Eukaryotic Gene regulation

• the expression of genes can be regulated at just about any step in the Central Dogma
• For transcription to be initiated (started), the RNA polymerase complex must bind to DNA at the beginning of the gene (the promoter)
• • Transcription initiation happens with the help of proteins called transcription factors that bind to the DNA at the promoter and “recruit” the RNA polymerase.
  • Even once RNA polymerase binds to the DNA, it can’t begin transcription until it is “released.”
• RNA polymerase is only released when different transcription factors bind to other regulatory DNA regions...
• In addition to non-coding promoter DNA sequence, eukaryotic genes also have non-coding enhancer sequences that contribute to regulating gene expression
• A gene can have many enhancers associated with it and they can be located anywhere on the chromosome (don’t have to be close to the gene)
• A gene’s enhancer will have a specific transcription factor(s) that will bind to it
• Once bound, enhancer TFs will attract a mediator complex, which interacts with TFs and RNA pol at the promoter and the “transcription initiation complex” is complete

  • At this point transcription can finally begin
• Enhancers regulate whether, where, when, and how much a promoter – and thus the gene it’s attached to – is active
• A gene often has multiple enhancers so that it can beregulated differently in different situations

  • B/c typically, a gene will code for a protein used for many different purposes
• Enhancers activate transcription; there can also be silencers that inhibit it
• Enhancers for a gene bind to activating transcription factors (activators). When this happens, the gene ispositively regulated (“activated”)
• Silencers for a gene bind to repressive transcription factors (repressors). When this happens, transcription of the gene is negatively regulated ("inhibit")
• Genes often have multiple enhancers and silencers
• Whether and how much the gene is transcribed in a particular cell depends on the exact combination of regulatory TFs (e.g., activators and/or repressors) present in that cell

  • This is called combinatorial control of gene expression
• The different possible combinations of various TF’s provides multiple layers of control over transcription (and thus gene activity) at a particular time, place, and speed
• Mutations in regulatory, non-coding regions of DNA (such as enhancers, silencers and promoters) often affect levels of transcription.
• What does “epigenetic” mean?

  • Epi = “above” or “beyond”
  • Epigenetic means “above the genes” (layered on top of the DNA sequence)
• Epigenetic regulation of transcription involves changes to the packaging of chromatin (what chromosomes are made of), which affects how easily genes can be transcribed (expressed)
• Epigenetic states are stable, but can be reversible and responsive to changes in the environment
• Just like genes, the epigenome (and thus how genes are expressed) is heritable through cell divisions, and sometimes across generations
• A eukaryotic chromosome is a single long, linear DNA double helix strand wrapped around clusters of proteins called histones
• histones + wound DNA is called a “nucleosome”
• The string of nucleosomes is further coiled to make a denser fiber of chromatin
• For a gene to be transcribed, the DNA must be accessible

  • When the chromatin is coiled and condense, theproteins that carry out transcription cannot access the DNA for that gene.
• If we want to express that gene, chromatin remodeling and unraveling must occur in that region so that transcription factors and RNA polymerase can bind to promoter and/or enhancers for that gene.
• Chromatin remodeling is a neat trick for turningon/off genes

  • Condensed: Not accessible for transcription
  • Open: accessible for transcription
• Chemical changes to either the histone proteins in the nucleosome or to the DNA itself can lead to chromatin remodeling

  • Be either open or condensed
• Genes in condensed chromatin can’t be accessed by RNA polymerase and transcription factors in order to be transcribed
• How is chromatin remodeled?Two major ways to remodel chromatin:

  1. Chemical changes to DNA bases
  2. Chemical changes to histone proteins
• Histones have tails

  • Methylating (adding a CH3 group to) histone tails can lead to either more open or more condensedchromatin (it depends...)
• Histones have tails

  • Acetylating histone tails leads to more open chromatin
• The most common chemical modification to DNA ismethylating (adding CH3 to) cytosine nucleotide bases

  • Cytosines that get methylated are usually right next to Guanine bases
  • Places (loci) in the DNA where C and G are next to each other are called CpG sites.
• Clusters of CpG sites are typically found in the promoter region of a gene

  • If these CpG sites are methylated, this will decrease gene expression
• If these CpG sites are methylated, this will decrease gene expression

  • Prevents activating transcription factors from binding.
  • Increases repressor binding
  • Recruits histone modifying enzymes to condense chromatin
• Like other epigenetic modifications, CpG methylation can change over time or in response to environmental cues, providing a way to turn genes on or off depending on circumstances.
• One of the major ways post- transcription regulation canhappen is via alternative splicing
• Translational regulation controls the rate, timing, and location of protein synthesis
• Post-translational modifications control the chemical properties – and thus the activity/function of – proteins once they’ve been made

  • Many proteins are modified by reversible addition of a phosphate to the R groups of an amino acid
  • This is a major regulator of protein activity
• The acetylation or methylation of histones is a post-translational modification