Eukaryote Gene Regulation

• Eukaryote gene regulation


  The expression of eukaryotic genes is different from prokaryotes
• Any human cell probably only expresses about 20% of its genes at a time, and this proportion is even lower in highly specialized cells (ex.: muscle cells, neurons)
• Multicellular organisms must activate or deactivate their genes according to

  • External stimuli
  • Internal stimuli
  • Regulate genes according to the type of cell (liver, skin, etc.)
• Chromatin


  A complex of DNA and protein found in eukaryotic cells
• Chromatin


  • The primary protein components are histones, which bind to DNA and wrap around the histone
  • The primary function is to pack DNA into more compact structures

  
• Regulation of the structure of chromatin

  1. Modification of histones

  2. DNA methylation

  3. Epigenetic inheritance
• Histone acetylation


  Leads to the loosening of the structure of chromatin
• Loose structure of chromatin

  Permits access of the RNA polymerase to the DNA and the initiation of transcription

  
• Histone methylation


  In general associated with transcriptional repression, but methylation of some lysine and arginine residues results in transcriptional activation
• ATP-dependent chromatin remodeling factors


  • Function as molecular motors that use energy from ATP hydrolysis to alter the relationships between histones and DNA
  • Make DNA more accessible to regulatory proteins that in turn affect gene expression

  
• DNA methylation


  Addition of methyl groups to certain bases in DNA is associated with reduced transcription in certain species (deactivates genes)
• Epigenetic inheritance


  The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence, such as DNA methylation and histone modification
• Structure of a gene typical of Eukaryotes

  Includes promoter, transcription factors, RNA polymerase II, and m-RNA
• Regulation of transcription initiation


  Transcription factors (general and specific) are necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase II to a promoter to initiate transcription
• General transcription factors


  Are necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase II to a promoter to initiate transcription, but do not increase the rate above this basal rate
• Specific transcription factors


  Increase the level of transcription in certain cell types or in response to signals
• Transcription


  The process of copying the genetic information from DNA into RNA
• RNA polymerase II


  • Enzyme that transcribes protein-coding genes in eukaryotes
• Initiation of the transcription complex

  1. Binding of general transcription factors to the promoter

  2. Recruitment of RNA polymerase II

  3. Initiation of transcription
• mRNA


  Messenger RNA, the RNA molecule that carries the genetic information from the nucleus to the ribosomes in the cytoplasm
• Promoter


  DNA sequence that serves as the binding site for the transcription machinery to initiate transcription
• Eukaryote gene regulation


  • Chromatin modification
  • Transcription
  • RNA maturation
  • Translation
  • Degradation of proteins
• General transcription factors


  • Are necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase II to a promoter to initiate transcription
  • Do not increase the rate of transcription above the basal level
• Specific transcription factors


  • Increase the level of transcription in certain cell types or in response to signals
  • Have a DNA-binding domain and an activation domain
• Regulation of transcription initiation


  1. General transcription factors bind to the promoter

  2. Specific transcription factors (activators) bind to enhancers

  3. Coactivator and mediator proteins facilitate interactions between activators and the transcription apparatus
• Activators


  Act in a specific tissue or in a time dependent manner to stimulate higher levels of transcription than the basal level
• Combination of control elements

  Can only activate transcription when the appropriate activator proteins are present
• Each enhancer is composed of approximately 10 control elements, each one can only link 1 or 2 specific coactivators, mediator proteins and transcription factors
• Virtually all genes transcribed by RNA polymerase II need the same suite of general factors to assemble an initiation complex
• The ultimate level of transcription depends on the presence of activators, coactivators, and mediator proteins
• Pre-mRNA alternative splicing


  • Different mRNA molecules are produced from the same primary transcript
  • Humans have about 21,000 genes but can make 100,000 proteins
• mRNA degradation


  • The lifespan of eukaryotic mRNA is higher (half life of 10 hrs) than prokaryotic mRNA (half life of 3 mins)
  • The nucleotide sequences that influence the lifespan of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3' end of the molecule
• microRNAs (miRNAs)


  • Small single-stranded RNA molecules coded in the DNA that do not produce proteins
  • Bind to mRNA and form a complex that cleaves the mRNA or blocks its translation
• Small interference RNAs (siRNAs)


  • Arise from a long piece of double-stranded RNA and are processed by Dicer to yield multiple siRNAs
  • The siRNAs are then associated with proteins that will cleave the mRNA when they find a complementary base pair

  
• Blocking of translation


  Regulatory proteins bind to mRNA sequences or structures (usually in the 5' or 3' UTR regions) and prevent the ribosome from binding
• Degradation of proteins


  • Proteins can be destroyed if they are not useful anymore or have been damaged
  • The labeling of a protein for destruction is carried out by attaching a small ubiquitin protein to the targeted protein
  • The proteasome is an organelle that degrades proteins marked with ubiquitin