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mirMachine: A One-Stop Shop for Plant miRNA Annotation
Published on: May 1, 2021
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R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants.
Lucia Gonzalo1, Ileana Tossolini1, Tomasz Gulanicz2,3
1Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina.
Nature Plants
|April 22, 2022
Summary
Plant microRNA (miRNA) biogenesis is coupled to transcription, with R-loops promoting this co-transcriptional processing. Some miRNAs are processed entirely during transcription, while others require a subsequent step.
Area of Science:
- Molecular Biology
- Plant Science
- Genetics
Background:
- RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) into pri-miRNAs in plants, which are structurally variable.
- miRNA biogenesis complex assembly initiates early during pri-miRNA transcription in plants.
- The co-transcriptional nature of plant miRNA processing remains largely unelucidated.
Purpose of the Study:
- To investigate whether plant miRNA biogenesis occurs co-transcriptionally.
- To elucidate the mechanisms and dynamics of miRNA processing in plants.
- To identify factors influencing co-transcriptional miRNA processing.
Main Methods:
- Native elongating transcript sequencing (NET-seq).
- Advanced imaging techniques.
- Analysis of pri-miRNA processing pathways.
Main Results:
- Plant miRNA biogenesis is coupled to transcription.
- Co-transcriptional processing occurs for pri-miRNAs from hairpin loops; base-processed pri-miRNAs require a second nucleoplasmic step.
- R-loops near MIRNA transcription start sites promote co-transcriptional pri-miRNA processing.
- Co- and post-transcriptional processing mechanisms coexist dynamically for most plant miRNAs.
Conclusions:
- Plant miRNA biogenesis is predominantly co-transcriptional, with distinct processing pathways.
- R-loops play a crucial role in facilitating co-transcriptional miRNA processing.
- Co-transcriptionally processed miRNAs may exhibit neofunctionalization, expanding regulatory networks.
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