Increased rate of RNA-polyadenylation. An early response in Concanavalin A activated lymphocytes

Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression

Alternative RNA processing mechanisms, including alternative splicing and alternative polyadenylation, are increasingly recognized as important regulators of gene expression. This article will focus on what has recently been described about alternative polyadenylation in development, differentiation, and disease in higher eukaryotes. We will also describe how the evolving global methodologies for examining the cellular transcriptome, both experimental and bioinformatic, are revealing new details about the complex nature of alternative 3(') end formation as well as interactions with other RNA-mediated and RNA processing mechanisms.

Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells

In cancer cells, genetic alterations can activate proto-oncogenes, thereby contributing to tumorigenesis. However, the protein products of oncogenes are sometimes overexpressed without alteration of the proto-oncogene. Helping to explain this phenomenon, we found that when compared to similarly proliferating nontransformed cell lines, cancer cell lines often expressed substantial amounts of mRNA isoforms with shorter 3' untranslated regions (UTRs). These shorter isoforms usually resulted from alternative cleavage and polyadenylation (APA). The APA had functional consequences, with the shorter mRNA isoforms exhibiting increased stability and typically producing ten-fold more protein, in part through the loss of microRNA-mediated repression. Moreover, expression of the shorter mRNA isoform of the proto-oncogene IGF2BP1/IMP-1 led to far more oncogenic transformation than did expression of the full-length, annotated mRNA. The high incidence of APA in cancer cells, with consequent loss of 3'UTR repressive elements, suggests a pervasive role for APA in oncogene activation without genetic alteration.

ERK is a novel regulatory kinase for poly(A) polymerase

Poly(A) polymerase (PAP), which adds poly(A) tails to the 3′ end of mRNA, can be phosphorylated at several sites in the C-terminal domain. Phosphorylation often mediates regulation by extracellular stimuli, suggesting PAP may be regulated by such stimuli. In this study, we found that phosphorylation of PAP was increased upon growth stimulation and that the mitogen-activated protein kinase ERK was responsible for the increase in phosphorylation. We identified serine 537 of PAP as a unique phosphorylation site by ERK. PAP phosphorylation of serine 537 by ERK increased its nonspecific polyadenylation activity in vitro. This PAP activity was also activated by stimulation of ERK with phorbol-12-myristate-13-acetate in vivo. These data suggest that ERK is a novel regulatory kinase for PAP and further, that PAP activity could be regulated by extracellular stimuli through an ERK-dependent signaling pathway(s).

Poly(A) polymerase phosphorylation is dependent on novel interactions with cyclins

We have previously shown that poly(A) polymerase (PAP) is negatively regulated by cyclin B-cdc2 kinase hyperphosphorylation in the M phase of the cell cycle. Here we show that cyclin B(1) binds PAP directly, and we demonstrate further that this interaction is mediated by a stretch of amino acids in PAP with homology to the cyclin recognition motif (CRM), a sequence previously shown in several cell cycle regulators to target specifically G(1)-phase-type cyclins. We find that PAP interacts with not only G(1)- but also G(2)-type cyclins via the CRM and is a substrate for phosphorylation by both types of cyclin-cdk pairs. PAP's CRM shows novel, concentration-dependent effects when introduced as an 8-mer peptide into binding and kinase assays. While higher concentrations of PAP's CRM block PAP-cyclin binding and phosphorylation, lower concentrations induce dramatic stimulation of both activities. Our data not only support the notion that PAP is directly regulated by cyclin-dependent kinases throughout the cell cycle but also introduce a novel type of CRM that functionally interacts with both G(1)- and G(2)-type cyclins in an unexpected way.

Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis

Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.

