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List the major steps of RNA processing
- Splicing
- Addition of 5' cap
- Addition of poly A tail
Describe how pre-mRNA processing contributes to differential regulation
- Pre-mRNA processing, specifically splicing, facilitates the regulation of protein expression in a cell by producing various protein variants from a single gene.
Contrast mRNA stabilization and destabilization
- Stability is influenced by the presence of the 5' cap and poly A tail. Stability directly contributes to protein production; without these elements, mRNA degrades quickly.
Explain RNA interference (RNAi)
- RNA interference is a regulatory process that can regulate gene expression, particularly at the transcription level.
- Example of RNAi: Specific microRNAs can target and degrade complementary mRNAs, thus influencing the transcription of certain proteins.

5' Cap Addition
- Occurs at the beginning of the 5' UTR while transcription is ongoing.
- A 5-Methyl Guanosine Triphosphate is added to the mRNA strand.
Ribosome Binding
- The 5' cap is crucial for ribosome binding during translation.
- mRNA lacking a cap is marked for destruction.
Poly A Tail Addition
- Cleavage of pre-mRNA occurs at the poly A addition site located in the 3' UTR, followed by the addition of approximately 200 adenine bases.
- The poly-A tail indicates that mRNA is available for translation.
- The tail shortens with each translation cycle, analogous to a burning fuse; when it becomes too short, the mRNA is destroyed.
- Both the 5' cap and 3' poly A tail are essential for mRNA stability and longevity.
- A stable mRNA can produce more protein as long as it retains both features.

Definition of Splicing
- Splicing is the process by which introns are removed and exons are retained in the pre-mRNA.
- The sequence at the borders of introns and exons recruits spliceosomes, which perform the splicing process.
Impact of Splicing on Protein Production
- Splicing, particularly alternative splicing, greatly impacts the final protein produced.
- Alternative Splicing:
  - Forms different mature mRNAs from a single pre-mRNA, affecting protein diversity.
  - For example, in Type II procollagen, alternative splicing results in variations between precursor chondrocytes and mature chondrocytes.
Examples of Alternative Splicing
- FGF Receptor 2 gene: Produces two different proteins that respond differently to paracrine signals during limb development.
- Bcl-X gene: Produces two protein variants where the small protein encourages apoptosis (programmed cell death), while the large protein inhibits it.
  - Apoptosis: A regulated process by which cells systematically dismantle their internal structures.
- Drosophila Dscam gene: Can generate 38,016 unique proteins through alternative splicing, important for neuronal dispersal in the fly body.
- Troponin gene: In humans, the gene is alternatively spliced to produce different forms tailored for different muscle cell types.

Overview
- RNA interference is a biological process where RNA molecules inhibit gene expression or translation, effectively regulating protein levels.
- A significant portion of the genome is made up of RNAs that do not code for proteins.
Non-coding RNAs
- Do not code for proteins, but perform various functions in cells:
  - Regulatory RNAs: Include micro RNAs (miRNAs) and small interfering RNAs (siRNAs).
  - Task RNAs: Include ribosomal RNA (rRNA), transfer RNA (tRNA), telomeric RNA, and splicing RNA.
- Non-coding RNAs are transcribed like mRNAs but are not processed in the same way as pre-mRNA is.
Mechanism of Action
- Micro RNAs (miRs):
  - Bind to approximately 20 base pair complementary sequences on the 3' UTR of target mRNAs, triggering quick removal of their poly A tails.
  - Devoid of a poly A tail, the mRNA is marked for degradation.
  - This leads to the cessation of protein translation.
Application in Development
- miR430: Transcription starts at the Maternal-Zygotic Transition (MZT) and targets many maternal mRNAs for degradation shortly after the transition.