Involvement of long terminal repeat U3 sequences overlapping the transcription control region in human immunodeficiency virus type 1 mRNA 3' end formation.

523

486

Polyadenylation [poly(A)] signals (PAS) are a defining feature of eukaryotic protein-coding genes. The central sequence motif AAUAAA was identified in the mid1970s and subsequently shown to require flanking, auxiliary elements for both 39-end cleavage and polyadenylation of premessenger RNA (pre-mRNA) as well as to promote downstream transcriptional termination. More recent genomic analysis has established the generality of the PAS for eukaryotic mRNA. Evidence for the mechanism of mRNA 39-end formation is outlined, as is the way this RNA processing reaction communicates with RNA polymerase II to terminate transcription. The widespread phenomenon of alternative poly(A) site usage and how this interrelates with pre-mRNA splicing is then reviewed. This shows that gene expression can be drastically affected by how the message is ended. A central theme of this review is that while genomic analysis provides generality for the importance of PAS selection, detailed mechanistic understanding still requires the direct analysis of specific genes by genetic and biochemical approaches.

Section: Polyadenylation Signals and 39 Noncoding Rna (Ncrna) Sequencesmentioning

confidence: 99%

Ending the message: poly(A) signals then and now

Proudfoot¹

2011

523

486

“…These 'Coiiesponding author. elements do not conform to a consensus sequence but are characterized as either U-rich or GU-rich. Upstream efficiency elements (USEs) have also been described in several systems, including the SV40 late RNAs (Carswell and Alwine 1989;Schek et al 1992), ground squirrel hepatitis virus (Russnak and Ganem 1990;Russnak 1991), cauliflower mosaic virus (Sanfacon et al 1991), HIV-1 (Brown et al 1991;DeZazzo et al 1991;Valsamakis et al 1991Valsamakis et al , 1992, and adenovirus type 2 (DeZazzo and Imperiale 1989). The USE of the SV40 late polyadenylation signal has three motifs with the consensus AUUU-GURA, located between 15 and 50 nucleotides upstream of the AAUAAA (Fig.…”

mentioning

confidence: 99%

Direct interaction of the U1 snRNP-A protein with the upstream efficiency element of the SV40 late polyadenylation signal.

Lutz¹,

Alwine²

1994

138

152

An integral component of the splicing machinery, the Ul snRNP, is here implicated in the efficient polyadenylation of SV40 late mRNAs. This occurs as a result of an interaction between Ul snRNP-A protein and the upstream efficiency element (USE) of the polyadenylation signal. UV cross-linking and immunoprecipitation demonstrate that this interaction can occur while Ul snRNP-A protein is simultaneously bound to Ul RNA as part of the snRNP. The dual reactivity of Ul snRNP-A occurs because the protein has two RNA recognition motifs (RRMs). The target RNA of the first RRM (RRMl) has been shown previously to be the second stem-loop of Ul RNA. We have found that a target for the second RRM (RRM2) is within the AUUUGURA motifs of the USE of the SV40 late polyadenylation signal. RNA substrates containing the wild-type USE efficiently bind to Ul snRNP-A protein, whereas substrates fail to bind when motifs of the USE were replaced by linker sequences. The addition of an oligoribonucleotide containing a USE motif to an in vitro polyadenylation reaction inhibits polyadenylation of a substrate representing the SV40 late polyadenylation signal, whereas a mutant oligoribonucleotide, a nonspecific oligoribonucleotide, and an oligoribonucleotide containing the Ul RNA-binding site had much reduced or no inhibitory effects. In addition, antibodies to bacterially produced, purified Ul snRNP-A protein specifically inhibit in vitro polyadenylation of the SV40 late substrate. These data suggest that the Ul snRNP-A protein performs an important role in polyadenylation through interaction with the USE. Because this interaction can occur when Ul snRNP-A protein is part of the Ul snRNP, our data provide evidence to support a link between the processes of splicing and polyadenylation, as suggested by the exon definition model.

“…Sequences that enhance 3' processing have been identified upstream of the SV40 late (Carswell and Alwine 1989;Schek et al 1992), adenovirus L1 (DeZazzo and Imperiale 1989;DeZazzo et al 1991a), L3 (Prescott andFalck-Pedersen 1992, 1994), and L4 (Sittler et al 1994), hepatitis B virus (Russnak and Ganem !990;Russnak 1991;Cherrington et al 1992), and HIV-1 (Brown et al 1991;DeZazzo et al 1991b;Valsamakis et al 1991;Cherrington and Ganem 1992) core poly(A) sites. These elements function in an orientationand position-dependent manner, and several appear to be functionally analogous (Russnak and Ganem 1990;Valsamakis et al 1991).…”

mentioning

confidence: 99%

CPSF recognition of an HIV-1 mRNA 3'-processing enhancer: multiple sequence contacts involved in poly(A) site definition.

Gilmartin¹,

Fleming²,

Oetjen³

et al. 1995

119

141

The endonucleolytic cleavage and polyadenylation of a pre-mRNA in mammalian cells requires two c/s-acting elements, a highly conserved AAUAAA hexamer and an amorphous U-or GU-rich downstream element, that together constitute the "core" poly(A) site. The terminal redundancy of the HIV-1 pre-mRNA requires that the processing machinery disregard a core poly(A) site at the 5' end of the transcript, and efficiently utilize an identical signal that resides near the 3' end. Efficient processing at the 3' core poly(A) site, both in vivo and in vitro, has been shown to require sequences 76 nucleotides upstream of the AAUAAA hexamer. In this report we demonstrate that this HIV-1 upstream element interacts directly with the 160-kD subunit of CPSF (cleavage polyadenylation specificity factor), the factor responsible for the recognition of the AAUAAA hexamer. The presence of the upstream element in the context of the AAUAAA hexamer directs the stable binding of CPSF to the pre-mRNA and enhances the efficiency of poly(A) addition in reactions reconstituted with purified CPSF and recombinant poly(A) polymerase. Our results indicate that the dependence of HIV-1 3' processing on upstream sequences is a consequence of the suboptimal sequence context of the AAUAAA hexamer. We suggest that poly(A) site definition involves the recognition of multiple heterogeneous sequence elements in the context of the AAUAAA hexamer.