Regulation of Gene Expression (finished)

• Gene: a segment of DNA that is transcribed into RNA and its associated transcriptional control regions
• Transcription factor: Protein capable of regulating transcription of a gene
• DNA binding protein: Protein that forms a complex with DNA, may or may not have transactivating ability
• Enhancer: DNA sequence that modulated DNA transcription in an orientation and location independent fashion
• Activator: transcription factor that increases gene expression
• Repressor: transcription factor that decreases gene expression
• Helix-loop-helix: structural feature in transcription factors consisting of a helices bound by a looping stretch of amino acids
• Zinc finger: transciption factor with a bound Zn atom associated with the protein that is required for the protein to achieve the proper confirmation to bind DNA and/or regulate transcription
• Helix-turn-helix: DNA binding motif consisting of two alpha helices joined by a short stretch of amino acids
• Leucine zipper: two proteins each with an alpha-helix (formed largely by consecutive leucine residues) form a Y-shaped coiled-coil structure. Results in both protein and DNA binding
• Response Element: DNA sequence (in a promoter, enhancer, or silencer element that serves to bind transcriptional regulatory proteins
• Topological Associated Domains (TAD): a segment of the chromosomal DNA that is bounded by insulator elements

  • Typically contained numerous gene
  • Looping within TADs facilitates the interaction between transcription factor-bound enhancers/silencers and promoters to determine the level of transcriptional activation and often the tissue-specificity of activation
• Gene nomenclature is different between humans and mice

  • Human genes are all capitalized and italicized (i.e. LRP5)
  • Mice genes have the first letter capitalized and all letters italicized (i.e. Lrp5)
• Letters of a gene name typically give clues as to the function of its encoded protein and how it's identified. Examples:

  • LRP5: LDL receptor-related protein 5
  • BMP4: bone morphongenetic protein 4
• Gene expression: process of transcribing DNA chemical sequence code into RNA, then RNA is translated to protein
• Not all genes encode for a protein but rather, they code for a functional RNA
• Genes:

  • Are segments of DNA that are transcribed into RNA
  • Possess association regions that control how, when, where, and how much RNA is transcribed
• All 23 chromosomes are throughout the body that can encode about 25,000 genes so...

  • All chromosomes and genes are in every cell of the body
  • But not every gene is expressed in every cell of the body
• Housekeeping genes: carry out basic and general functions within the cell

  • Can encode for cells involved in metabolism
  • Found in almost every cell of the body
• Hemoglobin is an example of genes with cell-type specific functions. Mature RBCs will expel their DNA after maturation
• Importance of Gene Regulation:

  • Creating specialized functions
  • How the cell responds to environmrental change
  • Maintenance of tissue homeostasis (based on temp., pH, nutrience)
  • Morphogenesis (cell proliferation and adhesion)
  • Cell communication
  • Evolutionary adaptation (new traits/features)
  • Immune responses
• Gene Regulatory Elements:

  • Promoters & transcriptional start sites
  • Enhancers
  • Silencers/repressor elements
  • Response elements
  • Insulators/boundary elements
  • CpG Islands
• Promoters are like TATA boxes that help with the position of RNA polymerase
• Enhancers often function far from the transcriptional start site but with enhance gene expression through transcription level/rate
• Silencer/repressor elements with shut down or turn off gene expression
• Response elements are specific sequences within enhancers or silencers that respond to signaling pathways and environmental cues
• Insulators/Boundary Elements act like barriers to restrict action of enhancers/silencers to particular genes
• CpG islands are stretches of DNA that have high concentration of CpG dinucleotides (cytosine followed by guanine) that are islands that are often targeted for methylation
• To control gene expression, you need:

  • Core transcriptional machinery
  • Gene specific requirements
• Proteins involved in regulating gene expression:

  • Activators
  • Repressors
  • Mediators and DNA binding proteins
  • Chromatin remodeling proteins
  • Histone acetylase/deacetylase
  • Histone methylation
  • DNA methylation
• DNA is protected/wrapped by chromatin to prevent degradation, damage, and controls gene expression
• There's 2 meters or 6 feet of DNA in every human cell
• Histones are highly basic proteins that bind loosely to DNA

  • Five families of histones (linker, core)
  • Has lots of positively charged amino acids that can bind to negatively charged DNA
  • Responsible for wrapping DNA and opening chromatin - histones can control transcription factor access to gene regulatory elements
• Histone tails contain modifications that determines whether chromatin is opened, if the transcription factor will interact, whether gene expression is turned on or off

  • Types: acetylation, methylation, phosphorylation
• Acetylations occur on positive charges to start opening up and weakening chromatin
• Histone methylation regulates interactions with DNA methyltransferases that methylate DNA at the CpG dinucleotides
• Transcription factor DNA binding motifs:

  • Helix-loop-helix: alpha helices bound by looping stretch of amino acids
  • DNA binding zinc finger: alpha helix and beta sheet structure that have bound zinc metal ions
  • Helix-turn-helix: 2 alpha helices joined by a short amino acid sequence
  • Leucine zipper: 2 proteins with alpha-helix to form a Y-shaped coiled-coil structure
• DNA is a right-handed helix
• Helix-turn-helix motif has a recognition helix that binds to the major groove of DNA and usually forms hydrogen bonds
• Transcription factors are very specific to where they bind