Coupled transcription-polyadenylation in a cell-free system

Influence of Friedreich ataxia GAA noncoding repeat expansions on pre-mRNA processing

The intronic GAA repeat expansion in the frataxin (FXN) gene causes the hereditary neurodegenerative disorder Friedreich ataxia. Although it is generally believed that GAA repeats block transcription elongation, direct proof in eukaryotic systems is lacking. We tested in hybrid minigenes the effect of GAA and TTC repeats on nascent transcription and pre-mRNA processing. Unexpectedly, disease-causing GAA(100) repeats did not affect transcriptional elongation in a nuclear HeLa Run On assay, nor did they affect pre-mRNA transcript abundance. However, they did result in a complex defect in pre-mRNA processing. The insertion of GAA but not TTC repeats downstream of reporter exons resulted in their partial or complete exclusion from the mature mRNAs and in the generation of a variety of aberrant splicing products. This effect of GAA repeats was observed to be position and context dependent; their insertion at different distances from the reporter exons had a variable effect on splice-site selection. In addition, GAA repeats bind to a multitude of different splicing factors and induced the accumulation of an upstream pre-mRNA splicing intermediate, which is not turned over into mature mRNA. When embedded in the homologous frataxin minigene system, the GAA repeats did not affect the pre-mRNA transcript abundance but did significantly reduce the splicing efficiency of the first intron. These data indicate an association between GAA noncoding repeats and aberrant pre-mRNA processing because binding of transcribed GAA repeats to a multitude of trans-acting splicing factors can interfere with normal turnover of intronic RNA and thus lead to its degradation and a lower abundance of mature mRNA.

The preparation and applications of cytoplasmic extracts from mammalian cells for studying aspects of mRNA decay

HeLa S100 cytoplasmic extracts have been shown to effectively recapitulate many aspects of mRNA decay. Given their flexibility and the variety of applications readily amenable to extracts, the use of such systems to probe questions relating to the field of RNA turnover has steadily increased over time. Cytoplasmic extract systems have contributed greatly to the field of RNA decay by allowing valuable insight into RNA-protein interactions involving both the decay machinery and stability/instability factors. A significant advantage of these systems is the ability to assess the behaviors of several transcripts within an identical static environment, reducing errors within experimental replications. The impact of the cytoplasmic extract/in vitro RNA decay technology may be further advanced through manipulations of the extract conditions or the environment of the cells from which it is made. For instance, an extract may be produced from cells after depletion of a specific factor by RNAi, giving insight into the role of that factor in a particular process. The goals of this chapter are threefold. First, we will familiarize the reader with the process of producing high-quality, reliable HeLa-Cell cytoplasmic extracts. Second, a method for the standardization of independent extracts is described in detail to allow for dependable extract-to-extract comparisons. Finally, the use and application of cytoplasmic extracts with regard to assaying several aspects of mRNA turnover are presented. Collectively these procedures represent an important tool for the mechanistic analysis of RNA decay in mammalian cells.

Functional coupling of last-intron splicing and 3'-end processing to transcription in vitro: the poly(A) signal couples to splicing before committing to cleavage

We have developed an in vitro transcription system, using HeLa nuclear extract, that supports not only efficient splicing of a multiexon transcript but also efficient cleavage and polyadenylation. In this system, both last-intron splicing and cleavage/polyadenylation are functionally coupled to transcription via the tether of nascent RNA that extends from the terminal exon to the transcribing polymerase downstream. Communication between the 3' splice site and the poly(A) site across the terminal exon is established within minutes of their transcription, and multiple steps leading up to 3'-end processing of this exon can be distinguished. First, the 3' splice site establishes connections to enhance 3'-end processing, while the nascent 3'-end processing apparatus makes reciprocal functional connections to enhance splicing. Then, commitment to poly(A) site cleavage itself occurs and the connections of the 3'-end processing apparatus to the transcribing polymerase are strengthened. Finally, the chemical steps in the processing of the terminal exon take place, beginning with poly(A) site cleavage, continuing with polyadenylation of the 3' end, and then finishing with splicing of the last intron.

