered the ability of wild-type polymerase to transcribe. Interestingly, while 6AU depressed RNA levels in both wild-type and mutant cells, wild-type cells reestablished normal RNA levels, whereas double-mutant cells could not. This work shows the importance of an optimally functioning elongation machinery for in vivo RNA synthesis and identifies an initial set of candidate genes with which SII-dependent transcription can be studied.

Nucleotide sequence context effect of a cyclobutane pyrimidine dimer upon RNA polymerase II transcription

We have studied the role of sequence context upon RNA polymerase II arrest by a cyclobutane pyrimidine dimer using an in vitro transcription system consisting of templates containing a specifically located cyclobutane pyrimidine dimer (CPD) and purified RNA polymerase II (RNAP II) and initiation factors. We selected a model sequence containing a well characterized site for RNAP II arrest in vitro, the human histone H3.3 gene arrest site. The 13-base pair core of the arrest sequence contains two runs of T in the nontranscribed strand that impose a bend in the DNA. We hypothesized that arrest of RNAP II might be affected by the presence of a CPD, based upon the observation that a CPD located at the center of a dA6.dT6 tract eliminates bending (Wang, C.-I., and Taylor, J.-S. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 9072-9076). We examined the normal H3.3 sequence and a mutant sequence containing a T --> G transversion, which reduces bending and efficiency of arrest. We show that a CPD in the transcribed strand at either of two locations in the arrest site is a potent block to transcription. However, a CPD in the nontranscribed strand only transiently pauses RNAP II. The CPD in concert with a mutation in the arrest site can reduce the extent of bending of the DNA and improve readthrough efficiency. These results demonstrate the potential importance of sequence context for the effect of CPDs within transcribed sequences.

Assays for investigating transcription by RNA polymerase II in vitro

With the availability of the general initiation factors (TFIIB, TFIID, TFIIE, TFIIF, and TFIIH), it is now possible to investigate aspects of the mechanism of eukaryotic messenger RNA synthesis in purified, reconstituted RNA polymerase II transcription systems. Rapid progress in these investigations has been spurred by use of a growing number of assays that are proving valuable not only for dissecting the molecular mechanisms of transcription initiation and elongation by RNA polymerase II, but also for identifying and purifying novel transcription factors that regulate polymerase activity. Here we describe a variety of these assays and discuss their utility in the analysis of transcription by RNA polymerase II.

Glutamic acid-371 of the barnase homology domain in RNA polymerase II is not required for SII-activated RNA cleavage

RNA polymerase II contains a ribonuclease activity which is stimulated by the transcription elongation factor SII. This nuclease shortens the nascent RNA and facilitates relief of transcriptional arrest by allowing the enzyme to make multiple attempts to read through an obstacle to transcription. The catalytic center of this ribonuclease is unknown, although a region of the enzyme's second largest subunit shares local sequence similarly with barnase and other bacterial ribonucleases. To test the role of the barnase homology region in SII-activated cleavage, we engineered a single amino acid change in the Saccharomyces cerevisiae enzyme at a position homologous to a catalytic residue of barnase (Glu-371) and has been suggested as a participant in active site chemistry of RNA polymerase II. We purified RNA polymerase II from mutant yeast and assayed its ability to cleave and re-extend the nascent RNA following SII treatment. We find no defects in this function of the mutant enzyme, suggesting that the barnase homology region does not represent the active site of the SII-activated nuclease. These mutant yeast cells were also resistant to mycophenolic acid, which slows the growth of some yeast mutants bearing elongation defective RNA polymerase II or mutant elongation factor SII.

