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Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data.

ABSTRACT: Intronic polyadenylation (IpA) usually leads to changes in the coding region of an mRNA, and its implication in diseases has been recognized, although at its very beginning status. Conveniently and accurately identifying IpA is of great importance for further evaluating its biological significance. Here, we developed IPAFinder, a bioinformatic method for the de novo identification of intronic poly(A) sites and their dynamic changes from standard RNA-seq data. Applying IPAFinder to 256 pan-cancer tumor/normal pairs across six tumor types, we discovered 490 recurrent dynamically changed IpA events, some of which are novel and derived from cancer-associated genes such as TSC1, SPERD2, and CCND2 Furthermore, IPAFinder revealed that IpA could be regulated by factors related to splicing and m⁶A modification. In summary, IPAFinder enables the global discovery and characterization of biologically regulated IpA with standard RNA-seq data and should reveal the biological significance of IpA in various processes.

SUBMITTER: Zhao Z

PROVIDER: S-EPMC8559711 | biostudies-literature |

REPOSITORIES: biostudies-literature

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flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data.

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Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq.

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Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq.

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scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data.

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scAPAmod: Profiling Alternative Polyadenylation Modalities in Single Cells from Single-Cell RNA-Seq Data.

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