Cloning and Detection of Genomic Retrozymes and Their circRNA Intermediates.

@article{Cervera2021CloningAD,  title={Cloning and Detection of Genomic Retrozymes and Their circRNA Intermediates.},  author={Amelia Cervera and Marcos de la Pe{\~n}a},  journal={Methods in molecular biology},  year={2021},  volume={2167},  pages={          27-44        },  url={https://api.semanticscholar.org/CorpusID:220797209}}
This chapter describes the procedures needed to carry out the cloning of genomic retrozymes, and to detect by northern blot their circular RNA retrotransposition intermediates.
2 Citations

2 Citations

Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining.

Viroids, the agents of several plant diseases, are the smallest and simplest known replicators that consist of covalently closed circular (ccc) RNA molecules between 200 and 400 nucleotides in size.…

Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?

Although viroid-like replicators are unlikely to be direct descendants of primordial RNA replicators, the study of the diversity and evolution of these ultimate genetic parasites can yield insights into the earliest stages of the evolution of life.

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Circular RNAs with hammerhead ribozymes encoded in eukaryotic genomes: The enemy at home

It is proposed that retrozymes in time could have evolved from the ancient family of Penelope-like retroelements, which also harbour hammerhead ribozymes, and could have given origin to infectious circRNAs with self-cleaving motifs among eukaryotes.

Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs

This work reveals that circular RNAs with hammerhead ribozymes are frequently occurring molecules in plant and, most likely, metazoan transcriptomes, which explains the ubiquity of these genomic Ribozymes and suggests a feasible source for the emergence of circular RNA plant pathogens.

Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs

The bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes, confirming the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eUKaryotic genomes.

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The hammerhead ribozyme motif is unveiled as a widespread motif in DNA genomes, which would be involved in new forms of retrotransposable elements.

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This work discusses possible biological functions of the genomic motifs of the hammerhead ribozyme, which has been shown to reside in a large number of genomes.

Intronic hammerhead ribozymes are ultraconserved in the human genome

In vitro characterization confirmed a high self-cleavage activity, whereas analysis of RECK‐expressed sequence tags revealed fusion events between the in vivo self‐cleaved intron and U5 or U6 small nuclear RNA fragments, which suggest a conserved role for these ribozymes in messenger RNA biogenesis.

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations

Genomic contexts of many hammerhead ribozymes indicate that they perform biological functions different from their known role in generating unit-length RNA transcripts of multimeric viroid and satellite virus genomes, suggesting that core mutations are occasionally tolerated or preferred.

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The hammerhead ribozyme has been regarded as a biological oddity typical of small circular RNA pathogens of plants, but numerous and new variations of this ribo enzyme have been found to inhabit the genomes of organisms from all life kingdoms, although their precise biological functions are not yet well understood.

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Methods for the generation of DNA templates for the subsequent in vitro transcription of hammerhead ribozymes and their kinetic analysis are described.

Involvement of the Chloroplastic Isoform of tRNA Ligase in the Replication of Viroids Belonging to the Family Avsunviroidae

Results support the conclusion that the chloroplastic isoform of the plant tRNA ligase is the host enzyme mediating circularization of both (+) and (−) monomeric linear intermediates during replication of the viroids belonging to the family Avsunviroidae.

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