mRNA 3'end processing: A tale of the tail reaches the clinic

Abstract

Recent advances reveal mRNA 3'end processing as a highly regulated process that fine-tunes posttranscriptional gene expression. This process can affect the site and/or the efficiency of 3'end processing, controlling the quality and the quantity of substrate mRNAs. The regulation of 3'end processing plays a central role in fundamental physiology such as blood coagulation and innate immunity. In addition, errors in mRNA 3'end processing have been associated with a broad spectrum of human diseases, including cancer. We summarize and discuss the paradigmatic shift in the understanding of 3'end processing as a mechanism of posttranscriptional gene regulation that has reached clinical medicine.

Figure 1

Endonucleolytic cleavage of pre-mRNAs and their subsequent polyadenylation requires the four multisubunit complexes CPSF, CstF, cleavage factor I (CFIm) and cleavage factor II (CFIIm) as well as the single-subunit polyadenylation-polymerase PAP. At the PAS CPSF and CstF bind to the central hexameric sequence (AA/UUAAA) and to the GU/U-rich DSE, respectively, as the first step in mRNA 3′end processing. The other protein complexes assemble at specific RNA sequence elements both up- and down-stream of the PAS, including several UGUA-repeats, thereby ensuring efficient cleavage and polyadenylation of an mRNA. The pre-mRNA is cleaved at the CS by the endonuclease CSPF73 before the nuclear poly(A) polymerase adds ∼200 As to the 3′end. This poly(A) tail stabilizes the processed mRNA for nuclear export upon binding of the nuclear poly(A) binding protein (PABPN1) which is subsequently exchanged for its cytoplasmic counterpart PABPC which promotes translation and RNA stability.

Figure 2

In a quantitative manner, the regulation of 3′end processing stimulates or inhibits the gene expression via the formation of specific mRNPs. Qualitatively, mRNAs containing more than one polyadenylation signal (PAS) can be subjected to APA. In case both PAS are present in the 3′UTR (PAS1 and PAS 2a), APA results in the expression of mRNA isoforms that encode the same protein (protein 1) but differ in the length of their 3′UTR (mRNA 1, mRNA 2a), including or excluding regulatory elements such as miRNA or RBP binding sites. If one poly(A) signal is contained within the coding region (PAS 2b), APA produces mRNA isoforms with distinct C-terminal coding regions (mRNA 2a and mRNA 2b), which leads to the expression of different protein isoforms (protein 1 and protein 2).

Figure 3

The control of 3′end processing post-transcriptionally adjusts mRNA and protein levels in response to environmental conditions, such as stress or inflammation. Further, it plays a role in development and differentiation, as in the case of the immunoglobulin heavy chain class switch and in the development of the central nervous system (CNS). In addition, alternative 3′end processing functions as a regulatory mechanism upon cell activation, e.g. T-cell activation, and proliferation. While a progressive lengthening of 3′UTRs via APA is typically observed during development and differentiation, higher proliferation states are associated with global 3′UTR shortening.

Figure 4

Misregulation of mRNA 3′end processing can be caused by constitutive errors incis-acting RNA elements, mutations of trans-acting proteins or changes in poly(A) site usage of otherwise normal transcripts. Mutations in RNA sequence elements or trans-acting proteins both potentially interfere with the interaction of RBPs and the RNA, leading to gain or loss of function. APA triggers the production of mRNAs varying in the length of their 3′UTR or in their C-terminal coding region, which leads to the expression of different protein isoforms. Certain diseases, such as cancer, are characterized by a polyadenylation pattern significantly different from the one in a healthy state.