RNA-seq, bioinformatic identification of potential microRNA-like small RNAs in the edible mushroom Agaricus bisporus and experimental approach for their validation
| Autor: | Francisco R. Marin, Alberto Dávalos, Dylan Kiltschewskij, Maria C. Crespo, Murray Cairns, Eduardo Andrés-León, Cristina Soler-Rivas |
|---|---|
| Přispěvatelé: | Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Junta de Andalucía, UAM. Departamento de Química Física Aplicada |
| Rok vydání: | 2022 |
| Předmět: |
miRNAs
milRNAs fungi Agaricus bisporus white button mushroom RT-qPCR White button mushroom Agaricus Organic Chemistry Fungi Computational Biology RNA Fungal General Medicine Química Catalysis Computer Science Applications Inorganic Chemistry MicroRNAs RNA-Seq Physical and Theoretical Chemistry Molecular Biology Spectroscopy |
| Zdroj: | Digital.CSIC. Repositorio Institucional del CSIC instname International Journal of Molecular Sciences; Volume 23; Issue 9; Pages: 4923 |
| Popis: | This article belongs to the Special Issue Bioactive Compounds: From Diet to Therapeutic Use. Although genomes from many edible mushrooms are sequenced, studies on fungal micro RNAs (miRNAs) are scarce. Most of the bioinformatic tools are designed for plants or animals, but the processing and expression of fungal miRNAs share similarities and differences with both kingdoms. Moreover, since mushroom species such as Agaricus bisporus (A. bisporus, white button mushroom) are frequently consumed as food, controversial discussions are still evaluating whether their miRNAs might or might not be assimilated, perhaps within extracellular vesicles (i.e., exosomes). Therefore, the A. bisporus RNA-seq was studied in order to identify potential de novo miRNA-like small RNAs (milRNAs) that might allow their later detection in diet. Results pointed to 1 already known and 37 de novo milRNAs. Three milRNAs were selected for RT-qPCR experiments. Precursors and mature milRNAs were found in the edible parts (caps and stipes), validating the predictions carried out in silico. When their potential gene targets were investigated, results pointed that most were involved in primary and secondary metabolic regulation. However, when the human transcriptome is used as the target, the results suggest that they might interfere with important biological processes related with cancer, infection and neurodegenerative diseases. This research was funded by grants from the Spanish “Agencia Estatal de Investigación” and European FEDER Funds (PID2019-109369RB-I00 to A.D., AGL2018-78922-R to FRM and C.S.-R.). E.A.-L. was recipient of a postdoctoral fellowship from Regional Andalusian Government (2020_DOC_00541). |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|