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Poly(A)-specific ribonuclease sculpts the 3' ends of microRNAs
Dooyoung Lee1, Daechan Park2, June Hyun Park1
1Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.
Abstract:
The 3' ends of metazoan microRNAs (miRNAs) are initially defined by the RNase III enzymes during maturation, but subsequently experience extensive modifications by several enzymatic activities. For example, terminal nucleotidyltransferases (TENTs) elongate miRNAs by adding one or a few nucleotides to their 3' ends, which occasionally leads to differential regulation of miRNA stability or function. However, the catalytic entities that shorten miRNAs and the molecular consequences of such shortening are less well understood, especially in vertebrates. Here, we report that poly(A)-specific ribonuclease (PARN) sculpts the 3' ends of miRNAs in human cells. By generating PARN knockout cells and characterizing their miRNAome, we demonstrate that PARN digests the 3' extensions of miRNAs that are derived from the genome or attached by TENTs, thereby effectively reducing the length of miRNAs. Surprisingly, PARN-mediated shortening has little impact on miRNA stability, suggesting that this process likely operates to finalize miRNA maturation, rather than to initiate miRNA decay. PARN-mediated shortening is pervasive across most miRNAs and appears to be a conserved mechanism contributing to the 3' end formation of vertebrate miRNAs. Our findings add miRNAs to the expanding list of noncoding RNAs whose 3' end formation depends on PARN.
Insights
Poly(A)-specific ribonuclease (PARN) shortens microRNAs (miRNAs) in human cells, finalizing their 3' end maturation. This conserved process affects most miRNAs without impacting their stability, adding to PARN's known roles in noncoding RNA processing.
Area of Science:
- Molecular Biology
- RNA Biology
- Biochemistry
Background:
- MicroRNA (miRNA) 3' end processing involves RNase III enzymes and subsequent modifications like elongation by terminal nucleotidyltransferases (TENTs).
- The enzymes responsible for shortening miRNAs and the functional outcomes of this process, particularly in vertebrates, remain largely uncharacterized.
Purpose of the Study:
- To identify the enzymatic activity responsible for shortening microRNAs (miRNAs) in human cells.
- To investigate the role of poly(A)-specific ribonuclease (PARN) in miRNA 3' end processing and its impact on miRNA stability and function.
Main Methods:
- Generation and characterization of PARN knockout human cells.
- Comprehensive analysis of the miRNAome in PARN knockout cells to assess the impact of PARN on miRNA length and abundance.
Main Results:
- Poly(A)-specific ribonuclease (PARN) was identified as the enzyme that sculpts the 3' ends of miRNAs by digesting 3' extensions.
- PARN-mediated shortening reduces miRNA length but does not significantly affect miRNA stability, suggesting a role in maturation rather than decay.
- This shortening mechanism is widespread across most miRNAs and appears to be conserved in vertebrates.
Conclusions:
- PARN plays a crucial role in the 3' end formation of vertebrate miRNAs, acting as a shortening enzyme.
- The findings expand the known functions of PARN to include the processing of miRNAs, in addition to other noncoding RNAs.
- PARN-mediated miRNA shortening is a key step in finalizing miRNA maturation, ensuring proper processing without triggering degradation.