Elongation factor SII contacts the 3'-end of RNA in the RNA polymerase II elongation complex

Elongation factor SII (also known as TFIIS) is an RNA polymerase II binding protein that allows bypass of template arrest sites by activating a nascent RNA cleavage reaction. Here we show that SII contacts the 3'-end of nascent RNA within an RNA polymerase II elongation complex as detected by photoaffinity labeling. Photocross-linking was dependent upon the presence of SII, incorporation of 4-thio-UMP into RNA, and irradiation and was sensitive to treatment by RNase and proteinase. A transcriptionally active mutant of SII lacking the first 130 amino acids was also cross-linked to the nascent RNA, but SII from Saccharomyces cerevisiae, which is inactive in concert with mammalian RNA polymerase II, failed to become photoaffinity labeled. SII-RNA contact was not detected after a labeled oligoribonucleotide was released from the complex by nascent RNA cleavage, demonstrating that this interaction takes place between elongation complex-associated but not free RNA. This shows that the 3'-end of RNA is near the SII binding site on RNA polymerase II and suggests that SII may activate the intrinsic RNA hydrolysis activity by positioning the transcript in the enzyme's active site.

The RNA polymerase II general elongation factors

Synthesis of eukaryotic messenger RNA by RNA polymerase II is governed by the concerted action of a set of general transcription factors that control the activity of polymerase during both the initiation and elongation stages of transcription. To date, five general elongation factors [P-TEFb, SII, TFIIF, Elongin (SIII) and ELL] have been defined biochemically. Here, we discuss these transcription factors and their roles in controlling the activity of the RNA polymerase II elongation complex.

Transcription elongation factor SII (TCEA) maps to human chromosome 3p22 --> p21.3

Transcription elongation factors assist RNA polymerase II through transcriptional blockages. The human transcriptional elongation factor SII or Trascription Elongation Factor A (TCEA) releases RNA polymerase II from transcriptional arrest and is encoded by a 2.5-kb intronless gene. Using PCR primers, verified by RT-PCR to amplify the authentic, transcriptionally active SII gene, this locus was mapped to human chromosome 3 by examination of a human/rodent somatic cell hybrid panel. PCR analysis of somatic cell hybrids with chromosome 3 translocations and FISH studies utilizing a human YAC clone containing the SII gene further refine the map position of this locus to human chromosome 3p22 --> p21.3. Since another elongation factor, SIII, has been implicated in human carcinogenesis and since the interval within which the human SII gene maps is frequently deleted in certain cancers, elongation factor SII may therefore be considered a candidate gene for human malignancies involving 3p22 --> p21.3.

Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest

RNA polymerases encounter specific DNA sites at which RNA chain elongation takes place in the absence of enzyme translocation in a process called discontinuous elongation. For RNA polymerase II, at least some of these sequences also provoke transcriptional arrest where renewed RNA polymerization requires elongation factor SII. Recent elongation models suggest the occupancy of a site within RNA polymerase that accommodates nascent RNA during discontinuous elongation. Here we have probed the extent of nascent RNA extruded from RNA polymerase II as it approaches, encounters, and departs an arrest site. Just upstream of an arrest site, 17-19 nucleotides of the RNA 3'-end are protected from exhaustive digestion by exogenous ribonuclease probes. As RNA is elongated to the arrest site, the enzyme does not translocate and the protected RNA becomes correspondingly larger, up to 27 nucleotides in length. After the enzyme passes the arrest site, the protected RNA is again the 18-nucleotide species typical of an elongation-competent complex. These findings identify an extended RNA product groove in arrested RNA polymerase II that is probably identical to that emptied during SII-activated RNA cleavage, a process required for the resumption of elongation. Unlike Escherichia coli RNA polymerase at a terminator, arrested RNA polymerase II does not release its RNA but can reestablish the normal elongation mode downstream of an arrest site. Discontinuous elongation probably represents a structural change that precedes, but may not be sufficient for, arrest by RNA polymerase II.

