Polyploidy and Epigenetics Notes

Polyploidy

  • Polyploidy: Possession of more than two complete sets of chromosomes.
  • Caused by non-disjunction during mitosis or meiosis.
  • Heritable condition.
  • Polyploid organisms are well-adapted to their environments.
  • High incidence in some taxa.

Terminology

  • Species A: 2n = AA
  • Species B: 2n = BB
  • Species C: 2n = CC
  • Auto triploid: 3n = AAA
  • Auto tetraploid: 4n = AAAA
  • F1: 2n = AB
  • Auto hexaploid: 6n = AAAAAA
  • Auto pentaploid: 5n = AAAAA
  • Allo tetraploid: 4n = AABB
  • Auto triploid: 3n = BBB
  • Allo triploid: 3n = ABC
  • Autoallo hexaploid: 6n = AABBBB
  • Autoallo octaploid: 8n = AAAABBBB
  • Autoallo hexaploid: 6n = AABBCC

Causes

  • Non-disjunction during mitosis.
  • Colchicine as a possible inducer.
  • Tetraploid cells: Gametes produced by a flower on a tetraploid branch (via meiosis) are diploid instead of haploid.
  • First division non-disjunction.
  • Second division non-disjunction.

Autopolyploidy

  • Caused by non-disjunction during meiosis and self-fertilization.
  • Unreduced gamete with 6 chromosomes combines with another unreduced gamete with 6 chromosomes, resulting in a zygote with 4n = 12 (tetraploid).

Autoallopolyploidy

  • Caused by non-disjunction during meiosis and fertilization by another species.
  • Species A (2n=6) produces a normal gamete (n=3).
  • Species B (2n=4) experiences meiotic error producing an unreduced gamete with 4 chromosomes . Another unreduced gamete with 7 chromosomes
  • Hybrid offspring results with 2n = 10, creating a viable fertile allopolyploid.

Commonality

  • Different species are tolerant to different degrees of polyploidy.
  • High frequency in flowering plants, fish, and frogs.
  • Higher vertebrates do not appear to tolerate polyploidy.

Polyploid Examples

  • Tetraploid (4x): Salmonidae fish, the frog Xenopus laevis.
  • Octoploid (8x): Acipenser (genus of sturgeon fish).
  • Dodecaploid (12x): Ugandan clawed frog Xenopus ruwenzoriensis.
  • Triploid crops (3x): Apple, banana, citrus, ginger, watermelon.
  • Tetraploid crops (4x): Apple, durum or macaroni wheat, cotton, potato, etc.
  • Octaploid crops (8x): Strawberry, dahlia, pansies, sugar cane.

Xenopus Example

  • X. laevis: allotetraploid, 2n = 36 chromosomes, genome size 3.1 \times 10^9 bp, adult size 10 cm, egg size 1-1.3 mm, 1000-3000 eggs/spawn, generation time 1-2 years.
  • X. tropicalis: diploid, 2n = 20 chromosomes, genome size 1.7 \times 10^9 bp, adult size 4-5 cm, egg size 0.7-0.8 mm, 300-1000 eggs/spawn, generation time 4 months, temp. optima 25-30° C. 16-22° C.

Brassica Family

  • Oil seed.
  • Turnip.
  • Swede turnip.
  • Cauliflower.
  • Cabbage.
  • Broccoli.
  • Black mustard.
  • Abyssinian mustard.
  • Indian mustard.

Evolutionary Benefits

  • Polyploidy can make the plant bigger.
  • Bigger flowers.
  • Bigger fruits.
  • Bigger leaves.

Summary

  • Polyploidy: Possession of more than two complete sets of chromosomes.
  • Arises from non-disjunction during mitosis or meiosis.
  • Different species exhibit different levels of tolerance for polyploidy.
  • Advantages:
    • Hybrid vigor.
    • More resistant to effects of recessive mutations.
    • Redundancy allows faster evolution/adaptation.

Epigenetics

  • 'Epi' – on top of.
  • Chemical reactions that switch parts of the genome off and on.
  • Epigenetic regulation modulates gene expression without altering the DNA sequence.
  • Facilitates rapid adjustments to dynamically changing environment.
  • Formation of an epigenetic memory.

Transcription Regulation

  • Epigenetics is the regulation of transcription.
  • A transcription factor molecule binds DNA at a binding site and regulates the production of protein from a gene.
  • Genotype --(Epigenetics = regulation of transcription)--> phenotype

Mechanisms

  • DNA methylation / Histone modification determines 'tightness' of chromatin structure.
  • Chromatin status controls access of transcription machinery (DNA -> mRNA).
  • RNA interference regulates amount of mRNA produced.

DNA Methylation

  • Methylation occurs at CpG islands.
  • C is methylated.
  • Methylation of CpG islands can lead to the 'silencing' of genes (i.e. not transcribed).

Histone Modification

  • Histone modifications (e.g., methylations, acetylations, etc.) can tighten (condense) chromatin structure.
  • Condensed chromatin (heterochromatin) blocks Transcription Factors (TF) from accessing DNA.

MicroRNA (miRNA)

  • Produced by cell to regulate gene's translation.
  • If miRNA is perfect match -> mRNA degradation.
  • If miRNA is imperfect match -> translational repression.

Trait Expression

  • Phenotype formed by interaction of genotype with environment.

Development

  • Before conception: Exposure of gametes influences parental epigenome and genome.
  • Fetal life: In utero exposures affect offspring's genome and epigenome at birth.
  • Childhood and adult life: Early life and adult life exposures shape epigenome in childhood and adulthood, programming disease risks.

Cancer

  • Epigenetics plays a significant role in cancer development.

Aging

  • Factors influencing aging epigenetics: Tobacco, metal exposure, air pollution, endocrine disruptors, diet.

Summary

  • Chemical reactions that switch genomic sections off / on in response to environmental stimuli (e.g., toxins, diet, stress, behavior).
  • Epigenetic regulation modulates gene expression without altering the DNA sequence.
  • Facilitates rapid adjustments to dynamically changing environmental conditions.
  • Formation of an epigenetic memory (matter of controversial debate).