Increase in the 64-kDa subunit of the polyadenylation/cleavage stimulatory factor during the G0 to S phase transition

The amount of the 64-kDa subunit of polyadenylation/cleavage stimulatory factor (CstF-64) increases 5-fold during the G0 to S phase transition and concomitant proliferation induced by serum in 3T6 fibroblasts. Higher levels of CstF-64 result in an increase in CstF trimer. The rise in CstF-64 occurs at a time when the amount of poly(A)-containing RNA rose at least 5-8 fold in the cytoplasm. Primary human splenic B cells, resting in G0, show a similar 5-fold increase in CstF-64 when cultured under conditions inducing proliferation (CD40 ligand exposure). Therefore, the increase in CstF-64 is associated with the G0 to S phase transition. As B cell development progresses, RNA processing changes occur at the Ig heavy chain locus resulting in a switch from the membrane- to the upstream secretory-specific poly(A) site. Treating resting B cells with agents triggering this switch in Ig mRNA production along with proliferation (CD40 ligand plus lymphokines or Staphylococcus aureus protein A) induces no further increase in CstF-64 above that seen for proliferation alone. The rise in CstF-64 is therefore insufficient to induce secretion. After stimulation of a continuously growing B cell line with lymphokines, a switch to Ig micrometer secretory mRNA and protein occurs but without a change in the CstF-64 level. Therefore, an increase in CstF-64 levels is not necessary to mediate the differentiation-induced switch to secreted forms of Ig-micrometer heavy chain. Because augmentation of CstF-64 levels is neither necessary nor sufficient for Ig secretory mRNA production, we conclude that other lymphokine-induced factors play a role.

Alternative poly(A) site selection in complex transcription units: means to an end?

Many genes have been described and characterized which result in alternative polyadenylation site use at the 3'-end of their mRNAs based on the cellular environment. In this survey and summary article 95 genes are discussed in which alternative polyadenylation is a consequence of tandem arrays of poly(A) signals within a single 3'-untranslated region. An additional 31 genes are described in which polyadenylation at a promoter-proximal site competes with a splicing reaction to influence expression of multiple mRNAs. Some have a composite internal/terminal exon which can be differentially processed. Others contain alternative 3'-terminal exons, the first of which can be skipped in some cells. In some cases the mRNAs formed from these three classes of genes are differentially processed from the primary transcript during the cell cycle or in a tissue-specific or developmentally specific pattern. Immunoglobulin heavy chain genes have composite exons; regulated production of two different Ig mRNAs has been shown to involve B cell stage-specific changes in trans -acting factors involved in formation of the active polyadenylation complex. Changes in the activity of some of these same factors occur during viral infection and take-over of the cellular machinery, suggesting the potential applicability of at least some aspects of the Ig model. The differential expression of a number of genes that undergo alternative poly(A) site choice or polyadenylation/splicing competition could be regulated at the level of amounts and activities of either generic or tissue-specific polyadenylation factors and/or splicing factors.

Transfer ribonucleic acid populations in concanavalin-A-stimulated bovine lymphocytes

Transfer RNA isolated from lymphocytes stimulated by concanavalin A and that from resting cells were compared with respect to amino-acid acceptance, integrity of the CCA-terminus, extent of modification and isoacceptor distribution. Following growth stimulation the overall amino-acid acceptance of the tRNA is elevated, in particular the relative acceptor activities for threonine and arginine are increased. The reduced acceptor activity of the tRNA from the quiescent cells is not due to a preferential degradation of the CCA-end, since it persists even in the presence of ATP(CTP):tRNA nucleotidyltransferase. We therefore conclude that this reduced activity is caused by structural differences of the tRNAs. The content of modified nucleotides in newly synthesized tRNA from lymphocytes cultured in the presence and absence of concanavalin A was determined. tRNA from resting cells was found to be undermodified with respect to pseudouridine and dihydrouridine. Upon monitoring the tRNA isoacceptor distribution by affinity chromatography on immobilized elongation factor Tu and subsequent two-dimensional gel electrophoresis, a preferential synthesis of particular lysine- and threonine-accepting tRNAs was observed upon mitogenic stimulation. Evidently, a specific tRNA population is needed by the proliferating cells. These results are discussed in view of the hypothesis that the commitment of lymphocytes to proliferation is at least in part under translational control.

