The Dynamic Genome Transposons

Transposable element (transposon, TE): What are Transposons? Transposable element (transposon, TE): DNA sequence competent to insert into new places Left image are sketches of McClintock’s observation of chromosomes in Maize. Transposition of DNA explains mottled kernels in maize Some definitions and figures from Lisch 2009: Annu. Rev. Plant Biol. 2009.60:43-66.

What are Transposons? Transposable element (transposon, TE): DNA sequence competent to insert into new places (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. Learn more at: weedtowonder.org/jumpingGenes.html

What are Transposons? “Cut & Paste” “Copy & Paste” (Ac/Ds) (Alu) Transposable element (transposon, TE): DNA sequence competent to insert into new places (Ac/Ds) “Cut & Paste” (Alu) “Copy & Paste”

Nonautonomous elements What are Transposons? 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. Autonomous element Nonautonomous elements Gene(s) Class I transposons are being copied  multiplicative. Class II transposons can undergo copying, too, if transposing during DNA replication

Transposons make up most of (most) eukaryotic genomes 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

Effect of transposons & genome duplications on genomes What are Transposons? Effect of transposons & genome duplications on genomes Rice 450 Mb Sorghum 700 Mb Maize 2,500 Mb Barley 5,000 Mb Wheat 20,000 Mb Oats ~20,000 Mb

How do organisms live with TEs? Most TEs are broken (cannot tranpose; “fossils”). Active TEs evolved to insert into “safe-havens.” Host regulates TE movement. TEs can provide advantages.

MITEs are being amplified to high copy numbers Ping/mPing mPing: MITE (Multi-insertional TE) Deletion-derivative of Ping Requires Ping transposase to jump MITEs are being amplified to high copy numbers

Transposons in Action The majority of transposition events are ancient, but in Sue Wessler’s story, we se tranpsons in action.

mPing copy number in O. japonica OVER 1000 mPing copies mPing mPing copy number Japonica strains Over 1000 copies of mPing in 4 related strains…. Naito et al PNAS (2006)) Takatoshi Tanisaka lab (Kyoto University)

mPing insertions in genome predominantly in genic regions in euchromatin even inserts in heterochromatin are in genes where does mPing insert in and around genes?

mPing insertions in genes UTR Exon mPing insertions rare in coding-exons

TEs can alter gene expression mPing found to confer cold and salt inducibility

TEs can alter gene expression Can this have phenotypic consequences? Nipponbare EG4 EG4 is salt tolerant

Rapid mPing amplification (burst) Massive amplification largely benign Subtle impact on the expression of many genes Produces stress-inducible networks (cold, salt, others?) Generates dominant alleles Naito et al, Nature, 2009

TEs as tools of evolutionary change 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 for student research projects (relatively) simple incredibly abundant evolve rapidly promote rapid genome evolution largely ignored (discovery)

Suppl.: DNA transposons can be copied, too Gap repair from sister chromatid Jump into site that is then replicated

Yellow Line Walk-through (Advanced Yellow Line Example) 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