Small RNA expression and deep sequencing analyses of the nucleolus reveal the presence of nucleolus-associated microRNAs

Autor: Marikki Laiho, Baoyan Bai, Hester Liu
Rok vydání: 2013
Předmět:
Zdroj: FEBS Open Bio
FEBS Open Bio, Vol 4, Iss C, Pp 441-449 (2014)
ISSN: 2211-5463
Popis: Highlights • miRNA expression arrays and RNA Seq were employed for unbiased spatial analyses of miRNAs. • Small RNomics of subcellular compartments revealed the presence of miRNAs in the nucleolus. • Several miRNAs were detected at low abundance in cancer cell nucleoli. • The nucleolar abundance of miR-31 was dependent on CRM1 export factor.
Micro RNAs (miRNA) are non-coding RNAs expressed in the cytoplasm as their mature, 21–22-nucleotide short forms. More recently, mature miRNAs have also been detected in the nucleus, raising the possibility that their spatial distribution may be more complex than anticipated. Here we undertook comprehensive systematic analyses of miRNA distribution in several subcellular compartments of human cancer cells. In particular, we focused on the potential presence of miRNAs in the nucleolus, which contains an abundance of small non-coding RNAs. We employed two miRNA expression array platforms and small RNA deep sequencing of small RNAs isolated from cells, nuclei, cytoplasm and the nucleoli. We developed an assay to compare RNAs of isolated nucleoli before and after denaturation and used Northern hybridization to verify the presence of miRNAs in the subcellular compartments. Consistently, we found more than 10 miRNAs associated with the nucleolar preparations. Several miRNAs had greater relative abundance in the nucleolus compared to the other compartments. The nucleolar presence of miRNAs was independent of Dicer and the main activity of the nucleolus, RNA polymerase I transcription, but was dependent on CRM1 previously associated with nucleolar trafficking of small nucleolar RNAs. These results highlight the complexity of miRNA spatial arrangement and regulation.
Databáze: OpenAIRE
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