Video animation: RNA interference

RNA interference (RNAi)

RNA interference (RNAi) is an important pathway that is used in many different organisms to regulate gene expression. This animation introduces the principles of RNAi involving small interfering RNAs (siRNAs) and microRNAs (miRNAs). We take you on an audio-visual journey through the steps of gene expression and show you an up-to-date view of how RNAi can silence specific mRNAs in the cytoplasm.

The accompanying slideshow provides further information about RNAi and small RNAs.

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Learn more about RNA interference

  1. Introduction

    This slideshow provides further information to accompany the animation on RNA interference (RNAi). Please enjoy learning more about small silencing RNAs.

    Nature Reviews Genetics / Arkitek

  2. Cytoplasm

    RNA interference — or RNAi — is a cellular process that can silence specific genes: that is, it can stop proteins being produced from specific genes. RNAi can involve different types of small RNA molecule. The best known types of RNAi act by targeting messenger RNA (mRNA) in the cytoplasm.

    Nature Reviews Genetics / Arkitek


    In eukaryotic cells, protein-coding genes are transcribed by RNA polymerase II (RNAPII). During transcription, an RNA molecule — the primary transcript — is synthesized using the DNA sequence as a template. The primary transcript is processed to form mRNA; regions of sequence that do not code for the protein (introns) are removed by splicing and a 'cap' is added to the 5′ end of the RNA.

    Nature Reviews Genetics / Arkitek

  4. MRNA

    The mRNA travels from the nucleus into the cytoplasm through the nuclear pore complex. The nuclear pore complex is one of the largest protein complexes in the cell and is made up of many copies of approximately 30 different proteins. The central cylinder has an eightfold symmetry. The filaments on the cytoplasmic side help to channel the mRNA towards the protein synthesis machinery.

    Nature Reviews Genetics / Arkitek

  5. Translation

    In the cytoplasm, ribosomes carry out translation of the mRNA to form a polypeptide chain, which folds to form a protein. Ribosomes are made up of proteins and RNA molecules (called ribosomal RNAs, or rRNAs). Some protein folding happens during translation, but the endoplasmic reticulum is an important site of protein folding and many ribosomes are associated with it. RNAi needs to target the mRNAs to stop this synthesis of proteins.

    Nature Reviews Genetics / Arkitek

  6. Injection

    The power of RNAi to silence specific genes is now widely used in the laboratory to explore the functions of genes. A popular approach is to use 'hairpin' RNAs (RNA molecules that fold back on themselves so that they become double-stranded). Specific siRNAs are now available to silence almost any gene in human cells or model organisms. Researchers hope to use siRNAs to correct faulty gene expression in humans. The delivery method is an important consideration for the development of RNAi-based therapies; the siRNA trigger needs to be delivered efficiently and may need to be targeted to a specific tissue.

    Nature Reviews Genetics / Arkitek

  7. Dicer

    Dicer is a double-stranded-RNA-specific ribonuclease from the RNase III protein family. In most species, cleavage of longer double-stranded RNAs by Dicer produces double-stranded siRNAs that are ∼21 nucleotides long. These have a two-nucleotide overhang at their 3′ end, as well as a 5′ phosphate and a 3′ hydroxyl group. (The model is approximately based on human Dicer; the positions are not accurate.)

    Nature Reviews Genetics / Arkitek

  8. RISC

    Argonaute catalyses cleavage near the centre of the region of the mRNA that is bound by the siRNA. The repertoire of different Argonaute proteins varies among species. For example, there are more than 25 Argonautes in the nematode worm Caenorhabditis elegans compared with five in the fly Drosophila melanogaster.

    Nature Reviews Genetics / Arkitek

  9. Degradation

    Because siRNAs can trigger degradation of specific mRNAs, they stop production of specific proteins. They are used in the lab to 'knock down' the products of genes that are being studied. It is hoped that RNAi can be used in the clinic to reduce the production proteins that are not functioning correctly.

    Nature Reviews Genetics / Arkitek

  10. RNAPII

    In animals, the pri-miRNA is cleaved by an RNAse III endonuclease called Drosha to form a 60–70-nucleotide precursor miRNA (pre-miRNA). Drosha works with a double-stranded RNA-binding protein; in flies, this protein is called Pasha. In plants, a protein called DCL1 performs the functions of Drosha and Dicer.

    Nature Reviews Genetics / Arkitek

  11. Exportin

    The pre-miRNA is shaped like a hairpin with a double-stranded region and a loop. It has a two-nucleotide overhang at the 3′ end and a 5′ phosphate group. In animals, it is bound by a protein called exportin 5 and travels through the nuclear pore into the cytoplasm.

    Nature Reviews Genetics / Arkitek

  12. Dicer miRNA

    In animals, Dicer acts in the cytoplasm to cut pre-miRNA to generate a small RNA duplex with strands known as the miRNA and miRNA*. Dicer can work with double-standed RNA-binding protein partners.

    Nature Reviews Genetics / Arkitek

  13. Argonaute

    One strand is 'chosen' to remain bound to Argonaute and will guide Argonaute to the target mRNA. The choice of strand may be influenced by many factors, including the thermodynamic stabilities of the ends of the strands in the duplex RNA.

    Nature Reviews Genetics / Arkitek

  14. RISC miRNA

    In flies and mammals, most miRNAs only pair with target mRNAs through a part of the miRNA sequence. Often, this is a region at the 5′ end known as the 'seed'. This means that an miRNA can target many mRNAs. Most miRNA-binding sites are in the 3′UTR of the mRNAs, but sometimes they are also in the coding region or 5′UTR. In plants, miRNAs were originally thought to match their target mRNAs perfectly, but it is now known that plant miRNAs can also pair with mRNAs through smaller parts of their sequence.

    Nature Reviews Genetics / Arkitek

  15. miRNA mechanisms

    The ways in which miRNAs cause silencing of their target mRNAs are still debated. The mechanisms involved are likely to include: inhibition of translation; triggering removal of the poly(A) tail from mRNAs (deadenylation); disruption of cap–tail interactions; and degradation of mRNAs by exonucleases.

    Nature Reviews Genetics / Arkitek

  16. Chromatin

    PIWI-interacting RNAs (piRNAs): these RNAs bind to particular Argonaute proteins called PIWI proteins. piRNAs are 25–30 nucleotides in length and have been found in most metazoans. siRNAs: in plants and fungi, endogenous siRNAs are important in the formation of heterochromatin, which is a specialized form of DNA packaging that is associated with repressed gene expression. There are roles for siRNAs in the nucleus in animals too, but these are less well-understood at the moment. miRNAs: miRNAs are also found in the nucleus, but their functions here are not well understood.

    Nature Reviews Genetics / Arkitek