The RNA tether from the poly(A) signal to the polymerase mediates coupling of transcription to cleavage and polyadenylation

We have investigated the mechanism by which transcription accelerates cleavage and polyadenylation in vitro. By using a coupled transcription-processing system, we show that rapid and efficient 3' end processing occurs in the absence of crowding agents like polyvinyl alcohol. The continuity of the RNA from the poly(A) signal down to the polymerase is critical to this processing. If this tether is cut with DNA oligonucleotides and RNaseH during transcription, the efficiency of processing is drastically reduced. The polymerase is known to be an integral part of the cleavage and polyadenylation apparatus. RNA polymerase II pull-down and immobilized template experiments suggest that the role of the tether is to hold the poly(A) signal close to the polymerase during the early stages of processing complex assembly until the complex is sufficiently mature to remain stably associated with the polymerase on its own.

Functional coupling of cleavage and polyadenylation with transcription of mRNA

Cleavage and polyadenylation define the 3' ends of almost all eukaryotic mRNAs and are thought to occur during transcription. We describe a human in vitro system utilizing an immobilized template, in which transcripts in RNA polymerase II elongation complexes are efficiently cleaved and polyadenylated. Because the cleavage rate of free RNA is much slower, we conclude that cleavage is functionally coupled to transcription. Inhibition of positive transcription elongation factor b (P-TEFb) had only a modest negative effect on cleavage, as long as transcripts were long enough to contain the polyadenylation signal. In contrast, removal of the carboxyl-terminal domain of the large subunit of RNA polymerase II had a dramatic negative effect on cleavage. Unexpectedly, the 5' portion of transcript after cleavage remained associated with the template in a functional, polyadenylation-competent complex. Efficient cleavage required 5' capping by the human capping enzyme, but the reduction of cleavage seen of transcripts in COOH-terminal domain-less polymerase elongation complexes, was not because of lack of capping.

A history of poly A sequences: from formation to factors to function

Biological polyadenylation, first recognized as an enzymatic activity, remained an orphan enzyme until poly A sequences were found on the 3' ends of eukarvotic mRNAs. Their presence in bacteria viruses and later in archeae (ref. 338) established their universality. The lack of compelling evidence for a specific function limited attention to their cellular formation. Eventually the newer techniques of molecular biology and development of accurate nuclear processing extracts showed 3' end formation to be a two-step process. Pre-mRNA was first cleaved endonucleolytically at a specific site that was followed by sequential addition of AMPs from ATP to the 3' hydroxyl group at the end of mRNA. The site of cleavage was specified by a conserved hexanucleotide, AAUAAA, from 10 to 30 nt upstream of this 3' end. Extensive purification of these two activities showed that more than 10 polypeptides were needed for mRNA 3' end formation. Most of these were in complexes involved in the cleavage step. Two of the best characterized are CstF and CPSF, while two other remain partially purified but essential. Oddly, the specific proteins involved in phosphodiester bond hydrolysis have yet to be identified. The polyadenylation step occurs within the complex of poly A polymerase and poly A-binding protein, PABII, that controls poly A length. That the cleavage complex, CPSF, is also required for this step attests to a tight coupling of the two steps of 3' and formation. The reaction reconstituted from these RNA-free purified factors correctly processes pre-mRNAs. Meaningful analysis of the role of poly A in mRNA metabolism or function was possible once quantities of these proteins most often over-expressed from cDNA clones became available. The large number needed for two simple reactions of an endonuclease, a polymerase and a sequence recognition factor, pointed to 3' end formation as a regulated process. Polyadenylation itself had appeared to require regulation in cases where two poly A sites were alternatively processed to produce mRNA coding for two different proteins. The 64-KDa subunit of CstF is now known to be a regulator of poly A site choice between two sites in the immunoglobulin heavy chain of B cells. In resting cells the site used favors the mRNA for a membrane-bound protein. Upon differentiation to plasma cells, an upstream site is used the produce a secreted form of the heavy chain. Poly A site choice in the calcitonin pre-mRNA involves splicing factors at a pseudo splice site in an intron downstream of the active poly site that interacts with cleavage factors for most tissues. The molecular basis for choice of the alternate site in neuronal tissue is unknown. Proteins needed for mRNA 3' end formation also participate in other RNA-processing reactions: cleavage factors bind to the C-terminal domain of RNA polymerase during transcription; splicing of 3' terminal exons is stimulated port of by cleavage factors that bind to splicing factors at 3' splice sites. nuclear ex mRNAs is linked to cleavage factors and requires the poly A II-binding protein. Most striking is the long-sought evidence for a role for poly A in translation in yeast where it provides the surface on which the poly A-binding protein assembles the factors needed for the initiation of translation. This adaptability of eukaryotic cells to use a sequence of low information content extends to bacteria where poly A serves as a site for assembly of an mRNA degradation complex in E. coli. Vaccinia virus creates mRNA poly A tails by a streamlined mechanism independent of cleavage that requires only two proteins that recognize unique poly A signals. Thus, in spite of 40 years of study of poly A sequences, this growing multiplicity of uses and even mechanisms of formation seem destined to continue.

