Unusual aspects of in vitro RNA processing in the 3' regions of the GAL1, GAL7, and GAL10 genes in Saccharomyces cerevisiae

The nuclear exosome and adenylation regulate posttranscriptional tethering of yeast GAL genes to the nuclear periphery

GAL genes and other activated yeast genes remain tethered to the nuclear periphery even after transcriptional shutoff. To identify factors that affect this tethering, we designed a plasmid-based visual screen. Although many factors affected GAL tethering during transcription, fewer specifically affected posttranscriptional tethering. Tw o of these, Rrp6p and Lrp1p, are nuclear exosome components known to contribute to RNA retention near transcription sites (dot RNA). Moreover, these exosome mutations lead to a substantial posttranscriptional increase in polyadenylated GAL1 3' ends. This accompanies a loss of unadenylated (pA-) GAL1 RNA and a loss of posttranscriptional gene-periphery tethering, as well as a decrease in dot RNA levels. This suggests that the exosome inhibits adenylation of some GAL1 transcripts, which results in the accumulation of pA- RNA adjacent to the GAL1 gene. We propose that this dot RNA, probably via RNP proteins, contributes to the physical tether linking the GAL1 gene to the nuclear periphery.

Rna15 interaction with the A-rich yeast polyadenylation signal is an essential step in mRNA 3'-end formation

In Saccharomyces cerevisiae, four factors [cleavage factor I (CF I), CF II, polyadenylation factor I (PF I), and poly(A) polymerase (PAP)] are required for maturation of the 3' end of the mRNA. CF I and CF II are required for cleavage; a complex of PAP and PF I, which includes CF II subunits, participates in polyadenylation, along with CF I. These factors are directed to the appropriate site on the mRNA by two sequences: one A-rich and one UA-rich. CF I contains five proteins, two of which, Rna15 and Hrp1, interact with the mRNA through RNA recognition motif-type RNA binding motifs. Previous work demonstrated that the UV cross-linking of purified Hrp1 to RNA required the UA-rich element, but the contact point of Rna15 was not known. We show here that Rna15 does not recognize a particular sequence in the absence of other proteins. However, in complex with Hrp1 and Rna14, Rna15 specifically interacts with the A-rich element. The Pcf11 and Clp1 subunits of CF I are not needed to position Rna15 at this site. This interaction is essential to the function of CF I. A mutant Rna15 with decreased affinity for RNA is defective for in vitro RNA processing and lethal in vivo, while an RNA with a mutation in the A-rich element is not processed in vitro and can no longer be UV cross-linked to the Rna15 subunit assembled into CF I. Thus, the recognition of the A-rich element depends on the tethering of Rna15 through an Rna14 bridge to Hrp1 bound to the UA-rich motif. These results illustrate that the yeast 3' end is defined and processed by a mechanism surprisingly different from that used by the mammalian system.

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.

Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae

We have investigated transcriptional interactions between the GAL10 and GAL7 genes of Saccharomyces cerevisiae. Both genes are part of the galactose (GAL) gene cluster which is transcriptionally activated to high levels in the presence of galactose. Since GAL7 is positioned downstream of GAL10 and both genes are expressed co-ordinately at high levels, the possibility that GAL10 transcription influences GAL7 was analysed. Using transcriptional run-on assays, we show that high levels of polymerase are found in the 600 bp GAL10-7 intergenic region that accumulate over the GAL7 promoter. Furthermore, GAL7 transcription is enhanced when the GAL10 upstream activating sequence (UASG) is deleted, indicating that interference between GAL10 and GAL7 is likely to occur in the chromosomal locus. Deletions in the GAL10 poly(A) signal result in complete inactivation of the GAL7 promoter and cause a dramatic increase in bi-cistronic GAL10-7 mRNA, predominantly utilizing the downstream, GAL7 poly(A) site. These data demonstrate a pivotal role for the GAL10 poly(A) site in allowing the simultaneous expression of GAL10 and GAL7. In effect, this RNA processing signal has a direct influence on both transcriptional termination and initiation.

