In vitro cleavage of the simian virus 40 early polyadenylation site adjacent to a required downstream TG sequence

Polyadenylation precedes splicing in vitro

Vertebrate premessenger RNAs are usually spliced and polyadenylated. In vivo analysis of the relative kinetics of the two reactions is difficult. We have used in vitro processing systems to investigate the order of splicing and polyadenylation of chimeric precursor RNAs containing a single intron and a poly(A) site. Polyadenylated, but not spliced, intermediate RNA appeared first and reached a low steady-state level early during incubation, properties consistent with its being a reaction intermediate in the production of doubly-processed spliced and polyadenylated product RNA. The kinetics of polyadenylation suggested that polyadenylated RNA was the only intermediate in the production of doubly-processed RNA. Spliced, but not polyadenylated, RNA also appeared. This species, however, continued to accumulate during reaction, and could not be chased into product spliced and polyadenylated RNA. These data support a preferred order of reaction for 3' terminal introns and exons in which polyadenylation precedes splicing.

Optimizing In Vitro Pre-mRNA 3' Cleavage Efficiency: Reconstitution from Anion-Exchange Separated HeLa Cleavage Factors and from Adherent HeLa Cell Nuclear Extract

Eukaryotic RNA processing steps during mRNA maturation present the cell with opportunities for gene expression regulation. One such step is the pre-mRNA 3' cleavage reaction, which defines the downstream end of the 3' untranslated region and, in nearly all mRNA, prepares the message for addition of the poly(A) tail. The in vitro reconstitution of 3' cleavage provides an experimental means to investigate the roles of the various multi-subunit cleavage factors. Anion-exchange chromatography is the simplest procedure for separating the core mammalian cleavage factors. Here we describe a method for optimizing the in vitro reconstitution of 3' cleavage activity from the DEAE-sepharose separated HeLa cleavage factors and show how to ensure, or avoid, dependence on creatine phosphate. Important reaction components needed for optimal processing are discussed. We also provide an optimized procedure for preparing small-scale HeLa nuclear extracts from adherent cells for use in 3' cleavage in vitro.

An investigation into the role of ATP in the mammalian pre-mRNA 3' cleavage reaction

RNA Polymerase II transcribes beyond what later becomes the 3' end of a mature messenger RNA (mRNA). The formation of most mRNA 3' ends results from pre-mRNA cleavage followed by polyadenylation. In vitro studies have shown that low concentrations of ATP stimulate the 3' cleavage reaction while high concentrations inhibit it, but the origin of these ATP effects is unknown. ATP might enable a cleavage factor kinase or activate a cleavage factor directly. To distinguish between these possibilities, we tested several ATP structural analogs in a pre-mRNA 3' cleavage reaction reconstituted from DEAE-fractionated cleavage factors. We found that adenosine 5'-(β,γ-methylene)triphosphate (AMP-PCP) is an effective in vitro 3' cleavage inhibitor with an IC50 of ∼300 μM, but that most other ATP analogs, including adenosine 5'-(β,γ-imido)triphosphate, which cannot serve as a protein kinase substrate, promoted 3' cleavage but less efficiently than ATP. In combination with previous literature data, our results do not support ATP stimulation of 3' cleavage through cleavage factor phosphorylation in vitro. Instead, the more likely mechanism is that ATP stimulates cleavage factor activity through direct cleavage factor binding. The mammalian 3' cleavage factors known to bind ATP include the cleavage factor II (CF IIm) Clp1 subunit, the CF Im25 subunit and poly(A) polymerase alpha (PAP). The yeast homolog of the CF IIm complex also binds ATP through yClp1. To investigate the mammalian complex, we used a cell-line expressing FLAG-tagged Clp1 to co-immunoprecipitate Pcf11 as a function of ATP concentration. FLAG-Clp1 co-precipitated Pcf11 with or without ATP and the complex was not affected by AMP-PCP. Diadenosine tetraphosphate (Ap4A), an ATP analog that binds the Nudix domain of the CF Im25 subunit with higher affinity than ATP, neither stimulated 3' cleavage in place of ATP nor antagonized ATP-stimulated 3' cleavage. The ATP-binding site of PAP was disrupted by site directed mutagenesis but a reconstituted 3' cleavage reaction containing a mutant PAP unable to bind ATP nevertheless underwent ATP-stimulated 3' cleavage. Fluctuating ATP levels might contribute to the regulation of pre-mRNA 3' cleavage, but the three subunits investigated here do not appear to be responsible for the ATP-stimulation of pre-mRNA cleavage.

