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Alternative cleavage and polyadenylation in health and disease

Nature Reviews Genetics volume 20, pages 599–614 (2019)Cite this article

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Abstract

Most human genes have multiple sites at which RNA 3ʹ end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3′ ends have generated comprehensive catalogues of polyadenylation (poly(A)) sites; their analysis using innovative computational methods has revealed how poly(A) site choice is regulated by core RNA 3ʹ end processing factors, such as cleavage factor I and cleavage and polyadenylation specificity factor, as well as by other RNA-binding proteins, particularly splicing factors. Here, we review the experimental and computational methods that have enabled the global mapping of mRNA and of long non-coding RNA 3ʹ ends, quantification of the resulting isoforms and the discovery of regulators of alternative cleavage and polyadenylation (APA). We highlight the different types of APA-derived isoforms and their functional differences, and illustrate how APA contributes to human diseases, including cancer and haematological, immunological and neurological diseases.

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Fig. 1: Overview of core 3ʹ end processing factors and their interaction elements in RNAs.
Fig. 2: Types of isoforms generated by alternative cleavage and polyadenylation.
Fig. 3: Consequences of alternative cleavage and polyadenylation.
Fig. 4: Impact of RNA-binding proteins on pre-mRNA processing.
Fig. 5: Dysregulation of cleavage and polyadenylation in human diseases.

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Acknowledgements

The authors thank G. Martin and W. Keller for numerous discussions.

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Authors and Affiliations

  1. Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK

    Andreas J. Gruber

  2. Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland

    Mihaela Zavolan

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Related links

ENSEMBL: https://www.ensembl.org/

STRINGTIE: https://ccb.jhu.edu/software/stringtie/

The Cancer Genome Atlas: https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga

Glossary

Poly(A) sites

(Also referred to as CPA sites or 3ʹ end processing sites). Single nucleotides after which a pre-mRNA is cleaved and the non-template synthesis of the poly(A) tail is initiated.

Alternative cleavage and polyadenylation

(APA). The process by which the distinct poly(A) sites of a gene are processed under distinct conditions to give rise to different transcript isoforms.

3′ UTR isoforms

Isoforms that differ only in their 3′ untranslated regions (UTRs). They are generated through RNA 3′ end processing at alternative poly(A) sites.

Poly(A) signal

(PAS). The main sequence element that defines 3′ end processing sites. It is bound by the WDR33 and CPSF4 proteins of the CPSF complex and most commonly has the sequence AAUAAA.

Terminal exon

The last exon of a transcript.

Cassette TEs

Exons that are included as terminal exons in some transcripts generated from a gene but spliced out in others.

Effector T cells

Relatively short-lived T lymphocytes that have been ‘primed’ by various signals and are ready to interact with the pathogen.

Small nuclear ribonucleoprotein

(snRNP). An RNA–protein complex that participates in RNA splicing, together with proteins and pre-mRNAs. The snRNPs are U1, U2, U4, U5, U6, U11, U12 and U4atac.

Adaptive immune response

The defence mechanism against microbial pathogens in vertebrates. It is based on a complex immune system that is trained during development to distinguish structures germane to the organism (self) from external structures (non-self).

Cis-regulatory elements

Regions in a nucleic acid that regulate the expression of the associated gene and transcript.

Telescripting

The small nuclear ribonucleoprotein U1 suppresses premature cleavage and polyadenylation at cryptic poly(A) sites in nascent RNA polymerase II transcripts. As this suppressive activity of U1 is required for full-length gene transcription, it is termed ‘telescripting’.

Alu transposable elements

Short, mobile DNA elements that can change (transpose) their position in the genome with the help of trans-acting factors.

Crosslinking and immunoprecipitation

A method for identifying the targets of RNA-binding proteins (RBPs). It involves crosslinking a protein of interest to RNAs using ultraviolet irradiation, followed by partial RNA digestion, immunoprecipitation of the protein with bound RNAs and sequencing of RBP-bound RNA fragments.

Single-nucleotide polymorphisms

(SNPs). Variations at a defined position in the genome; some individuals in the population carry a particular nucleotide at that position, while other individuals carry a different nucleotide.

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Gruber, A.J., Zavolan, M. Alternative cleavage and polyadenylation in health and disease. Nat Rev Genet 20, 599–614 (2019). https://doi.org/10.1038/s41576-019-0145-z

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