B11 Week 9

• mRNA stability


  Factors that influence the stability of mRNA, affecting how long the message is present to be used for translation

  
• 3' UTR


  Untranslated region at the 3' end of the mRNA, regulates mRNA stability, localization, and translation

  
• Regulating mRNA to impact protein amino acid sequence

  1. Alternative splicing

  2. Covalent modifications

  3. RNA editing

  
• Cis-acting regulatory elements


  • Sequences within the mRNA itself that regulate its processing, stability, localization, and translation

  
• Alternative splicing allows one gene to produce multiple different mRNA and protein isoforms

  
• Constitutive alternative splicing


  When the spliceosome cannot consistently distinguish correct pairings of 5' and 3' splice sites, resulting in alternative splicing in all cells

  
• Regulation of alternative splicing


  1. Exonic splicing enhancer elements

  2. Exonic splicing suppressor elements

  
• Nonsense-mediated decay is a quality control mechanism that degrades mRNAs with premature stop codons

  
• Exon junction complexes (EJCs)

  Complexes that mark completed splicing events

  
• Covalent modifications of mRNA


  Over 100 different modifications that can influence mRNA structure, stability, and interactions with regulatory proteins

  
• Alternate cleavage and polyadenylation


  Regulates which end of the mRNA and protein is produced

  
• Up to 50% of human genes are regulated by alternate cleavage and polyadenylation
• 5' UTR


  Untranslated region at the 5' end of the mRNA, regulates mRNA localization and translation

  
• mRNA stability


  Regulated by deadenylation pathways that shorten the poly(A) tail, triggering mRNA degradation

  
• mRNA degradation


  Can also occur through recruitment of endonucleases to specific internal sequences, often in the 3'UTR

  
• Translation initiation


  Regulated by exposing or blocking sequences like the Shine-Dalgarno sequence in prokaryotes

  
• mRNA localization


  Regulated by binding of regulators to sequences in the 5' and 3' UTRs, allowing localized translation

  
• Reasons for mRNA localization

  • Localized translation at sites of high protein demand
  • Unequal distribution to daughter cells during division to create cells with different fates

  
• Examples of mRNA localization

  • Localization of actin mRNA to the leading edge of migrating cells
  • Localization of bicoid and oskar mRNAs to establish body axes in Drosophila development

  
• mRNA localization


  Transport of mRNA allows localized translation of proteins needed at particular locations

  
• Early development for many organisms can proceed without any input from the organism's own DNA!
• Maternal contributions are proteins and RNA that are stored in the egg until they are needed to orchestrate early development (and determine the fate of particular cells)
• 1. P-bodies

  Sites of mRNA degradation or for storing translationally repressed mRNA

  
• Stress granules


  Membrane-less compartments where translation initiation is blocked until the stressful conditions are removed
• Long non-coding RNA (lncRNA)

  Long non-coding RNA molecules that fold into complex structures and can bind complementary sequences and recruit proteins to act on those genes (usually repressively)

  
• RNA interference (RNAi)


  Short single-stranded RNA binding to a complementary RNA sequence and directing protein machinery to that site, resulting in inhibition of translation or degradation of the mRNA

  
• microRNA (miRNA)


  Small non-coding RNA that can regulate a large number of eukaryotic genes by binding to complementary sequences on mRNA

  
• Humans have more than 1000 miRNA and at least half of human mRNA are regulated by miRNA
• RNAi is thought to have evolved as a cell defense system (and still functions this way)
• CRISPR/Cas9 Genome Editing


  Gene-specific guide RNA sequence directs the Cas9 nuclease to a specific site, where repair of the resulting double-strand break often results in small insertions or deletions (NHEJ), or specific changes can be created if a plasmid template with homology to the target region is provided to direct repair (Homologous recombination)