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Gene structure, expression and regulation in eukaryotes

Eukaryotic Gene Structure
1. Monocistronic - Each protein is coded for by a single separate gene
  1. Advantage - Flexible and Resilient
  2. Disadvantage - Complex
2. Promoter
  1. Controls expression level and timing
3. Enhancers
4. Coding region
  1. Nucleotides encoding peptide or RNA
  2. Exon
5. poly(A) site
  1. mRNA stability
    1. Expression Level
6. Splice sites
  1. Isoforms
7. Non coding regions
  1. Introns
    1. Help create genetic diversity
Transcription
1. Occurs in Nucleus
2. Transcription Units
  1. Simple
    1. 1 mRNA = 1 protein
    2. Mutation along entire length will impact protein
  2. Complex
    1. Encodes for multiple proteins through the use of Alternative Splicing
      1. Alternative in/exclusion
        Diff composition e.g. Fibronectin
      2. Alternative Promoters
        Diff timing e.g. Pax6, Diff N termini, Diff strength of expression
      3. Alternative poly(A) sites
        Different C-termini - Heavy chain IgM
3. 3 different polymerases
4. Initiation
  1. Promoter Recognition accessory proteins bind to promoter sequence promoter sequence --> recruitment of > recruitment of specific RNA polymerase
    1. Accessory Proteins
      1. General Transcription Factors
        Bind to core promoter to assemble Basal Transcription Apparatus (BTA)
        BTA includes TFs, mediator complex and RNA pol II for minimal transcription
        Core - immediately upstream of transcription start site
      2. Transcriptional Activator Proteins
        Bind to specific DNA sequences (regulatory, promoter, enhancers, etc) to stimulate assembly of BTA
        Leads to increased transcription
        Allows regulation in response to different stimuli
        Regulatory promoter is further upstream TAPs bind to DNA sequences then interacts with BTA, influences the rate of transcription initiation
        Includes enhancer region that is even further upstream
  2. TFIID binds to TATA box in core promoter
    1. Then TFs and RNA pol II bind to core promoter
      1. TAPs bind to sequences in enhancers
        DNA loops out allowing the proteins bound to the enhancer to interact with BTA
        TAP bind to sequences in the regulatory promoter and interact with BTA through the mediator
5. Elongation
  1. After 30 bp of mRNA After 30 bp of mRNA synthesis Pol leaves synthesis Pol leaves promoter and TF promoter and TF behind
  2. 8 nucleotides of RNA 8 nucleotides of RNA remains paired with remains paired with DNA
6. Termination
  1. RNA pol II transcribes well past the coding region of many genes
    1. Cleavage is near 3' end of RNA, while RNA pol II keeps transcribing
      1. The RAT1 exonuclease attaches to the 5' end of the trailing RNA and moves towards the RNA pol degrading the RNA as it goes along
        When RAT1 reaches the pol transcription is terminated
Translation
1. Occurs in Cytoplasm
2. Initiation
  1. Small subunit binds to 5’ cap and scans mRNA for start codon Kozak sequence aids recognition
    1. Initiation complex recognises 5' Cap
      1. Initiation Complex - small subunit, IF, initiator tRNA (Met small subunit, IF, initiator tRNA (Met--tRNA
    2. Start codon = AUG
    3. requires at least 7 IF (function: separation of SU of requires at least 7 IF (function: separation of SU of Ribosome, recognition of 5’ cap, RNA helicase activity, Ribosome, recognition of 5’ cap, RNA helicase activity, recruitment Met-tRNA
    4. poly(A) - bound proteins interact with 5' cap - enhances binding of small subunit at 5' of mRNA
      1. Eukaryotic Ribsomes - Bigger and more complex than complex than prokaryotes but prokaryotes but same structure and same structure and function
3. Elongation
  1. at least 3 elongation least 3 elongation factors equivalent to prokaryotic factors equivalent to prokaryotic EFs
    1. eeF2 - translocation
4. Termination
  1. Similar to prokaryotes
    1. eRF1 - recognises termination codons
    2. eRF2 GTP, stimulates release of polypeptide from ribosome
RNA processing
1. RNA molecules are processed before leaving Nucleus
2. Includes removal of parts of the primary transcript
3. Addition of 5' cap
  1. 5' cap functions include - Increases the stability of the transcript •Is recognised by the ribosome to begin translation •Has a role in transport of the mRNA from the nucleus to the cytoplasm
4. RNA editing
5. RNA splicing
  1. takes place in nucleus
  2. order of exons in DNA is usually maintained
  3. Occurs at short conserved sequences
  4. Proceeds via two sequential trans-esteriﬁcation reactions
  5. Catalysed by a spliceosome
    1. The spliceosome consists of: -5 small RNA molecules called snRNAs: U1, U2, U4, U5, U6. -Proteins.
      1. Each snRNA interacts with speciﬁc proteins to form snRNPs (small nuclear riboproteins, or snurps)
