Afasizheva, I. | Search bioRxiv

bioRxiv2022

A toolkit to handle T-less alignment for U insertion/deletion RNA editing

SummaryIn the mitochondrial genome of kinetoplastids, the targeted insertion and deletion of uridine in cryptic mRNA is essential to generate functional protein-coding mRNAs, but such process leads to a highly hetergenous and complex RNA population. Few tools were developped to perform alignment based on a T depleted strategy for such mRNA population, however to our knowledge no downstream analysis tool is available so far to allow easy data processing and interpretation. Here, we fill this gap with the T-less-Alignment-Toolkit, which provides useful functions such as duplication removal with UMI, alignment strandness analysis, statistical summary and visualization. Availability and ImplementationScripts and toolkits can be downloaded at https://gitee.com/Zhanglab/tless-alignment-toolkit

bioinformatics↗

bioRxiv2018

Pentatricopeptide repeat poly(A) binding protein from mitochondria of trypanosomes

In Trypanosoma brucei, most mitochondrial mRNAs undergo U-insertion/deletion editing, and 3' adenylation and uridylation. The internal sequence changes and terminal extensions are coordinated: Pre-editing addition of the short (A) tail protects the edited transcript against 3'-5' degradation, while post-editing A/U-tailing renders mRNA competent for ribosome recruitment. Participation of a poly(A) binding protein (PABP) in coupling of editing and 3' modification processes has been inferred, but its identity and mechanism of action remained elusive. We report identification of KPAF4, a pentatricopeptide repeat-containing PABP which sequesters the A-tail and impedes exonucleolytic degradation. Conversely, KPAF4 inhibits uridylation of A-tailed transcripts and, therefore, premature A/U-tailing of partially-edited mRNAs. This quality check point prevents translation of incompletely edited mRNAs. Our findings also implicate the RNA editing substrate binding complex (RESC) in mediating the interaction between the 5' end bound pyrophosphohydrolase MERS1 and 3' end associated KPAF4 to enable mRNA circularization. This event is critical for transcript stability during the editing process.

biochemistry↗