RNA interference review

What is RNA interference (RNAi)

RNA interference (RNAi) is a conserved biological response to double-stranded RNA (dsRNA) that mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids. It also regulates the expression of protein-coding genes and has been used experimentally to manipulate gene expression and probe gene function on a whole-genome scale.

Where was RNAi first discovered

RNAi was first discovered in the nematode worm Caenorhabditis elegans as a response to double-stranded RNA (dsRNA), which resulted in sequence-specific gene silencing.

What was the breakthrough discovery by Fire and Mello regarding RNAi

Fire and Mello discovered that a mixture of sense and antisense RNAs (dsRNA) was at least tenfold more potent as a silencing trigger than either sense or antisense RNA alone.

What is co-suppression in plants

Co-suppression is a phenomenon observed in plants where the introduction of exogenous transgenes leads to the silencing of both the transgene and the endogenous gene, resulting in variegated pigmentation or complete loss of pigment.

What role does dsRNA play in gene silencing

dsRNA is a potent inducer of gene silencing. It can be introduced from exogenous sources or transcribed from engineered inverted repeats, leading to the degradation of homologous mRNAs or transcriptional silencing through genomic methylation.

What is the role of Dicer in RNAi

Dicer is an enzyme that processes long dsRNA into small interfering RNAs (siRNAs) of about 21-25 nucleotides. These siRNAs are then incorporated into the RNA-induced silencing complex (RISC), which targets and degrades homologous mRNAs.

What is the RNA-induced silencing complex (RISC)

RISC is a protein-RNA effector complex that recognizes and destroys target mRNAs. It incorporates siRNAs, which guide the complex to homologous RNA sequences for degradation.

What is the significance of Argonaute proteins in RNAi

Argonaute proteins are key components of the RNAi machinery. They are involved in the assembly of silencing complexes and are required for the function of RISC. Mutations in Argonaute genes can disrupt RNAi and lead to developmental abnormalities.

What is transitive RNAi

Transitive RNAi refers to the spread of the silencing signal along a specific mRNA. In C. elegans, targeting one part of a transcript can lead to the production of siRNAs that target other regions of the same mRNA, resulting in broader silencing effects.

What is the role of RNA-directed RNA polymerase (RdRP) in RNAi

RdRP is thought to amplify the RNAi signal by synthesizing additional dsRNA from siRNA templates. This amplification mechanism is observed in plants and C. elegans but has not been definitively established in Drosophila.

How does RNAi spread systemically in organisms

In C. elegans and plants, RNAi can spread systemically throughout the organism. In plants, the silencing signal can move through plasmodesmata and the vasculature. In C. elegans, the protein SID-1 is required for the import of the silencing signal into cells.

What are small temporal RNAs (stRNAs)

Small temporal RNAs (stRNAs), such as lin-4 and let-7, are small RNAs that regulate gene expression at the translational level rather than through mRNA degradation. They are processed by Dicer and are involved in developmental timing.

How is RNAi used as a tool in genomics

RNAi is used to probe gene function on a whole-genome scale. In C. elegans, RNAi has been used to test the function of nearly all predicted genes. It is also being applied in other organisms, including plants and mammals, for large-scale loss-of-function genetic screens.

What are the challenges of using RNAi in mammalian cells

Mammalian cells exhibit nonspecific responses to dsRNA, such as activation of the RNA-dependent protein kinase (PKR) pathway, which can obscure sequence-specific silencing. However, the use of small interfering RNAs (siRNAs) has allowed effective RNAi in many mammalian cells without triggering these nonspecific responses.

What are the potential therapeutic applications of RNAi

RNAi has potential therapeutic applications, such as targeting disease-causing genes, including oncogenes, and creating RNAi-based therapeutics. For example, RNAi could be used to engineer stem cells to resist HIV infection by targeting viral RNA or host receptors like CCR5.

What is the relationship between RNAi and chromatin remodeling

RNAi can induce changes in chromatin structure, leading to transcriptional gene silencing (TGS). In some organisms, RNAi machinery is involved in forming heterochromatic domains, which are critical for genome organization and stability.

What are microRNAs (miRNAs)

MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression. They are processed by Dicer and are involved in various cellular functions, including development and differentiation. Over 100 miRNAs have been identified in Drosophila, C. elegans, and mammals.

How can RNAi be made stable and heritable

RNAi can be made stable and heritable by expressing the silencing trigger as an inverted repeat sequence, forming a hairpin structure in vivo. This approach has been used in plants, Drosophila, C. elegans, and trypanosomes to achieve long-term gene silencing.

What is the role of RNAi in pathogen resistance

RNAi plays a crucial role in pathogen resistance, particularly in plants. It forms the basis of virus-induced gene silencing (VIGS), where the RNAi machinery targets and degrades viral RNAs, providing a defense mechanism against viral infections.

What are the future prospects of RNAi research

RNAi research holds tremendous promise for understanding gene function and regulation. It is being applied on a whole-genome scale in various organisms, and efforts are underway to target every gene in the human genome using RNAi. This could lead to new insights into genetic interactions and the development of novel therapeutic strategie