Widespread Presence of Catalytic RNAs in All Domains of Life

Very few ribozymes have been found in complex eukaryotes. Here, we developed a novel method, AbRiDGed, for highly accurate and sensitive ab initio self-cleaving ribozyme discovery. Our results indicate the existence of millions of self-cleaving ribozymes in humans and other species. We characterized ~150 novel classes of self-cleaving ribozymes, including one class which exhibits noncanonical biochemical properties and widespread presence in all domains of life and appears to play specific functions in complex organisms. These results revealed that the true complexity of the "ribozyme-ome" is several orders of magnitude higher than previously estimated. We demonstrate that newly identified self-cleaving ribozymes influence organismal fitness by regulating gene expression and enhancing transcriptome complexity in vivo . Moreover, these ribozymes hold promise as foundational tools for biotechnological applications, such as direct RNA detection technologies. Overall, catalytic RNAs are prevalent and diverse, and may represent a hidden regulatory layer in various organisms.

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Publication Details

Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2026-10-28
DOI
https://doi.org/10.64898/2026.10.26.761763
Primary Topic
RNA and protein synthesis mechanisms
Type
preprint

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preprint

Widespread Presence of Catalytic RNAs in All Domains of Life

Fei Qi, Junjie Chen, Philipp Kapranov, Zipeng Chen et al.
bioRxiv (Cold Spring Harbor Laboratory)
RNA and protein synthesis mechanisms
preprint

Widespread Presence of Catalytic RNAs in All Domains of Life

Fei Qi, Junjie Chen, Philipp Kapranov, Zipeng Chen, Yonghong Zhao, David M.J. Lilley, Yue Chen, Yuhe Zhong, Meng Li, Wenjing Yin, Yiting Lin, Huang Lin, Siqi Chen, Qinling Tang, Fuchun Zhang, Wenzhui Zhang, Ilia Kruglikov, Kejia Li
preprint en

Abstract

Very few ribozymes have been found in complex eukaryotes. Here, we developed a novel method, AbRiDGed, for highly accurate and sensitive ab initio self-cleaving ribozyme discovery. Our results indicate the existence of millions of self-cleaving ribozymes in humans and other species. We characterized ~150 novel classes of self-cleaving ribozymes, including one class which exhibits noncanonical biochemical properties and widespread presence in all domains of life and appears to play specific functions in complex organisms. These results revealed that the true complexity of the "ribozyme-ome" is several orders of magnitude higher than previously estimated. We demonstrate that newly identified self-cleaving ribozymes influence organismal fitness by regulating gene expression and enhancing transcriptome complexity in vivo . Moreover, these ribozymes hold promise as foundational tools for biotechnological applications, such as direct RNA detection technologies. Overall, catalytic RNAs are prevalent and diverse, and may represent a hidden regulatory layer in various organisms.

bioRxiv (Cold Spring Harbor Laboratory)
Huaqiao University (CN), Sun Yat-sen University (CN), University of Dundee (GB), Xiamen University (CN)
National Natural Science Foundation of China
RNA and protein synthesis mechanisms
DOISourceOpenAlex
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