Week 32 Lecture 10 mRNA Stability_New

Gene Expression Basics

• Process: Transition from DNA to RNA to protein involves several steps:

  • DNA Replication

  • Transcription (DNA to RNA)

  • Reverse Transcription (rare)

  • Translation (RNA to protein)

mRNA Characteristics

• Structure: mRNA is single-stranded and highly processed.

• Processing Requirements: mRNA produced by RNA Pol II complex must undergo:

  • Splicing

  • Capping

  • Transport to the ER for Translation

• Stability: mRNA is inherently unstable and requires stabilization. Additional RNA and proteins can enhance or reduce stability.

Pre-mRNA vs. Mature mRNA

• Pre-mRNA: Located solely in the nucleus until fully processed.

• Mature mRNA: Contains joined exons, a 5' cap, and a 3' poly-A tail. Used for translation in the cytoplasm.

RNA Processing in Eukaryotes

• Stages of Processing:

  • 5' Capping: Addition of a protective cap at the 5' end.

  • RNA Splicing: Removal of introns and connecting exons.

  • 3' Polyadenylation: Addition of a poly-A tail at the 3' end.

Untranslated Regions (UTRs)

• 5' and 3' UTRs:

  • Help in maintaining mRNA stability.

  • Influence degradation, translation, and localization processes.

mRNA Structural Features

• Prokaryotic mRNA:

  • Not modified after transcription.

  • 3' terminus often forms a hairpin loop for stability.

• Eukaryotic mRNA:

  • Modified with a cap and poly-A tail.

  • Contains various base-paired structures.

mRNA Instability and Degradation

• Ribonucleases: Cause mRNA instability.

  • Endoribonucleases: Cleave RNA at internal sites.

  • Exoribonucleases: Remove ribonucleotides from RNA ends.

Prokaryotic mRNA Degradation

• Occurs during translation in prokaryotes.

• Mechanism:

  • E. coli mRNA degradation involves endonucleases and 3' to 5' exonucleases.

  • RNase E initiates degradation post removal of pyrophosphate from the 5' end.

  • Cleavage yields a downstream fragment that is then further degraded.

mRNA Lifetime and Variability

• mRNA half-lives vary significantly across organisms:

  • E. coli: ~3 min

  • Yeast: 3-100 min

  • Metazoans: Varies from minutes to days.

Capping and Poly-A Tails

• 5' Cap: Aids mRNA stability and translation initiation.

  • Formed during transcription by adding G to the first base of the transcript.

  • Involves modifications by methyltransferases.

• 3' Poly-A Tail: Protection from degradation and is crucial for translation efficiency.

Eukaryotic mRNA Degradation Pathways

• Deadenylation-Dependent Pathways: Two major pathways include:

  1. 5' to 3' Decay: Triggered by deadenylation and subsequent decapping.

  2. 3' to 5' Decay: Involves exonuclease digestion by the exosome complex.

Surveillance Mechanisms

• TRAMP complex: Recognizes improperly processed RNAs and aids in their degradation with the help of the exosome.

• Cytoplasmic Surveillance Systems: Detects translation-related defects (NMD, NSD, NGD).

Nonsense Mediated Decay (NMD)

• Targets mRNAs with premature termination codons (PTC).

• Processes include:

  • Recognition by an exon junction complex (EJC).

  • Involvement of Upf proteins in marking for degradation.

  • Link to disease pathology via PTCs and truncated proteins.

mRNA Localization

• mRNA localization regulates where proteins are synthesized within the cell leading to localized translation essential for cell functions and development.

  • Important for cell division, migration, and differentiation.

Conclusions

• Key Points:

  • mRNA stabilization relies on 5' capping and 3' poly-A tails.

  • Destabilization is often initiated by de-adenylation and decapping.

  • The TRAMP complex monitors mRNA integrity in the nucleus.

  • Localized translation impacts developmental processes.