Sequence requirements of the bidirectional yeast TRP4 mRNA 3'-end formation signal

The yeast TRP4 3'-end formation signal functions in both orientations in an in vivo test system. We show here that the TRP4 3'-end formation element consists of two functionally different sequence regions. One region of approximately 70 nucleotides is located in the untranslated region between the translational stop codon and the major poly(A) site. The major poly(A) site is not part of this region and can be deleted without a decrease in TRP4 3'-end formation. 5'and 3'deletions and point mutations within this region affected 3'-end formation similarly in both orientations. In the center of this region the motif TAGT is located on the antisense strand. Point mutations within this motif resulted in a drastic reduce of 3'-end formation activity in both orientations. A second region consists of the 3'-end of the TRP4 open reading frame and is required for 3'-end formation in forward orientation. A single point mutation in a TAGT motif of the TRP4 open reading frame abolished TRP4 mRNA 3'-end formation in forward orientation and had no effect on the reverse orientation.

Pre-mRNA topology is important for 3'-end formation in Saccharomyces cerevisiae and mammals

Various signal motifs that are required for efficient pre-mRNA 3'-end formation in the yeast Saccharomyces cerevisiae have been reported. None of these known signal sequences appears to be of the same general importance as is the mammalian AAUAAA motif. To establish the importance of yeast pre-mRNA termini in 3'-end formation, the ends of a pre-mRNA transcript synthesized in vitro were ligated before incubation in a yeast whole-cell extract. Such covalently closed circular RNAs were not cleaved at their poly(A) sites. Interestingly, pseudocircular RNAs with complementary 3'- and 5'-terminal sequences allowing the formation of panhandle structures were also resistant to cleavage. However, 3'-end processing was impeded neither by terminal hairpins at either or at both ends nor by RNA oligonucleotides complementary to either or both ends of a linear pre-mRNA. Intriguingly mammalian pseudocircular pre-mRNAs also were not cleaved at their poly(A) sites when incubated in a HeLa cell nuclear extract. These results provide evidence for the general importance of RNA topology in the formation of an active 3'-end processing complex in S. cerevisiae and higher eukaryotes. The possibility of a torus-shaped factor involved in 3'-end formation is discussed.

Redundant 3' end-forming signals for the yeast CYC1 mRNA

The cyc1-512 mutation is a 38-bp deletion in the 3' untranslated region of the CYC1 gene, which encodes iso-1-cytochrome c in Saccharomyces cerevisiae. This deletion caused a 90% reduction in the levels of the CYC1 mRNA and protein because of the absence of the normal 3' end-forming signal. Although the 3' end-forming signal was not defined by previous analyses, we report that concomitant alteration by base-pair substitution of three 3' end-forming signals within and adjacent to the 38-bp region produced the same phenotype as the cyc1-512 mutation. Furthermore, these signals appear to be related to the previously identified 3' end-forming signal TATATA. A computer analysis revealed that TATATA and related sequences were present in the majority of 3' untranslated regions of yeast genes. Although TATATA may be the strongest and most frequently used signal in yeast genes, the CYC1+ gene concomitantly employed the weaker signals TT-TATA, TATGTT, and TATTTA, resulting in a strong signal.

A complex unidirectional signal element mediates GCN4 mRNA 3' end formation in Saccharomyces cerevisiae

The yeast GCN4 3' element represents a class of polyadenylation sites which function unidirectionally and efficiently in test systems in vivo as well as in vitro. A complex signal element is required for polyadenylation activity with a minimal size of 116 nucleotides for the functional element. We subdivided this element into five regions (EL1 to EL5) of 16 to 26 nucleotides each. Each region was characterized by deletion analysis in an in vivo test system. Two TTTTTAT motifs are located in different regions (EL1 and EL4) upstream of the poly(A) site. The 3' end processing activity was significantly reduced when both motifs were mutated by site-directed mutagenesis and abolished when EL1 and EL4 were deleted. The major poly(A) site is located in EL5, 3 nucleotides downstream of the second TTTTTAT motif. Additional minor poly(A) sites are used in less than 10% of the mRNA 3' ends. Deletion of EL3 resulted in a changed pattern of mRNA 3' ends by increased usage of the minor poly(A) addition sites. The major poly(A) site in EL5 can be removed without loss of function when sequences upstream of EL1 are present. The tripartite TAG...TATGT...TTT sequence located downstream of EL5 is not required for function.