Growth-related changes in specific mRNAs upon lectin activation of human lymphocytes

A cDNA library in lambda gt10 was constructed from the cytoplasmic poly(A) +RNA of human peripheral blood lymphocytes after 72 hr of phytohemagglutinin stimulation, with the aim of assessing selective gene expression as a result of lymphocyte activation. Thirteen recombinants were isolated by the use of an enriched probe and differential screening. These clones were categorized into two groups with respect to their hybridization to mRNA. In the first group three recombinants were isolated, which hybridized to single discrete mRNAs in the size range 0.7-1.7 kb. The mRNAs corresponding to these clones were present at elevated levels in activated lymphocytes, but the kinetics of increase differed. The 0.7-kb mRNA coded for by clone p1L1 increased two-fold at 6 hr and remained elevated over 72 hr, as did beta-actin mRNA. The 1.7-kb mRNA coded for by clone p9L2 increased two- to three-fold after 6 hr and was maximally expressed after 24 hr exposure to phytohemagglutinin, coincident with the onset of DNA replication, and maintained this level up to 72 hr. The 1.0-kb mRNA coded by p10L2F which was rare in resting cells increased 25- to 30-fold after 6 hr, prior to overall transcriptional increases and reached peak levels after 72 hr when a substantial proportion of the cells were in the S and G2 + M phases of the cell cycle. This clone was undetectable or very rare in the leukemic T-lymphoblast cell line CCRF-CEM. The second group of clones, consisting of the remaining 10 recombinants, did not hybridize to discrete bands, but to a smear on RNA blots.(ABSTRACT TRUNCATED AT 250 WORDS)

Polyamine depletion results in impairment of polyribosome formation and protein synthesis before onset of DNA synthesis in mitogen-activated human lymphocytes

Lymphocytes, exposed to mitogens in culture, show enhanced protein and RNA synthesis before the onset of DNA synthesis. Inhibition by DL-alpha-difluoromethylornithine of polyamine synthesis in phytohaemagglutinin-activated human lymphocytes resulted in a suppression of protein synthesis, which was evident before the initiation of DNA synthesis. The mitogen-induced increase in the incorporation of [3H]thymidine into DNA was subsequently inhibited in parallel with the activity of thymidine kinase in the polyamine-depleted cells. Ultraviolet absorbance measurement of the ribosomes after sucrose gradient centrifugation revealed a suppression of polyribosome formation that coincided with the decrease in the rate of protein synthesis. The disturbance in the polysomal profiles did not appear to be due to a shortage of mRNA, since the synthesis of poly(A)-rich mRNA was reduced less than that of rRNA after inhibiting polyamine synthesis. Entry of both the pre-existing and newly synthesized ribosomal subunits into polysomal structures was found to be impaired. These results thus suggest an important role for polyamines in the initiation step of protein synthesis.

Early effects of triidothyronine on the complexity of rat heart messenger RNAs

Triiodothyronine (T3), injected daily into rats, induces heart hypertrophy. In a recent work we have shown that a single T3 injection stimulates RNA synthesis and modifies the translational products of myocardial mRNAs in reticulocyte lysates, quantitatively and qualitatively. In this work we show that T3 induces small but significant changes in mRNA size distribution after 4 h and much more important changes after 18 h. It also modifies the size distribution of their poly(A) tails. We studied the early effects of this compound on mRNA complexity, using the nucleic acid hybridization technique with DNA complementary to poly(A)+ RNAs. T3, 4 h after injection, suppresses approximately 15% of the sequences, mostly among rare sequences, and increases the frequency of the abundant sequences and of the sequences of intermediary abundance. A large part of this effect disappears 18 h after the injection. It may be concluded that T3 presents an early effect on gene expression, involving changes either at the gene level or and at some post transcriptional level.

Modulation of early mRNA synthesis in lectin-induced lymphocyte activation--an association with a possible factor

Two phases of early mRNA synthesis were observed in lectin-induced lymphocyte activation. At 0-2 h, lectin-treated lymphocytes showed a considerable decrease in nuclear RNA polymerase II activity as compared with that of untreated cells and, at later periods, a reverse increase was observed. Such modulation of mRNA synthesis is not due to the change of RNA polymerase II, but a possible factor in nuclei. This factor represses RNA chain initiation and stimulates chromatin-dependent RNA elongation catalyzed by RNA polymerase II. It was characterized to be a 10-30 kDa sugar-containing molecule and the physiological significance of this factor is discussed from the viewpoint of the transcriptional regulation.

