Alternative cleavage and polyadenylation: the long and short of it

Abstract

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.

Figure 1

Alternative cleavage and polyadenylation sites (pAs) in a gene. (A) Alternative cleavage and polyadenylation (APA) in 3′-most exon. A hypothetical gene is shown, with two pAs located in the 3′-most exon. The top gray line is genomic DNA with exons boxed, and bottom lines are mRNAs. Coding sequence (CDS) and 3′ untranslated region (UTR) are shown as thick and thin blue lines, respectively, as indicated in the graph, splicing as bent line, and pAs as arrowheads. AAA_n indicates the poly(A) tail. (B) APA in upstream regions. The type of terminal exon is indicated. The top mRNA shows only splicing. Skipped, skipped terminal exon; composite, composite (internal/terminal) exon; exonic, upstream exon.

Figure 2

Regulation of cis elements in 3′ untranslated regions (UTRs) by alternative cleavage and polyadenylation (APA). Two mRNA isoforms are shown. The 3′ UTR region upstream of the proximal cleavage and polyadenylation site (pA) is called the constitutive UTR (cUTR), and the downstream region is called the alternative UTR (aUTR). RNA-binding protein (RBP) and miRNA targeting to the aUTR are shown. Impacts on mRNA localization, translation, and degradation are indicated. CDS, coding sequence.

Figure 3

Regulation of the cleavage and polyadenylation machinery in 3′ end processing. (A) Some cleavage and polyadenylation (C/P) factors (yellow boxes) are recruited at the promoter by transcription activators (TAs) or other unknown mechanisms. (B) The pA is surrounded by several core cis elements, as indicated. The components of the C/P complex are indicated, and those binding to core elements are shown in red. Cleavage factor (CF)I and cleavage stimulation factor (CstF) are dimers, shown as two overlapping boxes. Phosphorylation of the RNA polymerase (RNAP) II carboxy terminal domain (CTD) is indicated. Splicing factors, such as U1 small nuclear ribonucleoprotein (snRNP), U2 snRNP, and U2AF65, interact with the C/P complex. Arrow indicates positive regulation of C/P and T-ended line indicates negative regulation. Two nucleosomes are shown (right), as well as attached symbols representing histone marks, such as H3K36me3. Other RNA-binding proteins (RBPs) can bind to sequences near the pA, thereby enhancing or inhibiting C/P. CPSF, cleavage and polyadenylation specificity factor; hFip1, human Fip1; PABPN, nuclear poly(A)-binding protein; PAP, poly(A) polymerase; PAS, polyadenylation signal; Wdr33, WD repeat domain 33.