Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation

Argonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA 'guide' sequences, and identifies its targets primarily via a 'seed' mediated partial complementarity process. Despite numerous studies, a definitive experimental dataset of AGO2 'guide'-'target' interactions remains elusive. Our study employs two experimental methods-AGO2 CLASH and AGO2 eCLIP, to generate thousands of AGO2 target sites verified by chimeric reads. These chimeric reads contain both the AGO2 loaded small RNA 'guide' and the target sequence, providing a robust resource for modeling AGO2 binding preferences. Our novel analysis pipeline reveals thousands of AGO2 target sites driven by microRNAs and a significant number of AGO2 'guides' derived from fragments of other small RNAs such as tRNAs, YRNAs, snoRNAs, rRNAs, and more. We utilize convolutional neural networks to train machine learning models that accurately predict the binding potential for each 'guide' class and experimentally validate several interactions. In conclusion, our comprehensive analysis of the AGO2 targetome broadens our understanding of its 'guide' repertoire and potential function in development and disease. Moreover, we offer practical bioinformatic tools for future experiments and the prediction of AGO2 targets. All data and code from this study are freely available at https://github.com/ML-Bioinfo-CEITEC/HybriDetector/ .

Evaluating automatic sentence alignment approaches on English-Slovak sentences

Parallel texts represent a very valuable resource in many applications of natural language processing. The fundamental step in creating parallel corpus is the alignment. Sentence alignment is the issue of finding correspondence between source sentences and their equivalent translations in the target text. A number of automatic sentence alignment approaches were proposed including neural networks, which can be divided into length-based, lexicon-based, and translation-based. In our study, we used five different aligners, namely Bilingual sentence aligner (BSA), Hunalign, Bleualign, Vecalign, and Bertalign. We evaluated both, the performance of the Bertalign in terms of accuracy against the up to now employed aligners as well as among each other in the language pair English-Sovak. We created our custom corpus consisting of texts collected in 2021 and 2022. Vecalign and Bertalign performed statistically significantly best and BSA the worst. Hunalign and Bleualign achieved the same performance in terms of F1 score. However, Bleualign achieved the most diverse results in terms of performance.