Heterogeneity in mammalian RNA 3' end formation

Precisely directed cleavage and polyadenylation of mRNA is a fundamental part of eukaryotic gene expression. Yet, 3' end heterogeneity has been documented for thousands of mammalian genes, and usage of one cleavage and polyadenylation signal over another has been shown to impact gene expression in many cases. Building upon the rich biochemical and genetic understanding of the 3' end formation, recent genomic studies have begun to suggest that widespread changes in mRNA cleavage and polyadenylation may be a part of large, dynamic gene regulatory programs. In this review, we begin with a modest overview of the studies that defined the mechanisms of mammalian 3' end formation, and then discuss how recent genomic studies intersect with these more traditional approaches, showing that both will be crucial for expanding our understanding of this facet of gene regulation.

Creatine phosphate, not ATP, is required for 3' end cleavage of mammalian pre-mRNA in vitro

The poly(A) tail of a mammalian mRNA is generated by endonucleolytic cleavage and poly(A) addition. Previous studies conducted with nuclear extracts suggested an ATP requirement for the cleavage step. We have reexamined the cofactor requirement, initially with the SV40 late pre-mRNA, which requires for cleavage four protein factors, cleavage and polyadenylation specificity factor, cleavage stimulation factor, cleavage factor I, and cleavage factor II. Using highly purified preparations of these factors, which lacked detectable creatine phosphokinase and ATPase activities, creatine phosphate (CP) was, surprisingly, found to be sufficient to promote efficient cleavage. Although other phosphate compounds substituted poorly or not at all for CP, another phosphoguanidine, arginine phosphate, was fully functional. Notably, ATP was neither necessary nor sufficient, and could in fact inhibit the reaction. Treatment of the purified factors with hexokinase plus glucose (to deplete any contaminating ATP) was without effect, as was addition of EDTA. Using 32P-labeled CP, we found that neither hydrolysis of CP nor phosphate transfer from CP occurred during the cleavage reaction. CP also allowed cleavage of the adenovirus 2 L3 pre-mRNA. However, in this case, ATP both enhanced the reaction and influenced the precise site of cleavage, perhaps reflecting the requirement of poly(A) polymerase for cleavage of this RNA. These results indicate that ATP is not essential for 3' pre-mRNA cleavage and that CP or a related compound can function as a necessary cofactor.

Expression of the laminin-A chain is down-regulated by a non-canonical polyadenylation signal

It is well accepted that 3' untranslated regions (UTR) are an essential part of mRNA. However, little is known in detail about the contribution of different regions of 3' UTR on synthesis, stability and translatability of their mRNA. In addition to the highly conserved hexanucleotide AAUAAA, some consensus sequences for 3'-end processing and polyadenylation have been characterized, but most of this work has been done with viral mRNA or beta-globin mRNA. We have studied the influence of the 3' UTR of the mRNA for the three chains A, B1, B2 of laminin on the expression of a reporter gene (galK). Laminin is a large glycoprotein of basement membranes and all three polypeptide chains are needed in equal amounts for a functional molecule. The three 3' UTR of the laminin mRNA differ widely with respect to length, number of polyadenylation signals and other consensus sequences. Nevertheless, all three 3' UTR reduce the expression of the reporter gene at least three-fold, when the corresponding cDNA sequences are inserted downstream of the reporter gene instead of the 3' UTR of simian virus 40 early genes. The 3' UTR of laminin-A mRNA contains the non-canonical polyadenylation signal AUUAAA which seems to be responsible for the limiting amounts of laminin-A mRNA and protein compared to those for laminin B1 and B2 [Speth and Oberbäumer (1993) Exp. Cell Res. 204, 302-310]. Mutation of the laminin-A polyadenylation signal to the canonical form AAUAAA increases expression by a factor of 2.5.

