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

Motivation 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 TAILcaller to empower researchers to perform analyses based on poly(A) tail length. TAILcaller is particularly useful for researchers utilizing nanopore sequencing, as it allows for direct analysis of data from BAM files generated by dorado, eliminating the need for complex scripts and intermediate tools. TAILcaller supports direct RNA sequencing data generated by dorado (—estimate-poly-a) and cDNA sequencing reads processed analogously. Results The TAILcaller program was utilized to investigate changes in poly(A) tail lengths in response to nanoplastic exposure and in Riccia fluitans 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 Riccia fluitans. Numerous genes with differential poly(A) tail lengths were effectively identified by TAILcaller’s adaptive statistical functions, thereby demonstrating its utility in detecting subtle biological responses. Availability and implementation TAILcaller is available at https://github.com/Mordziarz/TAILcaller.