The Dynamic Genome Transposons

What are Transposons? Transposable element (transposon): a sequence of DNA that is competent to move from place to place within a genome Left image are sketches of McClintock’s observation of chromosomes in Maize. Transposition of DNA on chromosome 9 of maize explains mottled kernels Some definitions and figures from Lisch 2009: Annu. Rev. Plant Biol. 2009.60:43-66.

What are Transposons? Transposable element (transposon): a sequence of DNA that is competent to move from place to place within a genome (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. Learn more at: weedtowonder.org/jumpingGenes.html

What are Transposons? “Cut & Paste” “Copy & Paste” Transposable element (transposon): a sequence of DNA that is competent to move from place to place within a genome “Cut & Paste” “Copy & Paste”

Nonautonomous elements What are Transposons? 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) Autonomous element Gene(s) Nonautonomous elements

Transposons make up the major content of eukaryotic genomes 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

Variation in cereal genomes - transposons & genome duplications What are Transposons? Variation in cereal genomes - transposons & genome duplications Rice 450 Mb Sorghum 700 Mb Maize 2,500 Mb Barley 5,000 Mb Wheat 20,000 Mb Oats ~20,000 Mb

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

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

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)

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

Genic distribution of mPing insertions 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)