transposable elements 1

biology of maize

• each pollen grain contains two identical haploid germ cells

• each endosperm (ovule, aleurone) contains the haploid egg cell (n) and a diploid cell called the central cell (2n) → 3n

• embryo contains the haploid sperm cell (n) and the haploid egg cell (n) → 2n

• kernel contains embryo and endosperm

maize pigment genes

• coloured aleurone (C) gene is important for production of purple pigment

• c is a recessive allele that is unable to make pigment

• C¹ is a dominant inhibitor allele that represses pigment production

• dominance: C¹ > C > c

• c/c or C¹/C → yellow pigment

• C/C or C/c → purple pigment

maize aleurone

arises from a single cell, all cells are genetically identical

observation of unstable pigment gene alleles

1. experiment: use pollen from a C¹ strain to fertilize C/C ovules

2. predicted result: all colourless kernels

3. unexpected result from one particular pollen parent: some kernels have blue pigment in sectors

4. hypothesis: C¹ allele is lost in some cells of the developing endosperm

5. experiment: look for breakage in chromosomes of the pollen parent

6. result: high rate of breakage in this strain

7. interpretation: loss of the C¹ allele is caused by chromosome breakage at specific locations

breakpoint Ds element

• dissociation element

• place on a chromosome at which it break

• requires the presence of the Ac element to mobilize

breaks occurring in a different location in a related strain

• in some strains, Ds has moved to a new location

• new location can be inferred from the phenotype of the sectors (which marker genes also got lost)

• in these sectors, pigment is restored but other kernel traits remain unchanged

Ac element

• activator element

• required for movement of the Ds element

non-autonomous transposable elements

requires a separate element to excise / transpose (ex: Ds requires Ac to jump out)

autonomous transposable elements

excises / transposes on its own, without requiring another element

c-Ds

when excised, the two ends of the chromosome are joined together, restoring a functional dominant C allele

size of pigmented sectors

• depends on when in development the Ds element jumped out and restored C function

• jump out early → large spot

• jump out late → small spot

Ds mobility in case of C pigment gene

• frequently can jump out of the c-Ds mutant and restore the original gene

• rarely can jump into the C gene to generate a mutant (c-m1)

  • low chance of landing in a small gene

transposons / transposable elements

• ancient

• found in all organisms (bacteria, plants, yeast, multicellular animals)

• contributed to placental evolution by inserting themselves into genes, enabling new functions and providing alternative promoters or enhancers

• TE-influenced regulatory elements play a critical role in placental function

• usually found in introns or in intergenic regions

• potential source of major phenotypic novelty and adaptive change

class 2 transposons / DNA transposons

• activator gene encodes transposase that catalyzes excision and integration

• each family had a transposase version that is specific for its own family

• cut and paste mechanism

class 1 transposons / retrotransposons

• similar to retroviruses

• move via an RNA intermediate

• transposition is meditated by reverse transcriptase

• replicative mechanism (copy and paste)

long interspersed element (LINE)

retrotransposon found in the human genome

LINE1 (L1)

• the only autonomous transposable element in humans

• comprises almost 17% of the whole human genome

steps of LINE1 (retrotransposon) movement

1. transcription

2. translation of LINE1 mRNAs to produce ORF1p and ORF2p

3. ORF1p is an RNA-binding protein with nucleic acid chaperone activity that binds to LINE1 transcript

4. ORF2p possesses endonuclease and reverse transcriptase activities

impacts of transposable element mobility over time

transposable elements are abundant in large genomes

• potential evolutionary impact via introducing genetic novelty

transposable elements as a source of phenotypic novelty in grapes

• Vvmby1A gene is required for production of purple pigment in Cabernet grapes

• initial insertion of a Gret1 long terminal repeat retrotransposon results in a loss-of-function allele of the Vvmby1A gene, leading to a loss of colour in Chardonnay variety

• subsequent rearrangement in Gret1 results in revertant, coloured grapes in varieties such as Ruby Okuyama

  • one of the two flanking regions of Gret1 remains

possible impacts of transposable element mobility in an individual

• disease mutations

• genetic instability

transposable element mobility leading to disease

• 1/600 spontaneous mutations causing important human diseases results from the transposition of a LINE or SINE element

• ex: Homo sapiens-specific LINE1 insertion in a patient with haemophilia (blood clotting disorder) interrupts a coding exon of factor VIII

  • insertion in an exon disrupts the gene’s coding sequence

transposable elements affecting genes

• insertion of an AluYa5 element in a patient with Dent disease (rare genetic kidney disorder) interrupts an exonic splice enhancer

• results in skipping of exon 11, which introduces a stop codon in exon 12

transposable element mobility is associated with human cancers

• numerous cancers including lung, colon, pancreatic, and ovarian cancers have been associated with markers for LINE1 mobility

• marker for LINE1 activity is found in cancerous tissue but not normal tissue