A decrease of RNA synthesis during macrophage activation with lipopolysaccharide--an association with novel regulating factors

RNA synthesis during macrophage activation with lipopolysaccharide (LPS) was analyzed in mice. The RNA synthesis of macrophages was considerably increased early after LPS stimulation, but drastically decreased at a later period. The decrease of RNA synthesis was observed in mouse strains responding to LPS such as BALB/c, ATL and ddY, but not in nonresponder strain, C3H/HeJ. Furthermore, the decrease of RNA synthesis occurred in both alpha-amanitin resistant and sensitive RNA polymerase reactions. However, RNA polymerases in nuclei were not changed significantly in LPS-treated macrophages, but the factors affecting RNA polymerase reactions were drastically changed. Amongst these factors, the stimulating factors were decreased and a novel repressing factor was remarkably increased. The factors were partially characterized and their significance in macrophage activation is discussed.

Lectin-induced changes among polyadenylated and non-polyadenylated mRNA in lymphocytes. mRNAs for actin, tubulin and calmodulin respond differently

The differentiation of T-cell-enriched concanavalin-A-stimulated bovine lymphocytes was studied in vitro. mRNA was isolated from resting and stimulated cells. The amount of polyadenylated RNA increases from 3.6 X 10(-9) to 12 X 10(-9) micrograms/cell during 40 h concanavalin A stimulation. The estimated maximum length of the 3'-poly(A) tract in this RNA is reduced from 240 to 220 residues in stimulated cells. During translation in the rabbit reticulocyte lysate in vitro mRNA from stimulated cells consistently incorporates about 1.6-3 times more radioactivity/micrograms RNA into proteins than mRNA from resting cells. Three translation products have been identified on two-dimensional gels as actin, tubulin and calmodulin. Large quantitative shifts are seen between proteins translated from mRNAs isolated from resting cells and stimulated cells respectively. Actin and calmodulin are already major products from resting cell mRNA. Actin, however, increases about fivefold after stimulation while calmodulin does not change. Tubulin appears in substantial amounts only among stimulated cell mRNA products. Tubulin and calmodulin, on the other hand, remain mainly in the polyadenylated RNA fraction after stimulation while 50% of the actin together with a group of about six other major products is found among proteins translated from non-polyadenylated RNA. We conclude that in lectin-stimulated lymphocytes, besides a general increase in the amount of mRNA, alterations in post-transcriptional processing reactions are active in determining the fate of individual mRNAs.

Stability of polyadenylated mRNA in pig lymphocytes

The stability of cytoplasmic poly(A)-containing mRNA in unstimulated pig lymphocytes has been determined by [3H]poly(U) hybridization after actinomycin D treatment. This approach has shown that the majority of the mRNA is much more unstable than has been suggested by earlier pulse-chase experiments, and has a half-life of between 1 and 2 h.

Metabolism of polyadenylated mRNA in growing human lymphocytes

The kinetics of degradation of newly synthesized, cytoplasmic polyadenylated RNA have been examined in normal human lymphocytes stimulated to grow with phytohemagglutinin. A single class of poly(A)-bearing RNA was identified with a half-life of approximately 50 h. In the presence of actinomycin D, the half-life was 5 to 6 h, and virtually no decay of pulse-labeled material was detectable after 6 h of chase incubation with cordycepin. These findings contrast sharply with data obtained from other growing human cells used as controls: polyadenylated mRNA in MOLT-4 cells, a cultured line of T lymphocytes, had a half-life of 2 h in the presence of actinomycin D. The stability of poly(A)-containing RNA in stimulated lymphocytes from normal donors is therefore not simply a manifestation of cell proliferation. In normal resting lymphocytes, Berger and Copper [(1975) Proc. Natl. Acad. Sci. U.S. 72, 3873--3877] reported the existence of 2 classes of polyadenylated mRNA with half-lives of under an hour and greater than 20 h, respectively. Since short-lived poly(A)-bearing mRNA is absent from mitogen-stimulated lymphocytes, the data suggest that stabilization of previously labile poly(A)-bearing RNA is one of many carefully regulated processes accompanying growth induction in normal lymphoid cells.