Effects of aminofluorene and acetylaminofluorene DNA adducts on transcriptional elongation by RNA polymerase II

A prominent model for the mechanism of transcription-coupled DNA repair proposes that an arrested RNA polymerase directs the nucleotide excision repair complex to the transcription-blocking lesion. The specific role for RNA polymerase II in this mechanism can be examined by comparing the extent of polymerase arrest with the extent of transcription-coupled repair for a specific DNA lesion. Previously we reported that a cyclobutane pyrimidine dimer that is repaired preferentially in transcribed genes is a strong block to transcript elongation by RNA pol II (Donahue, B.A., Yin, S., Taylor, J.-S., Reines, D., and Hanawalt, P. C. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 8502-8506). Here we report the extent of RNA polymerase II arrest by the C-8 guanine DNA adduct formed by N-2-aminofluorene, a lesion that does not appear to be preferentially repaired. Templates for an in vitro transcription assay were constructed with either an N-2-aminofluorene adduct or the helix-distorting N-2-acetylaminofluorene adduct situated at a specific site downstream from the major late promoter of adenovirus. Consistent with the model for transcription-coupled repair, an aminofluorene adduct located on the transcribed strand was a weak pause site for RNA polymerase II. An acetylaminofluorene adduct located on the transcribed strand was an absolute block to transcriptional elongation. Either adduct located on the nontranscribed strand enhanced polymerase arrest at a nearby sequence-specific pause site.

Mutations in the second largest subunit of RNA polymerase II cause 6-azauracil sensitivity in yeast and increased transcriptional arrest in vitro

Yeast RNA polymerase II enzymes containing single amino acid substitutions in the second largest subunit were analyzed in vitro for elongation-related defects. Mutants were chosen for analysis based on their ability to render yeast cells sensitive to growth on medium containing 6-azauracil. RNA polymerase II purified from three different 6-azauracil-sensitive yeast strains displayed increased arrest at well characterized arrest sites in vitro. The extent of this defect did not correlate with sensitivity to growth in the presence of 6-azauracil. The most severe effect resulted from mutation rpb2 10 (P1018S), which occurs in region H, a domain highly conserved between prokaryotic and eukaryotic RNA polymerases that is associated with nucleotide binding. The average elongation rate of this mutant enzyme is also slower than wild type. We suggest that the slowed elongation rate and an increase in dwell time of elongating pol II leads to rpb2 10's arrest-prone phenotype. This mutant enzyme can respond to SII for transcriptional read-through and carry out SII-activated nascent RNA cleavage.

Purification of RNA polymerase II general transcription factors from rat liver

Eukaryotic messenger RNA synthesis is a complex biochemical process requiring the concerted action of multiple “general” transcription factors (TFs) that control the activity of RNA polymerase II at both the initiation¹ and elongation^2,3 stages of transcription. Because the general transcription factors are present at low levels in mammalian cells, their purification is a formidable undertaking. For this reason we explored the feasibility of using rat liver as a source for purification of the general factors. Rat liver has proven to be an ideal model system for biochemical studies of transcription initiation and elongation by RNA polymerase II (Figs. 1 and 2). In our hands the yield of general transcription factors per gram of rat liver is roughly equivalent to their yield per gram of cultured HeLa cells. Moreover, we have been able to develop convenient and reproducible methods for preparation of rat liver extracts from as much as 1 kg of liver per day. Because it is both technically difficult and expensive to obtain such quantities of cultured cells on a daily basis, rat liver provides a significant logistic advantage for purification of the general transcription factors.

Variation in the size of nascent RNA cleavage products as a function of transcript length and elongation competence

RNA polymerase II arrested at specific template locations can be rescued by elongation factor SII via RNA cleavage. The size of the products removed from the 3'-end of the RNA varies. The release of single nucleotides, dinucleotides, and larger oligonucleotides has been detected by different workers. Dinucleotides tend to originate from SII-independent complexes and 7-14 base products from SII-dependent complexes (Izban, M. G., and Luse, D. S. (1993) J. Biol. Chem. 268, 12874-12885). Different modes of cleavage have also been recognized for bacterial transcription complexes and are thought to represent important structural differences between functionally distinct transcription intermediates. Using an elongation complex "walking" technique, we have observed factor-independent complexes as they approach and become arrested at an arrest site. Dinucleotides or 7-9-base (large) oligonucleotides were released from SII-independent or dependent complexes, respectively. The abrupt shift between the release of dinucleotide versus larger products accompanied the change from factor-dependent to factor-independent elongation, as described by others. However, not all factor-independent complexes showed cleavage in dinucleotide intervals since oligonucleotides 2-6 bases long were also liberated from elongation-competent complexes. These were all 5'-coterminal oligonucleotides indicating that a preferred phosphodiester bond is targeted for cleavage in a series of related complexes. This is consistent with recent models postulating a large product binding site that can hold RNA chains whose size increases as a function of chain polymerization. A specific transitional complex was identified that acquired the ability to cleave in a large increment one base insertion event prior to attaining the arrested configuration.

