Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 in HeLa cells was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects.

可变聚腺苷酸化（alternative polyadenylation）已被证实为基因表达的重要调控机制。在部分情境中，可变聚腺苷酸化可与可变剪接（alternative splicing）协同作用，参与最后一个内含子的移除过程。然而，目前尚不清楚可变聚腺苷酸化事件是否会对上游外显子处的可变剪接决策产生影响。本研究以海拉细胞（HeLa cells）中聚腺苷酸化因子CFIm25或CstF64的基因敲低（knockdown）为实验手段，在全基因组尺度上鉴定可变聚腺苷酸化与可变剪接事件。尽管在CstF64敲低组中发现了数百个差异可变剪接事件，但与可变聚腺苷酸化相关的基因并未表现出可变剪接发生率的显著升高。上述结果表明，可变聚腺苷酸化与可变剪接之间的协同耦合通常仅局限于对最后一个外显子的界定。CstF64敲低对可变剪接的显著影响，可通过其对已知剪接调控因子（如异质性核核糖核蛋白A2/B1（hnRNP A2/B1））的非翻译区（Untranslated Region，UTR）选择的调控作用得到解释，进而间接影响剪接位点的选择。综上，聚腺苷酸化因子CstF64的表达改变可通过间接效应影响可变剪接过程。