Post-Transcriptional Control

Post-transcriptional control

• Another level of regulation that occurs after transcription

• First, levels of mRNA can be controlled by other functional, NON-CODING RNAs

• Second, translation can be regulated by changes in the structure and/or protein binding partners of mRNA

Functional, non-coding RNAs

• After transcription, there can remain RNAs that are not translated to protein

• These include:

  • Ribosomal RNA (rRNA)

  • Transfer RNA (tRNA)

  • Small nuclear RNA (snRNA)

  • Micro RNA (miRNA)

miRNA

• Micro RNAs that are encoded in the genome and have evolved to regulate levels of particular mRNAs

• Process

  • Within the nucleus, miRNAs exist in long strands. The enzyme Drosha allows for miRNAs to turn into a hairpin-like structure called precursor miRNA

  • The precursor miRNA is what leaves the nucleus and goes into the cytoplasm, where it is diced by the enzyme Dicer into double-stranded RNA intermediates

  • The presence of RISC proteins catalyzes reactions that separate double-stranded RNA intermediates into their single-stranded miRNA components

  • The binding of single-stranded miRNA components to RISC proteins activates RISC, the RNA-induced silencing complex

  • This complex scans the cytoplasm for complementary target mRNA

    • Leading to either an extensive match, or less extensive match that, either way, lead to mRNA degradation

• Extensive match

  • Occurs when the bases within the single-stranded miRNA of the RISC exactly complementary base-pair with the target mRNA

  • mRNA is rapidly degraded by the nucleases within the RISC

• Less extensive match

  • Occurs when the bases within the single-stranded miRNA of the RISC only partially complementary base-pair with the target mRNA

  • Translation is reduced → Ultimately leading to mRNA degradation

    • In this case, mRNA degradation is performed by nucleases within the cytoplasm instead

• miRNAs can regulate several different genes because of the less extensive match component of its function

siRNA

• Small interfering RNAs that represent foreign sources of RNA that come from viruses or are experimentally introduced

  • In the case of viruses, the cells essentially use the viral RNA against the virus itself

• Process

  • Foreign double-stranded RNA is introduced into the genome and cleaved/diced by the enzyme Dicer into double-stranded siRNAs

    • This process is already directly happening in the cytoplasm

  • In the presence of RISC proteins, reactions are catalyzed to separate the double-stranded siRNAs into their single-stranded siRNA components

  • The binding of single-stranded siRNA to RISC proteins activates the RNA-induced silencing complex

  • The complex scans the cytoplasm for complementary foreign RNA

  • Once an exact match is created, the complementary foreign RNA is degraded and the RISC is released

• The siRNA mechanism is like an immune system strategy to kill invading viruses

  • RNA interference (RNAi)

• The siRNA mechanism specifically requires exact matches to be made

  • As a result, all degradation is performed by the nucleases within the complex machinery

Similarities between siRNA and miRNA

• Both mechanisms use complementary base pairing to “seek” out desired RNA (whether foreign RNA or mRNA) and target it for degradation

• Similar machinery are used to process the RNA and target mRNAs

  • Enzyme DICER and RISC (RNA-induced silencing complex)

Differences between siRNA and miRNA

• Purpose

  • The mechanism of siRNA acts like a “defender,” contributing to how the immune system of living organisms protect against foreign invaders like viruses

  • The mechanism of miRNA is more focused on gene regulation by controlling the levels of specific mRNA

• Origin

  • miRNA is originally encoded in the genome of living organisms

    • As a result, the process begins from the nucleus → cytoplasm

  • siRNA has to be introduced via viruses or experimental procedures into genomes

    • As a result, the process immediately starts in the cytoplasm

• Degradation Criteria

  • In the mechanism for miRNA, degradation can occur from both exact (extensive) or non-exact (less extensive) matches

    • As a result, degradation can be performed by both nucleases in the RISC itself (for extensive matches) or by nucleases in the cytoplasm (for less extensive matches)

  • In the mechanism for siRNA, degradation must occur from exact matches of single-stranded siRNA to complementary foreign RNA

    • As a result, degradation is always performed by nucleases in the RISC

Post-transcriptional control of translation

• Refers to how changes in the structure of the mRNA or protein-binding partners of mRNA can influence whether translation occurs

  • There is this common theme of limiting/allowing accessibility to required elements or proteins

• Prokaryotes

  • In bacterial cells, mRNA strands can take on hairpin-like structures in the 5’ UTR that block the ribosome’s access to the start codon

    • As a result, in the case of genes that code for toxins, these toxins can be prevented from being created

    • However, the hairpin structure is NOT permanent

      • In warmer temperatures, the hydrogen bonds in the hairpin structure can be “disrupted” to make translation possible again as the start codon is accessible once more

  • In bacterial cells, translation repressor proteins can also bind to block ribosome-binding site at the Shine-Dalgarno sequences, and prevent translation from occurring as the start codon isn’t accessible

• Eukaryotes

  • The ideas of the processes from prokaryotes are very similar

  • Protein binding in the 5’ UTR can repress translation by limiting access to the machinery