T7 RNA polymerase bypass of large gaps on the template strand reveals a critical role of the nontemplate strand in elongation

We show that T7 RNA polymerase can efficiently transcribe DNA containing gaps from one to five bases in the template strand. Surprisingly, broken template strands missing up to 24 bases can still be transcribed, although at reduced efficiency. The resulting transcripts contain the full template sequence with the RNA deleted for the gapped region missing on the template strand. These findings indicate that the end of a downstream template strand can be brought into the polymerase and transcribed as if it were a part of an intact polynucleotide chain by utilizing the unpaired nontemplate strand. This, as well as transcription of an intact template strand, relies heavily upon the non-template strand, suggesting that a duplex DNA-binding site on the leading edge of RNA polymerase is required for RNA chain elongation on DNA templates. This work contributes substantially to the emerging picture that the nontemplate strand is an important element of the transcription elongation complex.

Identification of a decay in transcription potential that results in elongation factor dependence of RNA polymerase II

The rate of RNA elongation by RNA polymerase II (pol II) is affected by DNA sequences called intrinsic arrest sites. Efficient transcription through these sites requires elongation factor SII. In addition to the sequence-specific features of the DNA, we show that the acquisition of SII-dependence is a function of its "dwell-time" at an arrest site. This temperature-dependent decay in elongation potential appears irreversible, implying that factor-dependent and factor-independent elongation complexes are not mutually interconvertible at this position. TFIIF and NH4Cl are known to increase the elongation rate of pol II. Both agents preempt arrest, consistent with the idea that elongation dwell time influences the process. TFIIF and SII act upon different steps in a complementary way to prevent or resolve arrest, respectively. They are probably instrumental in facilitating the efficient transcription of large eukaryotic genes in vivo.

Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template

A current model for transcription-coupled DNA repair is that RNA polymerase, arrested at a DNA lesion, directs the repair machinery to the transcribed strand of an active gene. To help elucidate this role of RNA polymerase, we constructed DNA templates containing the major late promoter of adenovirus and a cyclobutane pyrimidine dimer (CPD) at a specific site. CPDs, the predominant DNA lesions formed by ultraviolet radiation, are good substrates for transcription-coupled repair. A CPD located on the transcribed strand of the template was a strong block to polymerase movement, whereas a CPD located on the nontranscribed strand had no effect on transcription. Furthermore, the arrested polymerase shielded the CPD from recognition by photolyase, a bacterial DNA repair protein. Transcription elongation factor SII (also called TFIIS) facilitates read-through of a variety of transcriptional pause sites by a process in which RNA polymerase II cleaves the nascent transcript before elongation resumes. We show that SII induces nascent transcript cleavage by RNA polymerase II stalled at a CPD. However, this cleavage does not remove the arrested polymerase from the site of the DNA lesion, nor does it facilitate translesional bypass by the polymerase. The arrested ternary complex is stable and competent to resume elongation, demonstrating that neither the polymerase nor the RNA product dissociates from the DNA template.

