Using DNA Subway in the Classroom Yellow Line

Using DNA Subway in the Classroom Yellow Line

Using DNA Subway in the Classroom Yellow Line - Transposons The Dynamic Genome Transposons What are Transposons? Transposable element (transposon, TE): DNA sequence competent to insert into new places 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? Transposable element (transposon, TE): DNA sequence competent to insert into new places (Ac/Ds) Cut & Paste (Alu) Copy & Paste 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 Gen element e(s) Nonautonomous elements 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

What are Transposons? Effect of transposons & genome duplications on genomes Sorghum 700 Mb Rice 450 Mb Barley 5,000 Mb Wheat 20,000 Mb Maize 2,500 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. 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 mPing copy number in O. japonica mPing copy number

OVER 1000 mPing copies mPing Japonica strains Over 1000 copies of mPing in 4 related strains. 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

12 shared (n=926) 10 unshared (n=736) (%)

8 expect. 6 4 2 0 5'UTR UTR

exon Exon intron 3'UTR UTR mPing insertions rare in coding-exons TEs can alter gene expression Os02g0135500 (-41)

2.5 NB EG4 (mPing+) A123 (mPing+) A157 2 1.5 1 0.5

0 control cold salt dry 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

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