Mechanism of poly(A) signal transduction to RNA polymerase II in vitro

Termination of transcription by RNA polymerase II usually requires the presence of a functional poly(A) site. How the poly(A) site signals its presence to the polymerase is unknown. All models assume that the signal is generated after the poly(A) site has been extruded from the polymerase, but this has never been tested experimentally. It is also widely accepted that a "pause" element in the DNA stops the polymerase and that cleavage at the poly(A) site then signals termination. These ideas also have never been tested. The lack of any direct tests of the poly(A) signaling mechanism reflects a lack of success in reproducing the poly(A) signaling phenomenon in vitro. Here we describe a cell-free transcription elongation assay that faithfully recapitulates poly(A) signaling in a crude nuclear extract. The assay requires the use of citrate, an inhibitor of RNA polymerase II carboxyl-terminal domain phosphorylation. Using this assay we show the following. (i) Wild-type but not mutant poly(A) signals instruct the polymerase to stop transcription on downstream DNA in a manner that parallels true transcription termination in vivo. (ii) Transcription stops without the need of downstream elements in the DNA. (iii) cis-antisense inhibition blocks signal transduction, indicating that the signal to stop transcription is generated following extrusion of the poly(A) site from the polymerase. (iv) Signaling can be uncoupled from processing, demonstrating that signaling does not require cleavage at the poly(A) site.

Specific transcriptional pausing activates polyadenylation in a coupled in vitro system

We have developed a coupled in vitro transcription-polyadenylation system to investigate RNA polymerase II (Pol II) termination, which depends on active polyadenylation of the nascent RNA. Specific G-rich sequences originally identified as binding sites for the transcription factor MAZ both pause Pol II and activate polyadenylation of an upstream poly(A) signal. They do not affect polyadenylation efficiency in an uncoupled cleavage assay. In contrast, pausing of Pol II elongation induced by a high-affinity DNA-binding protein does not activate polyadenylation, indicating that G-rich MAZ sequences have a specific effect on polyadenylation. They also promote intrinsic pausing of purified Pol II, indicating a general role in the modulation of cotranscriptional RNA processing events.

The C-terminal domain of RNA polymerase II couples mRNA processing to transcription

Messenger RNA is produced by RNA polymerase II (pol II) transcription, followed by processing of the primary transcript. Transcription, splicing and cleavage-polyadenylation can occur independently in vitro, but we demonstrate here that these processes are intimately linked in vivo. We show that the carboxy-terminal domain (CTD) of the pol II large subunit is required for efficient RNA processing. Splicing, processing of the 3' end and termination of transcription downstream of the poly(A) site, are all inhibited by truncation of the CTD. We found that the cleavage-polyadenylation factors CPSF and CstF specifically bound to CTD affinity columns and copurified with pol II in a high-molecular-mass complex. Our demonstration of an association between the CTD and 3'-processing factors, considered together with reports of a similar interaction with splicing factors, suggests that an mRNA 'factory' exists which carries out coupled transcription, splicing and cleavage-polyadenylation of mRNA precursors.