Ch6 expression regulation

• Expression regulation by RNA degradation involves protein degradation, protein stability, protein synthesis, and mRNA degradation.
• Prokaryotes (P) and Eukaryotes (E) differ in mRNA degradation, mRNA abundance, mRNA stability, and mRNA synthesis.
• Dhh1p couples translation to mRNA decay by sensing codon optimality.
• Non-stop decay (NSD) was first observed on 1819/11/2023.
• The DEAD-box protein Dhh1p associates with the translating mRNP.
• The codon-dependent rate of translational elongation impacts mRNA stability.
• mRNA analysis can be done specifically through Northern blotting, qPCR (Real-time RT-PCR), and high-throughput methods such as transcriptomics.
• mRNA turnover can be measured through Pulse-chase, RNA pol II inactivation + cDNA labeling, and RNA pol II inactivation + RNA-seq.
• mRNA can be converted to cDNA with specific primer and reverse transcriptase (RT) and PCR-amplified with two specific primers (Taq polymerase or Tth polymerase).
• The amplification products in real-time PCR can be monitored using fluorescence detection and the mRNA abundance can be calculated using a standard curve.
• Not1 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• PAN3 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• Caf130 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• Not3 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• Not5 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• PABP is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• Caf44 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• PARN is a mRNA degrading enzyme that is inhibited by PABP and stimulated by 5’ cap.
• PAN2 is a mRNA degrading enzyme that is stimulated by PABP and has no effect of 5’ cap.
• Not4 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• Not2 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• Pop2 is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
• m7G is a mRNA degrading enzyme that is inhibited by PABP and has no effect of 5’ cap.
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