RNA-interference

Ajaydesouza December 18, 2023

 RNA- interference

RNAi in Eukaryotes

• Sequence-specific recognition of mRNAs.

• Represses expression through ribonuclease-directed degradation or translation prevention.


ribonuclease-directed degradation-

  • “ribonuclease-directed degradation” refers to the process of breaking down RNA molecules into smaller fragments by enzymes called ribonucleases. 

  • Ribonucleases are proteins that can recognize and cleave specific bonds between the nucleotides that make up RNA. 

  • Ribonuclease-directed degradation can occur as a natural mechanism of gene regulation, RNA maturation, or RNA surveillance in cells, or as a way of defending against foreign RNAs, such as those from viruses or bacteria.

  • Ribonuclease-directed degradation can also be induced artificially by introducing interfering RNAs, such as siRNAs(siRNA stands for small interfering RNA, which is a type of double-stranded RNA molecule that can silence gene expression by degrading target mRNA)

  • miRNAs(miRNA stands for microRNA, which is a type of small non-coding RNA molecule that regulates gene expression by binding to complementary sequences in messenger RNA (mRNA) and inhibiting its translation or stability.) that target specific RNA sequences for degradation. 

  • Ribonuclease-directed degradation is an important aspect of RNA interference, a technique that can be used to manipulate gene expression or control plant diseases.



the two main RNA interference pathways in plants

the miRNA pathway and the siRNA pathway. 

RNA interference is a natural mechanism that plants use to regulate gene expression and defend against pathogens by silencing specific RNAs

The miRNA pathway is a way for plants to control their own gene expression by producing small RNAs that target specific mRNAs. 

  • The process starts in the nucleus, where a gene encoding a miRNA is transcribed into a long RNA molecule that has a hairpin-like structure. This is called the primary miRNA (pri-miRNA). 

  • An enzyme called Dicer-like (DCL) cuts the pri-miRNA into a shorter RNA molecule that still has a hairpin shape. This is called the precursor miRNA. Then, DCL cuts the precursor miRNA into a small RNA duplex that has two strands of about 22 nucleotides each. This is called the miRNA duplex. 

  • The miRNA duplex is then transported to the cytoplasm, where it is loaded into a protein complex called the RNA-induced silencing complex (RISC). One strand of the miRNA duplex is removed and degraded. 

  • This is called the passenger strand. The other strand is kept by the RISC and serves as a guide to find the target mRNA. 

  • This is called the guide strand. The guide strand binds to the target mRNA by matching its sequence. 

  • This causes the RISC(RNA-induced silencing complex) to either cut the target mRNA or stop its translation into a protein. This way, the miRNA pathway reduces the expression of the target gene.



The siRNA pathway is a way for plants to defend against foreign or abnormal RNAs, such as those from viruses or transposons. 

  • The process starts in the cytoplasm, where a target RNA that has a double-stranded or highly structured shape is recognized by DCL. 

  • DCL cuts the target RNA into small RNA duplexes that have two strands of 21 to 24 nucleotides each. These are called siRNA duplexes. 

  • The siRNA duplexes are then loaded into the RISC (RNA-induced silencing complex), just like the miRNA duplexes. One strand of the siRNA duplex is discarded and degraded. This is called the passenger strand. 

  • The other strand is retained by the RISC (RNA-induced silencing complex) and serves as a guide to find the target RNA. This is called the guide strand. The guide strand binds to the target RNA by matching its sequence. This causes the RISC (RNA-induced silencing complex) to cut the target RNA and destroy it. 

  • This way, the siRNA pathway eliminates the foreign or abnormal RNA. Sometimes, the siRNA pathway can be amplified by an enzyme called RNA-dependent RNA polymerase (RdRP), which makes more copies of the target RNA or the siRNA duplexes. 

  • This increases the amount of siRNAs and the silencing effect.


Source

  • Source: Conversation with Bing, 18/12/2023

  • (1) siRNA (Small Interfering RNA): Structure And Function - Genetic Education. https://geneticeducation.co.in/sirna-small-interfering-rna-structure-and-function/.

  • (2) Small interfering RNA - Wikipedia. https://en.wikipedia.org/wiki/Small_interfering_RNA.

  • (3) siRNA FAQ - MilliporeSigma. https://www.sigmaaldrich.com/US/en/technical-documents/technical-article/genomics/gene-expression-and-silencing/sirna-faq.) or 

  • Source: Conversation with Bing, 18/12/2023

  • (1) microRNA - Wikipedia. https://en.wikipedia.org/wiki/MicroRNA.

  • (2) rna - Naming convention of miRNAs - Biology Stack Exchange. https://biology.stackexchange.com/questions/30651/naming-convention-of-mirnas.

  • (3) MiRNA | definition of miRNA by Medical dictionary. https://medical-dictionary.thefreedictionary.com/miRNA.),
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