A DNA minor groove-binding ligand both potentiates and arrests transcription by RNA polymerase II. Elongation factor SII enables readthrough at arrest sites

RNA polymerase II encounters various obstacles to transcript elongation both in vivo and in vitro. These include DNA sequence elements and protein bound to the major groove of DNA. Elongation factor SII binds to RNA polymerase II and enables the enzyme to bypass these impediments. SII also activates nascent RNA cleavage by the arrested transcription elongation complex, an activity intimately involved in the readthrough process. Here we identify another type of reversible blockage to RNA polymerase II transcription, the antitumor antibiotic distamycin, which binds in the minor groove of A + T-rich DNA. SII facilitates readthrough of arrest sites resulting from DNA-binding of the drug. In response to SII, these complexes cleave their nascent RNA chains. These findings confirm that SII is a general elongation factor that potentiates transcription through a variety of impediments. They also strengthen the idea that SII stimulates transcription by activating nascent RNA cleavage. In some cases, distamycin can potentiate transcription through a naturally occurring pause site. We also show that the template undergoes a conformational change in the presence of distamycin. This suggests that distamycin can transform DNA from an elongation-non-permissive configuration into an elongation-permissive form and we take this as independent evidence confirming that DNA structure influences transcription elongation by RNA polymerase II.

Nascent RNA cleavage by arrested RNA polymerase II does not require upstream translocation of the elongation complex on DNA

Obstacles incurred by RNA polymerase II during primary transcript synthesis have been identified in vivo and in vitro. Transcription past these impediments requires SII, an RNA polymerase II-binding protein. SII also activates a nuclease in arrested elongation complexes and this nascent RNA shortening precedes transcriptional readthrough. Here we show that in the presence of SII and nucleotides, transcript cleavage is detected during SII-dependent elongation but not during SII-independent transcription. Thus, under typical transcription conditions, SII is necessary but insufficient to activate RNA cleavage. RNA cleavage could serve to move RNA polymerase II away from the transcriptional impediment and/or permit RNA polymerase II multiple attempts at RNA elongation. By mapping the positions of the 3'-ends of RNAs and the elongation complex on DNA, we demonstrate that upstream movement of RNA polymerase II is not required for limited RNA shortening (seven to nine nucleotides) and reactivation of an arrested complex. Arrested complexes become elongation competent after removal of no more than nine nucleotides from the nascent RNA's 3'-end. Further cleavage of nascent RNA, however, does result in "backward" translocation of the enzyme. We also show that one round of RNA cleavage is insufficient for full readthrough at an arrest site, consistent with a previously suggested mechanism of SII action.

FMR1 protein: conserved RNP family domains and selective RNA binding

Fragile X syndrome is the result of transcriptional suppression of the gene FMR1 as a result of a trinucleotide repeat expansion mutation. The normal function of the FMR1 protein (FMRP) and the mechanism by which its absence leads to mental retardation are unknown. Ribonucleoprotein particle (RNP) domains were identified within FMRP, and RNA was shown to bind in stoichiometric ratios, which suggests that there are two RNA binding sites per FMRP molecule. FMRP was able to bind to its own message with high affinity (dissociation constant = 5.7 nM) and interacted with approximately 4 percent of human fetal brain messages. The absence of the normal interaction of FMRP with a subset of RNA molecules might result in the pleiotropic phenotype associated with fragile X syndrome.

Elongation factor SII-dependent transcription by RNA polymerase II through a sequence-specific DNA-binding protein

In eukaryotes the genetic material is contained within a coiled, protein-coated structure known as chromatin. RNA polymerases must recognize specific nucleoprotein assemblies and maintain contact with the underlying DNA duplex for many thousands of base pairs. Template-bound lac operon repressor from Escherichia coli arrests RNA polymerase II in vitro and in vivo [Kuhn, A., Bartsch, I. & Grummt, I. (1990) Nature (London) 344, 559-562; Deuschele, U., Hipskind, R. A. & Bujard, H. (1990) Science 248, 480-483]. We show that in a reconstituted transcription system, elongation factor SII enables RNA polymerase II to proceed through this blockage at high efficiency. lac repressor-arrested elongation complexes display an SII-activated transcript cleavage reaction, an activity associated with transcriptional read-through of a previously characterized region of bent DNA. This demonstrates factor-dependent transcription by RNA polymerase II through a sequence-specific DNA-binding protein. Nascent transcript cleavage may be a general mechanism by which RNA polymerase II can bypass many transcriptional impediments.

