Alternative Polyadenylation (APA) ​ 

Understanding Alternative Polyadenylation (APA) and Its Role in Gene Regulation 

Alternative polyadenylation (APA) is a crucial mechanism in gene regulation, producing mRNAs with distinct 3′ ends, and significantly contributing to the complexity of the transcriptome and proteome. Emerging as a prevalent mechanism, APA is found in more than 70% of yeast, Arabidopsis, and mammalian genes, about 50% of Drosophila and zebrafish genes, and roughly 30% of nematode protein-coding genes. This broad occurrence underscores APA’s importance in cellular function and gene diversity.

In mammalian cells, the 3′-end processing machinery involves several multi-subunit protein complexes, including:

• Cleavage and polyadenylation specificity factor (CPSF)
• Cleavage stimulation factor (CstF)
• Cleavage factor I (CFIm)
• Poly(A) polymerase
• Symplekin
• RNA polymerase II (Pol II)

The key players, CPSF30 and WDR33, bind to the poly(A) signal (5′-AAUAAA-3′ or its variant 5′-AUUAAA-3′), located 10-30 nucleotides upstream of the cleavage site, while CstF binds to the U/GU-rich region located downstream of the cleavage site. These interactions are critical for poly(A) site selection.

Temporal and spatial regulation of poly(A) site choice is mediated by trans-acting factors like RNA-binding proteins (RBPs), which, along with cis-elements (poly(A) signals, auxiliary sequences, and RNA secondary structures), orchestrate APA regulation.

Misregulation of APA has been linked to various pathophysiological diseases, carcinogenesis, and developmental defects, making it a crucial focus of research in cancer biology, developmental biology, and disease modeling.