Review
Alternative cleavage and polyadenylation: the long and short of it

https://doi.org/10.1016/j.tibs.2013.03.005Get rights and content

Highlights

  • Alternative cleavage and polyadenylation (APA) is widespread in eukaryotes.

  • APA impacts the cellular transcriptome and proteome.

  • APA is dynamic under different biological conditions.

  • APA is modulated by multiple mechanisms.

Cleavage and polyadenylation (C/P) of nascent transcripts is essential for maturation of the 3′ ends of most eukaryotic mRNAs. Over the past three decades, biochemical studies have elucidated the machinery responsible for the seemingly simple C/P reaction. Recent genomic analyses have indicated that most eukaryotic genes have multiple cleavage and polyadenylation sites (pAs), leading to transcript isoforms with different coding potentials and/or variable 3′ untranslated regions (UTRs). As such, alternative cleavage and polyadenylation (APA) is an important layer of gene regulation impacting mRNA metabolism. Here, we review our current understanding of APA and recent progress in this field.

Section snippets

APA is widespread in eukaryotes

The mechanism of 3′ end processing of nascent transcripts in eukaryotic cells is determined by the type of RNA polymerase used for transcription and specific signals embedded in the transcript (reviewed in [1]). Except for most replication-dependent histone mRNAs in metazoans, and some protozoans (reviewed in [2]), all pre-mRNAs are processed by C/P, which involves endonucleolytic cleavage of the nascent RNA and synthesis of a poly(A) tail (reviewed in [3]), and is a necessary prelude to

APA impacts the cellular transcriptome and proteome

A given gene can encode transcripts with multiple pAs located in different regions (Figure 1). With respect to the impact on protein-coding, alternative pAs in the 3′-most exon typically leads to variable 3′ UTRs, whereas pAs in upstream introns and exons cause both coding sequence (CDS) and 3′ UTR changes. Alternative pAs in introns can be further divided into two subtypes depending on the configuration of the terminal exon in which they reside: namely, skipped terminal exons (a whole exon is

Tissue specificity

Studies of individual genes over the past two decades have reported hundreds of cases in which APA isoforms are differentially expressed under different cellular conditions (some early studies are reviewed in [35]). Global analysis of APA isoforms using expressed sequence tag (EST) libraries has indicated variation of expression in different tissues 25, 36, suggesting that APA isoform expression is not stochastic. Some human tissues have been found to have a global tendency favoring certain

Regulation of core C/P factor expression

The core components of the mammalian C/P machinery include ~15 polypeptides, most of which exist in multisubunit subcomplexes (Box 3 and Figure 3). Regulation of APA by modulation of core factor expression was first demonstrated for cleavage stimulation factor (CstF)-64, one of the subunits of the CstF complex (Box 3), which is strongly upregulated during B cell maturation, resulting in higher usage of the upstream intronic pA in the IgM pre-mRNA [28] (discussed previously). This has been shown

Concluding remarks

Building upon biochemical studies of 3′ end processing in the past three decades, recent advances at the molecular and systems levels concerning APA have stimulated interest in comprehending this dynamic process and its widespread implications for regulation of gene expression and cell growth control. Many questions remain to be addressed in the coming years. For instance, with the availability of powerful deep sequencing methods to study APA isoforms, thorough understanding of APA in different

Acknowledgments

We thank our laboratory members for helpful discussions. We apologize for not citing many important papers related to the topic owing to space limitation. This work was funded by grants GM 84089 (B.T.) and GM 28983 (J.L.M.) from National Institutes of Health.

References (104)

  • S. Vorlova

    Induction of antagonistic soluble decoy receptor tyrosine kinases by intronic polyA activation

    Mol. Cell

    (2011)
  • P. Yao

    Coding region polyadenylation generates a truncated tRNA synthetase that counters translation repression

    Cell

    (2012)
  • K.C. Wang et al.

    Molecular mechanisms of long noncoding RNAs

    Mol. Cell

    (2011)
  • S.W. Flavell

    Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection

    Neuron

    (2008)
  • S. Danckwardt

    p38 MAPK controls prothrombin expression by regulated RNA 3′ end processing

    Mol. Cell

    (2011)
  • W. Li

    Star-PAP control of BIK expression and apoptosis is regulated by nuclear PIPKIalpha and PKCdelta signaling

    Mol. Cell

    (2012)
  • C. Mayr et al.

    Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells

    Cell

    (2009)
  • G. Martin

    Genome-wide analysis of pre-mRNA 3′ end processing reveals a decisive role of human cleavage factor I in the regulation of 3′ UTR length

    Cell Rep.

    (2012)
  • M. Jenal

    The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites

    Cell

    (2012)
  • H. Zhu

    Hu proteins regulate polyadenylation by blocking sites containing U-rich sequences

    J. Biol. Chem.

    (2007)
  • G.G. Simpson

    FY is an RNA 3′ end-processing factor that interacts with FCA to control the Arabidopsis floral transition

    Cell

    (2003)
  • A. Kyburz

    Direct interactions between subunits of CPSF and the U2 snRNP contribute to the coupling of pre-mRNA 3′ end processing and splicing

    Mol. Cell

    (2006)
  • S.I. Gunderson

    U1 snRNP inhibits pre-mRNA polyadenylation through a direct interaction between U1 70K and poly(A) polymerase

    Mol. Cell

    (1998)
  • M.G. Berg

    U1 snRNP determines mRNA length and regulates isoform expression

    Cell

    (2012)
  • A.R. Kornblihtt

    Promoter usage and alternative splicing

    Curr. Opin. Cell Biol.

    (2005)
  • M. Yonaha et al.

    Specific transcriptional pausing activates polyadenylation in a coupled in vitro system

    Mol. Cell

    (1999)
  • E. Rosonina

    Transcriptional activators control splicing and 3′-end cleavage levels

    J. Biol. Chem.

    (2003)
  • T. Nagaike

    Transcriptional activators enhance polyadenylation of mRNA precursors

    Mol. Cell

    (2011)
  • Y. Huang

    Mediator complex regulates alternative mRNA processing via the MED23 subunit

    Mol. Cell

    (2012)
  • T. Uhlmann

    The VP16 activation domain establishes an active mediator lacking CDK8 in vivo

    J. Biol. Chem.

    (2007)
  • R.F. Luco

    Epigenetics in alternative pre-mRNA splicing

    Cell

    (2011)
  • N. Spies

    Biased chromatin signatures around polyadenylation sites and exons

    Mol. Cell

    (2009)
  • L. Salmena

    A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?

    Cell

    (2011)
  • F. Ozsolak

    Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation

    Cell

    (2010)
  • P. Richard et al.

    Transcription termination by nuclear RNA polymerases

    Genes Dev.

    (2009)
  • W.F. Marzluff

    Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

    Nat. Rev. Genet.

    (2008)
  • D.F. Colgan et al.

    Mechanism and regulation of mRNA polyadenylation

    Genes Dev.

    (1997)
  • S. Danckwardt

    3′ end mRNA processing: molecular mechanisms and implications for health and disease

    EMBO J.

    (2008)
  • A. Derti

    A quantitative atlas of polyadenylation in five mammals

    Genome Res.

    (2012)
  • M. Hoque

    Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing

    Nat. Methods

    (2013)
  • C.H. Jan

    Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

    Nature

    (2011)
  • I. Ulitsky

    Extensive alternative polyadenylation during zebrafish development

    Genome Res.

    (2012)
  • N.J. Proudfoot

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

    Genes Dev.

    (2011)
  • Y. Shi

    Alternative polyadenylation: new insights from global analyses

    RNA

    (2012)
  • M.R. Fabian et al.

    The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC

    Nat. Struct. Mol. Biol.

    (2012)
  • R. Sandberg

    Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites

    Science

    (2008)
  • Z. Ji

    Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

    Proc. Natl. Acad. Sci. U.S.A.

    (2009)
  • N.L. Garneau

    The highways and byways of mRNA decay

    Nat. Rev. Mol. Cell Biol.

    (2007)
  • Y.K. Kim

    Staufen1 regulates diverse classes of mammalian transcripts

    EMBO J.

    (2007)
  • R.R. Graham

    Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus

    Proc. Natl. Acad. Sci. U.S.A.

    (2007)
  • Cited by (261)

    View all citing articles on Scopus
    View full text