MicroRNA biogenesis: coordinated cropping and dicing

Key Points

  • MicroRNA (miRNA) is a single-stranded RNA of 22 nucleotides in length, which is generated by an RNase-III-type enzyme from an endogenous transcript that contains a local hairpin structure.

  • miRNA functions as a guide molecule in post-transcriptional gene silencing, by base pairing with the target mRNAs, which leads to mRNA cleavage or translational repression. By silencing various target mRNAs, miRNAs have key roles in diverse regulatory pathways, including control of development timing, haematopoietic cell differentiation, apoptosis, cell proliferation and organ development.

  • miRNA genes belong to class II genes, which are transcribed by RNA polymerase II. A majority of miRNA loci are found in intronic regions of protein-coding or non-coding transcription units, whereas the others are found in exonic regions of non-coding transcription units.

  • In animals, miRNA genes are transcribed to generate long primary transcripts (pri-miRNAs), which are first cropped by RNase-III-type enzyme Drosha to release the hairpin intermediates (pre-miRNAs) in the nucleus. Drosha forms a large (500–650 kDa) complex, known as the Microprocessor complex, together with its essential cofactor DGCR8/Pasha, which contains two dsRNA-binding domains. Pre-miRNA then gets exported to the cytoplasm by exportin-5, which is a member of the Ran-dependent nuclear transport receptor family. Following arrival in the cytoplasm, pre-miRNAs are subjected to the second processing step, which is carried out by Dicer, the cytoplasmic RNase-III-type protein.

  • In plants that lack Drosha and DGCR8, it has been suggested that miRNA processing is executed by Dicer-like protein 1 (DCL1) in the nucleus and that nuclear export is mediated by HASTY, the exportin-5 homologue.

Abstract

The recent discovery of microRNAs (miRNAs) took many by surprise because of their unorthodox features and widespread functions. These tiny, 22-nucleotide, RNAs control several pathways including developmental timing, haematopoiesis, organogenesis, apoptosis, cell proliferation and possibly even tumorigenesis. Among the most pressing questions regarding this unusual class of regulatory miRNA-encoding genes is how miRNAs are produced in cells and how the genes themselves are controlled by various regulatory networks.

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Figure 1: The structure of five pri-miRNAs.
Figure 2: Model for microRNA biogenesis.
Figure 3: Domain organization of microRNA biogenesis factors.
Figure 4: Possible mechanisms of actions for Drosha and Dicer.
Figure 5: Generation of small hairpin RNAs.

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Acknowledgements

I am grateful to members of my laboratory, especially to Young Kook Kim for the bioinformatics analysis of the miRNA gene structure. This work was supported by a Molecular and Cellular BioDiscovery Research Program grant from the Ministry of Science and Technology and a Research Fellowship from the Ministry of Education and Human Resources Development of Korea.

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DATABASES

Entrez Gene

let-7

Swiss-Prot

CAF

DGCR8

Dicer

Drosha

exportin-5

HEN1

RDE-4

The miRNA Registry

miR-21

miR-38

FlyBase

AGO1

AGO2

Dicer-1

Dicer-2

FMR1

R2D2

TAIR

HST

HYL1

FURTHER INFORMATION

V. Narry Kim's laboratory

Noncoding RNAs Database

RNA & DNA Folding Applications

The miRNA Registry

Glossary

SMALL INTERFERING RNA

(siRNA; also known as short interfering RNA). A small (21–24 nucleotide), non-coding RNA that is generated from long double-stranded RNA. siRNAs function as guide molecules in small-RNA-mediated gene silencing.

POLYCISTRONIC TRANSCRIPTION UNIT

A transcript that includes regions representing multiple, non-overlapping gene products.

CAP STRUCTURE

A structure, which consists of m7GpppN (where m7G represents 7-methylguanylate, p represents a phosphate group and N represents any base), that is located at the 5′ end of eukaryotic mRNAs.

POLY(A) TAIL

A homopolymeric stretch of usually 25–200 adenine nucleotides that is present at the 3′ end of most eukaryotic mRNAs.

SMALL NUCLEOLAR RNA

(snoRNAs). A small RNA molecule that functions in ribosome biogenesis in the nucleolus by guiding the assembly of macromolecular complexes on the target RNA to allow site-specific modifications or processing reactions to occur.

TRANS-SPLICING

Intermolecular splicing that occurs in trypanosomes and worms where a short sequence (SL RNA) is linked to the 5′ end of many pre-mRNAs.

WW DOMAIN

A protein domain that binds to proline-rich regions.

DEAD-BOX RNA HELICASE DOMAIN

An evolutionarily conserved domain in a family of enzymes that use ATP hydrolysis to unwind RNA duplexes. The domain is named after the DEAD (Asp-Glu-Ala-Asp) motif.

PAZ DOMAIN

A conserved RNA-binding domain found in members of the Dicer and Argonaute protein families, and that preferentially interacts with the 3′ end of RNA.

ARGONAUTE PROTEINS

(also known as PPD proteins). A family of proteins that are characterized by the presence of two homology domains, PAZ and PIWI. These proteins are essential for diverse small-RNA pathways.

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Kim, V. MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6, 376–385 (2005). https://doi.org/10.1038/nrm1644

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