Transcription elongation by RNA polymerase II: mechanism of SII activation

RNA chain elongation by RNA polymerase is a dynamic process. Techniques that allow the isolation of active elongation complexes have enabled investigators to describe individual steps in the polymerization of RNA chains. This article will describe recent studies of elongation by RNA polymerase II (pol II). At least four types of blockage to chain elongation can be overcome by elongation factor SII: (a) naturally occurring "arrest" sequences, (b) DNA-bound protein, (c) drugs bound in the DNA minor groove, and (d) chain-terminating substrates incorporated into the RNA chain. SII binds to RNA polymerase II and stimulates a ribonuclease activity that shortens nascent transcripts from their 3' ends. This RNA cleavage is required for chain elongation from some template positions. As a result, the pol II elongation complex can repeatedly shorten and reextend the nascent RNA chain in a process we refer to as cleavage-resynthesis. Hence, assembly of large RNAs does not necessarily proceed in a direct manner. The ability to shorten and reextend nascent RNAs means that a transcription impediment through which only half the enzyme molecules can proceed per encounter, can be overcome by 99% of the molecules after six iterations of cleavage-resynthesis. Surprisingly, the boundaries of the elongation complex do not move upstream after RNA cleavage. The physico-chemical alterations in the elongation complex that accompany RNA cleavage and permit renewed chain elongation are not yet understood.

The RNA polymerase II elongation complex. Factor-dependent transcription elongation involves nascent RNA cleavage

Regulation of transcription elongation is an important mechanism in controlling eukaryotic gene expression. SII is an RNA polymerase II-binding protein that stimulates transcription elongation and also activates nascent transcript cleavage by RNA polymerase II in elongation complexes in vitro (Reines, D. (1992) J. Biol. Chem. 267, 3795-3800). Here we show that SII-dependent in vitro transcription through an arrest site in a human gene is preceded by nascent transcript cleavage. RNA cleavage appeared to be an obligatory step in the SII activation process. Recombinant SII activated cleavage while a truncated derivative lacking polymerase binding activity did not. Cleavage was not restricted to an elongation complex arrested at this particular site, showing that nascent RNA hydrolysis is a general property of RNA polymerase II elongation complexes. These data support a model whereby SII stimulates elongation via a ribonuclease activity of the elongation complex.

Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II

In addition to polynucleotide polymerization, DNA polymerases and bacterial RNA polymerase can also remove nucleotides from the growing end of nucleic acid chains. For DNA polymerases this activity is an important factor in establishing fidelity in DNA synthesis. This report describes a novel in vitro activity of RNA polymerase II whereby it cleaves an RNA chain contained within an active elongation complex. These elongation complexes are arrested at a previously identified, naturally occurring transcriptional pause site in a human gene. The new 3'-end revealed by this cleavage remains associated with an active elongation complex and is capable of being extended by RNA polymerase II. Nascent RNA cleavage is evident after removal of free nucleotides and is dependent upon a divalent metal cation and transcription elongation factor SII. This function of SII could be important in its function as an activator of transcription elongation. It is also possible that the transcript cleavage activity of RNA polymerase II represents a proofreading function of the enzyme.

Purification of RNA using an anti-RNA monoclonal antibody

Studies of the synthesis and modification of RNA employ many types of in vitro reactions. Often, the RNA product must be concentrated or purified away from other reaction components such as salts, unincorporated nucleotides, protein, or DNA. Here I describe an immunological approach suitable for the isolation of RNA from in vitro reactions. A variety of RNAs of differing size and nucleotide sequence were immunoprecipitated with a monoclonal antibody specific for RNA. RNA binding took place in seconds with nearly quantitative recoveries. Immunoprecipitation was more efficient than ethanol precipitation in removing unincorporated nucleotides. Proteins which do not bind to RNA remained soluble. The immunoprecipitated RNA sample was solubilized directly with a buffered solution suitable for gel electrophoresis under denaturing conditions. Thus, RNAs can be rapidly concentrated for electrophoresis in a single step. Antibody-RNA binding was reversible under nondenaturing conditions in the presence of excess rRNA. This procedure serves as a novel means of purifying RNA and RNA-binding proteins from in vitro reactions.