Flexibility and interchangeability of polyadenylation signals in Saccharomyces cerevisiae

Various signal motifs have been reported to be essential for proper mRNA 3'-end formation in the yeast Saccharomyces cerevisiae. However, none of these motifs has been shown to be sufficient to direct 3'-end processing and/or transcription termination. Therefore, several structural motifs have to act in concert for efficient 3'-end formation. In the region upstream of the three polyadenylation sites of the yeast gene for alcohol dehydrogenase I (ADH1), we have identified a hitherto unknown signal sequence contained within the octamer AAAAAAAA. This motif, located 11 nucleotides upstream of the first ADH1 polyadenylation site, is responsible for the utilization of this site in vitro and in vivo, since mutational alteration drastically reduced 3'-end formation at this position. Insertion of 38 ADH1-derived nucleotides encompassing the (A)8 motif into the 3'-end formation-deficient cyc1-512 deletion mutant restored full processing capacity in vitro. Insertion of the octamer alone did not restore 3'-end formation, although mutation of the (A)8 motif in the functional construct had abolished 3'-end processing activity almost completely. This demonstrates that the sequence AAAAAAAA is a necessary, although not sufficient, signal for efficient mRNA 3'-end formation in S. cerevisiae.

Flexibility and interchangeability of polyadenylation signals in Saccharomyces cerevisiae

Various signal motifs have been reported to be essential for proper mRNA 3'-end formation in the yeast Saccharomyces cerevisiae. However, none of these motifs has been shown to be sufficient to direct 3'-end processing and/or transcription termination. Therefore, several structural motifs have to act in concert for efficient 3'-end formation. In the region upstream of the three polyadenylation sites of the yeast gene for alcohol dehydrogenase I (ADH1), we have identified a hitherto unknown signal sequence contained within the octamer AAAAAAAA. This motif, located 11 nucleotides upstream of the first ADH1 polyadenylation site, is responsible for the utilization of this site in vitro and in vivo, since mutational alteration drastically reduced 3'-end formation at this position. Insertion of 38 ADH1-derived nucleotides encompassing the (A)8 motif into the 3'-end formation-deficient cyc1-512 deletion mutant restored full processing capacity in vitro. Insertion of the octamer alone did not restore 3'-end formation, although mutation of the (A)8 motif in the functional construct had abolished 3'-end processing activity almost completely. This demonstrates that the sequence AAAAAAAA is a necessary, although not sufficient, signal for efficient mRNA 3'-end formation in S. cerevisiae.

Saturation mutagenesis of a polyadenylation signal reveals a hexanucleotide element essential for mRNA 3' end formation in Saccharomyces cerevisiae

The cis-acting signal sequences required for mRNA 3' end formation are highly conserved and well characterized in higher eukaryotes. However, the situation in the yeast Saccharomyces cerevisiae is still unclear. Several sequences have been proposed which share only limited similarities. One difficulty in identifying yeast polyadenylylation signals might be the presence of redundant signal sequences in the 3' region of yeast genes. To circumvent this problem we have analyzed the heterologous 3' region from cauliflower mosaic virus which contains a yeast polyadenylylation signal. We have performed a saturation mutagenesis of the key element TAG-TATGTA, which is a condensed version of the polyadenylylation signal TAG ... TATGTA ... (TTT) which had previously been proposed. Each of the nine nucleotides was replaced by the three other possible nucleotides and all resulting 1-bp mutants were tested for their capacity to specify mRNA 3' end formation in yeast cells. The first three nucleotides of this condensed sequence are not required, but mutagenesis of the other six nucleotides had distinct effects on mRNA 3' end formation. All mutants that were significantly functional had the sequence TAYRTA, and the sequence TATATA had the best capacity for mRNA 3' end formation. The two thymidine residues at the first and fifth positions are the most essential nucleotides in this sequence. Our results suggest that a degenerate hexanucleotide is essential for mRNA 3' end formation in yeast. This is reminiscent of the conserved polyadenylylation signal in higher eukaryotes, AATAAA.

Functional analysis of mRNA 3' end formation signals in the convergent and overlapping transcription units of the S. cerevisiae genes RHO1 and MRP2

The Saccharomyces cerevisiae genes RHO1 and MRP2 are convergently transcribed, with 281 base pairs separating their termination codons. Transcript mapping revealed at least 111 base pairs within the RHO1-MRP2 intercoding region are transcribed in both directions. Transplacement experiments showed distinct sequences of 70 nt for MRP2 and 179 nt for RHO1 were sufficient for normal mRNA 3' end formation. The MRP2 signal functioned in either orientation, although relatively inefficiently in the non-native orientation. This element contains a polyAT sequence essential for 3' end formation in both orientations. RHO1 or MRP2 3' end formation was not affected by overproduction or elimination of the complementary, natural antisense transcript. In contrast, insertion of a strong promoter that extended antisense transcripts beyond their normal 3' ends inactivated either MRP2 or RHO1. These data suggest that transcript termination in the compact yeast genome can be important to prevent inactivation of downstream genes as a result of antisense transcription.