3' cleavage and polyadenylation of mRNA precursors in vitro requires a poly(A) polymerase, a cleavage factor, and a snRNP

We have separated and purified three factors from HeLa cell nuclear extracts that together can accurately cleave and polyadenylate pre-mRNAs containing the adenovirus L3 polyadenylation site. One of the factors is a poly(A) polymerase with a molecular weight of approximately 50-60 kd. The second activity is a cleavage factor with a native molecular weight in the range of 70-120 kd. The third component is a factor (cleavage and polyadenylation factor, CPF) that is needed for the cleavage reaction and, in addition, confers specificity to the poly(A) polymerase activity; the native molecular weight of CPF is approximately 200 kd. Poly(A) polymerase together with CPF is sufficient to specifically polyadenylate pre-mRNA substrates that have been precleaved at the poly(A) addition site. In contrast, all three components are required for accurate cleavage and polyadenylation of pre-mRNA substrates. Further purification of CPF by buoyant density centrifugation, ion exchange, and affinity column chromatography or by gel filtration demonstrates that CPF activity resides in a ribonucleoprotein and copurifies with U11 snRNP.

Separation and characterization of a poly(A) polymerase and a cleavage/specificity factor required for pre-mRNA polyadenylation

To study the mechanism and factors required to form the 3' ends of polyadenylated mRNAs, we have fractionated HeLa cell nuclear extracts carrying out the normally coupled cleavage and polyadenylation reactions. Each reaction is catalyzed by a distinct, separable activity. The partially purified cleavage enzyme (at least 360,000 MW) retained the specificity displayed in nuclear extracts, since substitutions in the AAUAAA signal sequence inhibited cleavage. In contrast, the fractionated poly(A) polymerase (300,000 MW) lost all specificity. When fractions containing the cleavage and polyadenylation activities were mixed, the efficiency and specificity of the polyadenylation reaction were restored. Interestingly, the cleavage activity by itself functioned well on only one of four precursor RNAs tested. However, when mixed with the poly(A) polymerase-containing fraction, the cleavage activity processed the four precursors with comparable efficiencies.

Functional analysis of the sea urchin U7 small nuclear RNA

U7 small nuclear RNA (snRNA) is an essential component of the RNA-processing machinery which generates the 3' end of mature histone mRNA in the sea urchin. The U7 small nuclear ribonucleoprotein particle (snRNP) is classified as a member of the Sm-type U snRNP family by virtue of its recognition by both anti-trimethylguanosine and anti-Sm antibodies. We analyzed the function-structure relationship of the U7 snRNP by mutagenesis experiments. These suggested that the U7 snRNP of the sea urchin is composed of three important domains. The first domain encompasses the 5'-terminal sequences, up to about nucleotides 7, which are accessible to micrococcal nuclease, while the remainder of the RNA is highly protected and hence presumably bound by proteins. This region contains the sequence complementarities between the U7 snRNA and the histone pre-mRNA which have previously been shown to be required for 3' processing (F. Schaufele, G. M. Gilmartin, W. Bannwarth, and M. L. Birnstiel, Nature [London] 323:777-781, 1986). Nucleotides 9 to 20 constitute a second domain which includes sequences for Sm protein binding. The complementarities between the U7 snRNA sequences in this region and the terminal palindrome of the histone mRNA appear to be fortuitous and play only a secondary, if any, role in 3' processing. The third domain is composed of the terminal palindrome of U7 snRNA, the secondary structure of which must be maintained for the U7 snRNP to function, but its sequence can be drastically altered without any observable effect on snRNP assembly or 3' processing.

Minute virus of mice (MVM) mRNAs predominantly polyadenylate at a single site

The polyadenylation sites for MVM(p) and MVM(i) mRNAs were determined by a quantitative hybridization-S1 protection assay. mRNAs produced by MVM(p) both early and late in infection of mouse A9 fibroblasts, and by MVM(p) and MVM(i) late in infection of human NB324K cells, polyadenylate predominantly at a single site, at nucleotide 4908 +/- 2 for MVM(p) and 4843 +/- 2 for MVM(i), shortly downstream of the final AATAAA in each viral genome. These results demonstrate that although the right-hand end of MVM has multiple AATAAA signals, and MVM(p) and MVM(i) vary significantly within this region, 3' end processing of viral mRNAs is not a prevalent mechanism for the regulation of MVM gene expression.

Conserved 12-bp element downstream from mRNA polyadenylation sites

Sequences downstream from the AATAAA motif in a number of cellular and viral transcription units have been compared. A 12-bp conserved element was identified in approximately half of the cases studied, and a consensus sequence TTGANNNTTTTTT was derived from a comparison of 74 such sequences. This element is located immediately (5-20 bp) downstream from the poly(A)-addition site in every case where this is known, and it is suggested that this element may be involved in the cleavage/polyadenylation reaction. This proposal is consistent with published studies on deletion mutants of downstream regions.