RNA polymerase II elongation complex. Elongation complexes purified using an anti-RNA antibody do not contain initiation factor alpha

Gene expression in eukaryotes can be regulated by controlling the efficiency of transcript elongation by RNA polymerase II. The composition of the elongation complex is, however, poorly understood. Previous work has identified DNA sequences which block RNA polymerase II transcription and factors which stimulate RNA chain elongation. Here, I have purified elongation complexes arrested at discrete template locations. Complexes were rapidly and efficiently precipitated from in vitro transcription reactions using a monoclonal antibody that binds RNA. The isolated complexes remained transcriptionally active. This technique enables the facile manipulation of transcription elongation complexes. Using this approach, I show that transcription initiation factor alpha is not associated with a RNA polymerase II elongation complex. Since others have shown that alpha associates stoichiometrically with DNA, RNA polymerase II, and other required factors in an initiation complex, this work suggests that alpha departs from the transcription complex after nucleotides are required but before extensive RNA chain synthesis. In this regard alpha resembles the bacterial promoter-recognition factor sigma.

Purified elongation factor SII is sufficient to promote read-through by purified RNA polymerase II at specific termination sites in the human histone H3.3 gene

Purified RNA polymerase II terminates transcription in vitro at sites within genes which also block transcript elongation in vivo. Studies on a termination site within the first intron of the human histone H3.3 gene have shown that transcription elongation factor SII can promote read-through at this site when the polymerase initiates transcription from a promoter in the presence of the accessory initiation factors. Using 3'-extended templates to direct specific initiation by purified RNA polymerase II, we show here that purified SII is sufficient to effect read-through of this terminator by the purified polymerase alone. Thus, the interaction of purified SII with an elongation complex containing only the polymerase, the template, and the nascent transcript can change the termination properties of RNA polymerase II and can effect read-through of a region that blocks elongation in the cell.

Transcription initiated by RNA polymerase II and purified transcription factors from liver. Cooperative action of transcription factors tau and epsilon in initial complex formation

Synthesis of accurately initiated transcripts has been reconstituted with RNA polymerase II and a set of five transcription factors purified from rat liver. In addition to three previously identified factors alpha, beta gamma, and delta (Conaway, R. C., and Conaway, J. W. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 7356-7360), transcription in the reconstituted liver system requires two novel factors designated tau and epsilon. These five transcription factors comprise two functional classes: (i) promoter recognition factors (tau and epsilon), which interact with template DNA to facilitate formation of a stable initial complex that is subsequently recognized and bound by RNA polymerase II, and (ii) RNA chain initiation factors (alpha, beta gamma, and delta), which do not participate in formation of the initial complex, but which are essential for transcription initiation.

Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a block to transcription in a human gene in vitro

Elongation and termination by RNA polymerase II are important regulatory steps for eukaryotic gene expression. We have previously studied the transcription of linear DNA templates where specific initiation of transcription by highly purified RNA polymerase II can be achieved in the absence of promoters and promoter-specific factors. Using these templates we have shown that a human histone gene, H3.3, contains sequences (intrinsic terminators) within which purified RNA polymerase II will efficiently terminate transcription (Reines, D., Wells, D., Chamberlin, M.J., and Kane, C. M. (1987) J. Mol. Biol. 196, 299-312). Curiously, these signals were found within an intron, 3'-untranslated, and protein-encoding regions of the gene suggesting that they might act to attenuate transcription of H3.3 in vivo. Here we show that intrinsic terminator sequences from an H3.3 gene intron also block in vitro transcript elongation by RNA polymerase II when the enzyme has initiated transcription from a promoter using highly purified transcription initiation factors. However, under the conditions used for promoter-specific transcription there is little transcript release. Instead the polymerase can pause at these sites for periods exceeding 60 min. We have identified and partially purified an activity from HeLa cells that causes the transcription complex to read through this block to transcription elongation. This readthrough activity fractionates with a previously characterized elongation factor (SII) over three chromatographic columns. A homogeneous preparation of calf thymus SII can also provide this activity in trans. This factor may facilitate passage of the RNA polymerase II transcription complex through such intragenic sites in cellular genes in vivo.

