TRITIUM CLOUD 氚

By Ao Zhang

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Understanding Genetic Variation

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Part A: Understanding Genetic Variation

Some Causes of Genetic Variation

  • Replication errors
  • Sponatneous mutation (自发突变): during DNA replication
    • Hydrolytic damage
    • Oxidative damage
  • Chemicl damage: caused by chemicals
    • Radiation (UV, X-ray, gamma-ray)
    • Chemicals (e.g. cigarette smoke)

Types of Genetic Variation

DNA replication errors

  • DNA polymerase could insert the wrong nucleotide, corrected by proofreading

  • Commonly occur in short tendem repeats

Unequal crossover (UEC)

Unequal crossover

Tom Strachan; Anneke Lucassen. Genetics and Genomics in Medicine: CRC Press, 2022. ISBN 9780367490812

Chromosomal segregation errors

Causing wrong number of chromosomes in gametes: trisomy, monosomy

Small-scale variation

Single base-pair substitution (Transition vs. Transversion)

  • Transition: purine to purine (A <-> G) or pyrimidine to pyrimidine (C <-> T)
  • Transversion: purine to pyrimidine or pyrimidine to purine (A <-> C, A <-> T, G <-> C, G <-> T)

SNV (Single nucleotide variant) (Synonymous vs. Non-synonymous)

  • Synonymous: no change in amino acid (ACC (Thr) -> ACA (Thr))
  • Non-synonymous: change in amino acid
    • Missense: change in amino acid (AGT (Ser) -> AGG (Arg))
    • Nonsense: change in amino acid to stop codon (TGG (Trp) -> TGA (Stop))
    • Stop-loss: stop codon to amino acid (TGA (Stop) -> TGC (Cys))

Conservative vs. Non-conservative

  • Conservative: Same Chemical class
  • Non-conservative: Different Chemical class

Splicing Mutation

Small insertion/deletion (indel) (<50 bp)

  • Frameshift Mutation: insertion/deletion of a number of nucleotides
    • Lead to premature stop codon
    • Degradation of mRNA by nonsense-mediated decay (NMD)
    • Sometimes, translate to a longer protein, which could infect the function of the normal protein

Large-scale variation

Structural variation (>50 bp) (balanced vs. unbalanced)

  • Types: Insertion, Deletion, Duplication, Inversion, Translocation
  • Can cause copy number variations
  • Effects on gene expression and protein function

Variants in gene regulation

  • Transcription factor binding sites
  • Affects Transcription factor binding motifs (TFBMs)

Effects of Mutation

A change in the sequence of the gene:

  • Gain of function
  • Loss of function
  • Altered function

Change in gene expression levels:

  • Copy number variation
  • Change in gene regulation
  • Premature termination codon

1.5B DNA Damage and Repair

DNA repair pathways

  • Direct reversal of damage
    • O6-alkyl guanine-DNA alkyltransferase (ATase)
    • Photolyase
    • AlkB
  • Nucleotide excision repair (NER)
    • UV damage
    • Bulky adducts
  • Base excision repair (BER)
    • Base and sugar-phosphate backbone damage
    • DNA single strand breaks (SSBs)
  • DNA damage tolerance
    • Translesion polymerases

Why DNA repair is important

  • DNA is the only molecule that can be repaired, others are replaced

  • 5% of proteins are involved in DNA repair

  • Cancer

    • Polygenic disease requiring changes in several class of genes.
    • Steps:
      • Loss of Genome Stability
      • Loss of a tumor suppressor gene
      • Activation of an oncogene
      • Escape from cell death process
      • Amplification of signal cascades

DNA repair for cancer therapy:

  • Good:
    • Defend against exogenous and endogenous agents
    • protect against cancer
  • Bad:
    • Resistance to therapy
    • responsible for chromosomal translocations

Main forms of DNA damage

  • Single strand breaks
  • Mismatches
  • Damaged bases
  • Double strand breaks
  • Intra-strand crosslinks
  • Inter-strand crosslinks

DNA repair pathways

Direct reversal

Removal of O6-alkyl groups by the suicide protein O6-ATase

Base excision repair

Base excision repair in Human Cells.

Lesion recognition in base excision repair - 'nucleotide flipping' is a common theme

Nucleotide excision repair

  • Recognise distorition

  • Formation of structure & recognition of damaged strand

  • Dual incision by structure-specific endonucleases

  • Excision DNA repair synthesis

Failed Transcription-coupled repair:
Cockayne syndrome

DNA Damage tolerance

Nearly all DNA lesions block DNA polymerase synthesis, and replication in S-phase

  • Interconnections and redundancy across repair pathways