Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation

Abstract

Messenger RNA (mRNA) 3' end formation is a nuclear process through which all eukaryotic primary transcripts are endonucleolytically cleaved and most of them acquire a poly(A) tail. This process, which consists in the recognition of defined poly(A) signals of the pre-mRNAs by a large cleavage/polyadenylation machinery, plays a critical role in gene expression. Indeed, the poly(A) tail of a mature mRNA is essential for its functions, including stability, translocation to the cytoplasm and translation. In addition, this process serves as a bridge in the network connecting the different transcription, capping, splicing and export machineries. It also participates in the quantitative and qualitative regulation of gene expression in a variety of biological processes through the selection of single or alternative poly(A) signals in transcription units. A large number of protein factors associates with this machinery to regulate the efficiency and specificity of this process and to mediate its interaction with other nuclear events. Here, we review the eukaryotic 3' end processing machineries as well as the comprehensive set of regulatory factors and discuss the different molecular mechanisms of 3' end processing regulation by proposing several overlapping models of regulation.

Figure 1.

The 3′ end processing at single or multiple pA signals and its interconnections with the splicing/transcription machineries. Alternative 3′ end processing occurs through the selection of pA signals in the same exon or in different alternative exons. The physical and functional interdependence between 3′ end processing and transcription/splicing is represented by red/green dotted lines.

Figure 2.

Schematic drawing of the eukaryotic 3′ end processing machineries. Known factors and cis-elements contributing to 3′ end processing of metazoan (A), yeast (B) and plant (C) pre-mRNAs, as described in the text. Homologous factors are color-matched while specific factors are in gray. The position of the different factors takes into account the RNA-binding specificity of each factor and, where possible, the protein contacts within the machinery. The sequence elements that comprise the poly(A) signals are indicated by black rectangles, and the site of cleavage [and subsequent poly(A) tail addition] is shown by a red dotted-line. In (C) ‘At’ stands for Arabidopsis thaliana.

Figure 3.

Mechanistic models of 3′ end processing regulation of eukaryotic pre-mRNAs. Based on different examples of pre-mRNA 3′ end processing regulation, eight mechanisms of action can be delineated. (A) Competition with pA factors for binding to a (C) Poly(A) signal (pA signal). (B) Inhibitory interaction between PAP and RNA-bound factors. (C) Poly(A) signal recognition in kinetic competition with splicing and transcription. (D) Recruitment of pA factors to a poly(A) signal. (E) Redirection to alternative poly(A) sites. (F) Redistribution of pA factors to the cytoplasm. (G) Redistribution of pA factors in nuclear complexes. (H) Post-translational modification (PTM) of pre-mRNA 3′ end processing factors and regulators. 3′ end processing regulators are in red (negative regulation) or in green (positive regulation) while pA factors are in white. Protein–protein interactions are indicated with double-headed harrows while the RNA-binding activity of regulatory or pA factors is depicted with a thick, simple arrow in gray.