Identification of intrinsic termination sites in vitro for RNA polymerase II within eukaryotic gene sequences

We have identified and mapped several DNA sequences within a human histone gene (H3.3) at which in-vitro transcription by highly purified RNA polymerase II is efficiently terminated. Since transcription in our system involves only RNA polymerase II acting on a linear DNA template, these sequences contain "intrinsic" termination signals recognized by the polymerase protein itself. The existence of such signals within a gene suggests that efficient antitermination systems probably exist for mammalian transcription units. Alternatively, there could be a high frequency of premature transcription termination, or "polarity" for genes such as H3.3. Intrinsic transcription termination sites in H3.3 are located in sequences of consecutive thymidylate residues (5 to 8 nucleotides) on the non-transcribed DNA strand (T-runs), from which it is likely that such T-runs are elements of the intrinsic termination signal for RNA polymerase II. However, transcription proceeds without significant termination through many similar T-runs, from which it follows that these intrinsic termination signals include other elements. Since transcription is also terminated efficiently at these sites when the transcript remains bound along its full length as a DNA-RNA hybrid, it is unlikely that formation of specific RNA secondary structures in the transcript is a general element of the intrinsic termination signal. Although DNA sequences downstream from the coding portion of the mouse beta-globin gene have been implicated as sites of transcription termination in vivo, these regions do not contain strong intrinsic termination signals, and transcription in vitro proceeds through these regions almost undiminished. Transcriptional termination in this region in vivo may depend on the presence of termination factors or other intracellular elements, and there may be multiple classes of DNA signals that control eukaryotic termination.

Immunochemical analysis of the supramolecular structure of myosin in contractile cytoskeletons of Dictyostelium amoebae

A collection of monoclonal antibodies against Dictyostelium myosin was screened to identify an antibody that could distinguish monomeric from polymeric myosin. An antibody was found that reacted only with monomeric myosin, provided that the antigen-antibody reaction was carried out in solution. This antibody was used in competition radioimmunoassays to probe the supramolecular structure of myosin in Triton-extracted cell models, or cytoskeletons, of Dictyostelium amoebae. The competition assay showed that, as isolated, cytoskeletal myosin was entirely filamentous, but could be converted to monomeric form by increasing the ionic strength of the surrounding buffer. As monomer, it remained associated with the cytoskeleton and could be cycled back to filament form by a second change of buffer. The ability of cytoskeletons to carry out ATP-dependent contraction was examined as a function of the assembly state of myosin. The results suggested that filamentous myosin is responsible for contraction of the cortical filament matrix.

Quantitative immunochemical studies of myosin in Dictyostelium discoideum

We have isolated monoclonal antibodies against myosin from the eukaryotic microorganism Dictyostelium discoideum. Immunoblot analysis using chymotryptic fragments of myosin has shown that the 17 antibodies are directed against at least five different sites on the myosin heavy chain. Using an antibody (M342) that reacts with an epitope on the tail portion of the myosin molecule, we have developed an assay to quantitate myosin in whole cells and subcellular fractions. Samples are deposited on nitrocellulose paper using a filtration manifold and are probed with metabolically labeled M342 antibodies. The assay is rapid and sensitive; it permits the measurement of myosin even in crude cell lysates that contain detergent. By use of the filtration immunoassay, we have found that myosin constitutes 0.72% of the total protein in vegetative amoebae. We have also determined that Triton-resistant cell residues (cytoskeletons or cortical actin matrices) prepared in the absence of ATP contain nearly half of the cell's myosin. If ATP is present, 98% of that myosin is released, although actin levels do not diminish.