TAILcaller: an R package for analyzing differences in poly(A) tail length for Oxford Nanopore RNA sequencing

<h4>Motivation</h4>Changes in poly(A) tail length were identified as a key post-transcriptional mechanism that controls protein synthesis. The length of the poly(A) tail was shown to directly impact mRNA stability and translation, broadening its regulatory scope. A thorough understanding of poly(A) tail dynamics is considered essential for deciphering how genes are regulated and what role they play in cellular function. Therefore, we developed <i>TAILcaller</i> to empower researchers to perform analyses based on poly(A) tail length. <i>TAILcaller</i> is particularly useful for researchers utilizing nanopore sequencing, as it allows for direct analysis of data from BAM files generated by <i>dorado</i>, eliminating the need for complex scripts and intermediate tools. <i>TAILcaller</i> supports direct RNA sequencing data generated by <i>dorado</i> (-estimate-poly-a) and cDNA sequencing reads processed analogously.<h4>Results</h4>The <i>TAILcaller</i> program was utilized to investigate changes in poly(A) tail lengths in response to nanoplastic exposure and in <i>Riccia fluitans</i> under varying environmental conditions. Significant differences in poly(A) tail lengths were revealed across different nanoplastic concentrations, with distinct patterns being observed between control and exposed groups. Furthermore, a global elongation in poly(A) tail lengths was noted in the aquatic environment compared to the terrestrial environment in <i>R. fluitans</i>. Numerous genes with differential poly(A) tail lengths were effectively identified by <i>TAILcaller</i>'s adaptive statistical functions, thereby demonstrating its utility in detecting subtle biological responses.<h4>Availability and implementation</h4><i>TAILcaller</i> is available at https://github.com/Mordziarz/TAILcaller.