J 2023

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

HEJRET, Václav; Nandan Mysore VARADARAJAN; Eva KLIMENTOVÁ; Katarína GREŠOVÁ; Ilektra-Chara GIASSA et al.

Basic information

Original name

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

Authors

HEJRET, Václav; Nandan Mysore VARADARAJAN; Eva KLIMENTOVÁ; Katarína GREŠOVÁ; Ilektra-Chara GIASSA; Štěpánka VAŇÁČOVÁ and Panagiotis ALEXIOU

Edition

SCIENTIFIC REPORTS, England, NATURE PORTFOLIO, 2023, 2045-2322

Other information

Language

English

Type of outcome

Article in a journal

Country of publisher

Germany

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Marked to be transferred to RIV

Yes

RIV identification code

RIV/00216224:14740/23:00133649

Organization

Středoevropský technologický institut – Repository – Repository

DOI

https://doi.org/10.1038/s41598-023-49757-z

UT WoS

001136279200030

EID Scopus

2-s2.0-85180195179

Keywords in English

Data processing; Machine learning; miRNAs

Links

GA20-19617S, research and development project. GA23-07372S, research and development project. GJ19-10976Y, research and development project. LQ1601, research and development project. NCMG III, large research infrastructures.
Changed: 26/10/2024 00:50, RNDr. Daniel Jakubík

Abstract

In the original language

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/.
Displayed: 2/5/2026 19:04