The Dynamic Genome Transposons. What are Transposons? Some definitions and figures from Lisch 2009:...

The Dynamic Genome

Transposons

What are Transposons?

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

Transposition of DNA explains mottled kernels in maize

Transposable element (transposon, TE):DNA sequence competent to insert into new places

What are Transposons?

Learn more at: weedtowonder.org/jumpingGenes.html

(1) At the beginning of kernel development, the Ds transposon inserts 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.

Transposable element (transposon, TE): DNA sequence competent to insert into new places

What are Transposons?

Transposable element (transposon, TE): DNA sequence competent to insert into new places

“Cut & Paste”

“Copy & Paste”

(Alu)

(Ac/Ds)

Autonomous element

Nonautonomous elements

Gene(s)

•Most genomes contain multiple transposon families.

•Each family contains autonomous and non-autonomous elements.

•Autonomous elements encode their own moving competency.

•Non-autonomous elements are moved by other elements.

What are Transposons?

Class I transposons are being copied multiplicative. Class II transposons can undergo copying, too, if transposing during DNA replication

What are Transposons?

Transposons make up most of (most) eukaryotic genomes•~50% of the genomes of human, chimp, mouse, gorilla

•~75% of the maize genome

•~85% of the barley genome

•~98% of the iris genome

Iris brevicaulis Iris fulva

Hs 11: http://dnalc.org/resources/3d/chr11.html

Sorghum 700 Mb

Barley 5,000 Mb

Maize 2,500 Mb

Oats ~20,000 MbWheat 20,000 Mb

Rice 450 Mb

Effect of transposons & genome duplications on genomes

What are Transposons?

• 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

Transposons in Action

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?

mPing insertions in genome

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

mPing insertions in genes

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

Suppl.: DNA transposons can be copied, tooGap repair from sister chromatid

Jump into site that is then replicated

• Find homologs using DNA

• Find homologs using protein

• Locate transposons

• Examine surroundings of transposon insertions

• Identify active transposons and “molecular fossils”

• Show recent transposon activity

Yellow Line Walk-through(Advanced Yellow Line Example)