the dynamic genome transposons. what are transposons? transposable element (transposon): a sequence...

The Dynamic Genome

Transposons

What are Transposons?Transposable element (transposon): a sequence of DNA that is competent to movefrom place to place within a genome

Some definitions and figures from Lisch 2009: Annu. Rev. Plant Biol. 2009.60:43-66.

Transposition of DNA on chromosome 9 of maize explains mottled kernels


Learn more at: weedtowonder.org/jumpingGenes.html

(1) At the beginning of kernel development, the Ds transposon is inserted into the colored (C) gene, resulting in colorless tissue. (2) Ds transposition early in kernel development restores the C gene, giving rise to a large colored sector. (3) Transposition later in kernel development results in smaller sectors.


“Cut & Paste”

“Copy & Paste”

Autonomous element

Nonautonomous elements

Gene(s)

•Plant genomes contain multiple transposon families.

•Each contains autonomous and non-autonomous elements.•Class I transposons do not move, but are being copied.

•Class II transposons move, but can undergo copying, too (if transposing during DNA replication)

What are Transposons?

What are Transposons?Transposons make up the major content of eukaryotic genomes

•~50% of the genomes of human, chimp, mouse, ape

•~75% of the maize genome

•~85% of the barley genome

•~98% of the iris genome

Iris brevicaulis Iris fulva

Sorghum 700 Mb

Barley 5,000 Mb

Maize 2,500 Mb

Oats ~20,000 MbWheat 20,000 Mb

Rice 450 Mb

Variation in cereal genomes - transposons & genome duplications

What are Transposons?

Transposons in Action

• Most TEs are broken (cannot tranpose; “fossils”).

• Active TEs evolved to insert into “safe-havens.”

• Host regulates TE movement.

• TEs can provide advantages.

How do organisms live with TEs?

mPing:

MITE (Multi-insertional TE)

Deletion-derivative of Ping

Requires Ping transposase to jump

MITEs are being amplified to high copy numbers

Ping/mPing

OVER 1000 mPing copies

Japonica strains

mP

ing

cop

y n

um

ber

Naito et al PNAS (2006))

mPing

Over 1000 copies of mPing in 4 related strains….

Takatoshi Tanisaka lab (Kyoto University)

mPing copy number in O.japonica

• predominantly in genic regions in euchromatin

• even inserts in heterochromatin are in genes

• where does mPing insert in and around genes?

Genomic distribution of mPing insertions

0

2

4

6

8

10

12

5'UTR exon intron 3'UTR

(%)

shared(n=926)

unshared(n=736)

expect.

mPing insertions rare in coding-exons

UTR Exon UTR

Genic distribution of mPing insertions

Os02g0135500 (-41)

0

0.5

1

1.5

2

2.5

control cold salt dry

NBEG4 (mPing+)A123 (mPing+)A157

mPing found to confer cold and salt inducibility

TEs can alter gene expression

Nipponbare EG4

EG4 is salt tolerant

TEs can alter gene expressionCan this have phenotypic consequences?

Naito et al, Nature, 2009

• Massive amplification largely benign• Subtle impact on the expression of many genes• Produces stress-inducible networks (cold, salt, others?)• Generates dominant alleles

Rapid mPing amplification (burst)

• TEs usually inactive.

• “Stress” conditions may activate TEs.

• Active TEs increase mutation frequency.

• Most mutations caused by TEs neutral or harmful.

• A rare TE-induced mutation (or rearrangement) may be adaptive.

Transposable elements can shake up otherwise conservative genomes and generate new genetic diversity.

TEs as tools of evolutionary change

• (relatively) simple

• incredibly abundant

• evolve rapidly

• promote rapid genome evolution

• largely ignored (discovery)

TEs for student research projects

the dynamic genome transposons. what are transposons? transposable element (transposon): a sequence...

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