  6. Exceptions to normal splicing
    1. Trans-splicing (e.g. nematodes and trypanosomes) joining of exons from different mRNAs
    2. minor splicing: different consensus sequences and different spliceosome composition
    3. Self-splicing introns (e.g. protists, mitochondria): remove themselves (no other enzyme/protein)
6. 3' cleavage and addition of poly(A) tail
  1. pre-mRNA is transcribed with a consensus sequence
    1. pre-mRNA is cleaved 11-30 bp upstream of consensus sequence - this cleave site contains a u rich sequence
      1. poly(A) tail is added through polyadenylation
        Functions of poly(A) tail include increasing stability and acting as a timer. Also is recognised in protein synthesis (attachment of ribosome)
Gene regulation
1. mRNA degradation control
  1. legnth of poly(A) tail controls stability and acts as a timer
  2. cleavage inside mRNA
  3. 3’->5’ removal nucleotide
  4. removal of 5’ CAP, 5’->3’ removal nucleotid
  5. 5’UTR, CDR, 3‘UTR can affect mRNA stability
  6. RNA interferecne
    1. Dicer
    2. RNA Induced Silencing Complex (RISC)
    3. pairing with complementary sequence of mRNA -> cleavage of mRNA
    4. 4 possible outcomes
      1. Cleavage of mRNA
        Double stranded RNA is cleaved by dicer enzyme to produce small interfereing RNAs (siRNAs)
        siRNAs combine with RISC complex and pair with complementary sequences of mRNA
        Complex cleaves mRNA and afterwards the RNA is degraded
      2. Inhibition of translation
        miRNAs produced then combine with RISC and pair imperfectly to an mRNA, which leads to inhibition of translation
      3. Transcriptional silencing
        miRNAs bind to comp sequences and attract methylating enzymes, this mehtylates the DNA or histones inhibiting (silencing) transcription
      4. Degradation of mRNA
2. Translation Control
  1. e.g. T cells activation mRNA already there, increase in available initiation factors for translation -> IF allow ribosomes to bind to mRNA -> TRANSLATION
3. RNA Processing Control
  1. Alternative splicing
    1. e.e sexual phenotype in drosophila
      1. In males upstream splice site used - premature stop codon so no functional protein is produced - and in females sxl protein causes downstream splice site to be used - stop codon is spliced out alongside intron and tra protein normally produced
4. Transcriptional Control
  1. Transcriptional Repressors
    1. - Bind to silencers: can be some distance from regulated gene, position and orientation independent they compete with activators
    2. may bind to sites near activator site -> prevents contact of activator with BTA
    3. Directly interfere with assembly of BTA
  2. Enhancers stimulate any promoter in vicinity
  3. Insulators block effect on promoters nearby, some also limit spread of de/condensation of chromatin
  4. Transcriptional Stalling
    1. transcription for few bp, then pause until external stimulus is encountere
    2. e.g. Heat shock in drosophila
  5. Coordinated Gene Regulation - certain genes activated by same stimulus -> response element (same regulatory sequence, that provides binding sites for transcriptional activators
    1. single gene can be activated by several different response elements - > activation through different stimuli
    2. One stimulus can be activated by several genes --> presence of same response element
  6. Combinatorial Gene Control
    1. e.g. ey gene in drosophila
5. Protein activity control
  1. Effects transport, function and activity
6. RNA Transport and localisation control
  1. Transport mRNA across nuclear envelope
    1. poly(A) and 5' cap involved
Epigenetics
1. changes in phenotype or gene expression by mechanisms other than changes in the underlying DNA sequence
  1. may be continuous over lifespan of cell or even hereditary
2. Chromatin remodelling
  1. Histone modification - A combination of diff molecules attach to tail of histone molecule. These alter the activity of the DNA surrounding them
  2. Can make oncogenes more active
3. DNA methylation
  1. Methyl marks added to certain bases represses gene activity
    1. e.g. Gene silencing by adding methyl group to cytosine
    2. Can play a role in cancer by silencing tumour suppresor genes
4. Plays a role in development - cell differentiation
  1. Epigenetic reprogramming = Reproductive cells: specialised cells, lots of epigenetic tags most epigenetic tags removed in early embryo, so that cells can form every type of cell in body: “blank slate"
    1. Some genes escape this reprogramming - Epigenetic inheritence

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Gene structure, expression and regulation in eukaryotes

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	Created by Natalina Laria over 8 years ago