Pre-mRNA 3'-end processing complex assembly and function

Abstract

The 3'-ends of almost all eukaryotic mRNAs are formed in a two-step process, an endonucleolytic cleavage followed by polyadenylation (the addition of a poly-adenosine or poly(A) tail). These reactions take place in the pre-mRNA 3' processing complex, a macromolecular machinery that consists of more than 20 proteins. A general framework for how the pre-mRNA 3' processing complex assembles and functions has emerged from extensive studies over the past several decades using biochemical, genetic, computational, and structural approaches. In this article, we review what we have learned about this important cellular machine and discuss the remaining questions and future challenges.

Figure 1. Comparison of the poly(A) signals from animals (canonical) the budding yeast (S. cerevisiae) and plants

USE: upstream element; DSE: downstream element; auxDSE: auxiliary downstream element; EE, efficiencty element; PE, positioning element; UUE, upstream U-rich element; DUE, downstream U-rich element; FUE, far upstream element; NUE, near upstream element; URE, U-rich element. Same colors are used for similar cis-element to illustrate the conservation of the basic tripartite poly(A) signal across different phylogenetic groups. Adapted from reference .

Figure 2. The protein-protein interaction network of the mammalian pre-mRNA 3’ processing complex

Circles represent individual proteins except for RNAP II CTD (pink rectangle). Colored rectangles represent subcomplexes. Experimentally verified interactions within subcomplexes are marked with thick black lines. Experimentally verified interactions among subcomplexes are marked with thin black line. Predicted interactions based on information on homologues from other species are marked with grey lines.

Figure 3. Domain structures of CstF 64 and CstF 64τ

Rectangular boxes represent individual domains, which include RRM (RNA recognition motif), hinge domain, Pro/Gly (proline/glycine-rich domain), 12/8× MEARA/G (12/8 tandem copies of MEARA/G repeats), and CTD (C-terminal domain). Adapted from reference .

Figure 4. Domain structures of the three nuclear mammalian PAPs

Rectangular boxes represent individual domains, which include NTP (Nucleotidyltransferase domain), RBP (PAP RNA-binding domain), NLS (nuclear localization signal), S/T (serine/threonine-rich domain), ZF (zinc finger domain), RRM (RNA recognition motif), PRR (proline-rich domain), and RS (RS domain). Adapted from reference .

Figure 5. Domain structure of yeast and human PABPs

Rectangular boxes represent individual domains, which include RRM (RNA recognition motif), 5H (a unique 5 conserved helices domain), RGG (RGG box involved in RNA binding), N-terminal (N-terminal domain), Q-rich (Q-rich domain) and CCCH (zinc finger domain). Adapted from reference .

Figure 6. A proposed model for the mammalian pre-mRNA 3’ processing complex

The core complex consists of CPSF bound to the A(A/U)UAAA element, CstF bound to the downstream U/GU-rich DSE as a dimer, CF Im bound to the UGUA sequences also as a dimer, and the RNAP II CTD. The nuclear PAPs (PAP/neo-PAP/star-PAP) and CF IIm associate with the core complex weakly and/or transiently.