Transposable Elements And Transposition integration of small DNA segments into chromosomes Can occur at many locations within genome transposable elements (TEs) “jumping genes” DNA segments that move 1st identified by Barbara McClintock in corn

McClintock Discovers Moving Loci in Corn Babara McClintock identified many unusual features of corn chromosomes in one strain of corn, chromosome 9 tended to break at a high rate at the same site termed this a mutable locus Mutable sites are locations where transposable elements have been inserted into the chromosomes She received Nobel Prize in 1983

Transposition Pathways 3 general types of transposition Simple transposition Replicative transposition Retrotransposition Class I Retrotransposons Class II DNA transposons

Simple Transposition Prokaryotic eukaryotic Insertion Sequences (IS# ) - only contains transposase gene Transposons (Tn#) - contain additional genes between 2 IS eukaryotic Ac/Ds

Regulatory Sequences of Transposable Elements Simple Transposons Direct repeats – Identical DNA sequences that are and run in the same direction (5’3’) Originate from bacterial chromosome at insertion site Inverted repeats - DNA sequences that are identical (or very similar) but run in opposite directions 5’ ATGACTGAC 3’ 3’ TACTGACTG 5’ 5’ ATGACTGAC 3’ 3’ TACTGACTG 5’ and 5’ CTGACTCTT 3’ 3’ GACTGAGAA 5’ 5’ AAGAGTCAG 3’ 3’ TTCTCAGTC 5’ and

Bacterial Insertion Sequence 9bp direct repeat 9bp direct repeat N1N2N3N4N5N6N7N8N9 N1N2N3N4N5N6N7N8N9 Figure 13.23 6

Bacterial Transposon Figure 13.25B 7

Simple & Replicative Transposons Both contain a gene encoding a transposase enzyme Transposase function recognizes direct and indirect repeats cuts DNA for both excision and insertion

Replicative Transposition Involves replication of the TE and insertion of the copy into another chromosomal location Only found in bacteria

Retrotranposons & Retrotransposition Very common but only occur in eukaryotes also known as retroelements Similar organization to retroviruses

Composite Transposons Contain additional genes that are not necessary for transposition per se Only the inverted repeats at the ends of the transposon are involved in the transposition event Only these are adjacent to direct repeats

Elements of Replicative Transposons Organization is similar to insertion sequences Resolvase gene is found between the inverted repeats Both enzymes are needed to catalyze the transposition of these types of elements

Transposase Catalyzes Excision & Insertion The enzyme transposase catalyzes the removal of a TE and the its reinsertion at another location Transposase recognize the inverted repeats at the ends of a TE and bring them closer together

Cut & Paste Transposition by Transposase

Retrotransposons – Retroviral-Like Elements Evolutionarily related to known retroviruses Retroviruses - RNA viruses that make a DNA copy that integrates into the host’s genome LTR – long terminal repeat act as promoters to transcribe viral genes RT – reverse transcriptase (pol) uses RNA as a template to synthesize a cDNA (complementary DNA) Int – integrase recognizes DR sequences, cuts host DNA and inserts retroelement sequences There is no excision of retroelements or retroviruses There are ~850,000 copies of LINE retroelements in humans Virtually all have lost function of RT and/or Int genes

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Non-viral Retroelements Share little sequence similarity with retroviruses derived from normal eukaryotic genes some have RT or RT-like gene, many such genes are not functional Alu family of non-viral retroelements derived from a single ancestral gene known as the 7SL RNA gene has been copied by retroposition to > 500,000 copies ~ 6% of the human genome An example of a SINE – short interspersed element

Describing Function of Transposable Elements Autonomous contain all the information necessary for transposition to occur functional transposase, RT, Int etc… DNA elements – DRs, IRs, LTR, etc… Nonautonomous lack a gene or sequence element necessary for transposition If element is missing – transposon will not transpose if Transposase is mutated, element can still transpose if enzyme from another transposon “helps” it McClintock’s Ds element is nonautonomous lacks transposase gene McClintock’s Ac locus (Activator) is autonomous has functional transposase enzyme If Ds and Ac are both present in genome, transposition of Ds can occur

Transposable Elements Influence Mutation & Evolution Over the past few decades, researchers have found that transposable elements occur in the genomes of all species 17-74 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Repetitive Sequences on Chrom 22

Telomere probe Centromere probe Alu repeat probe rDNA probe

In some cases, repetitive sequences in eukaryotic genomes are due to the proliferation of TEs In mammals, for example LINEs Long interspersed elements Usually 1,000 to 5,000 bp long Found in 20,000 to 100,000 copies per genome SINEs Short interspersed elements Less than 500 bp in length Example: Alu sequence Present in 500,000 to 1,000,000 copies in the human genome

There are two schools of thought biological significance of transposons in evolution remains a matter of debate There are two schools of thought 1. TEs exist because they simply can In other words they are like parasites They can proliferate within the host as long as they do not harm the host to the extent that they significantly disrupt survival This has been termed the selfish DNA theory 2. TEs exist because they offer some advantage Bacterial TEs carry antibiotic-resistance genes TEs may cause greater genetic variability through recombination TEs may cause the insertion of exons into the coding sequences of structural genes This phenomenon, called exon shuffling, may lead to the evolution of genes with more diverse functions

Transposable elements can rapidly enter the genome of an organism and proliferate quickly Drosophila melanogaster A TE known as the P element was introduced into the species in the 1950s Remarkably, in the last 50 years, the P element has expanded throughout D. melanogaster populations worldwide The only strains without the P element are lab stocks collected prior to 1950 Transposable elements have a variety of effects on chromosome structure and gene expression

Transposons Have Become Important Tools in Biology The features of transposons have made them an important experimental tool in molecular biology 1. The introduction of transposons into a cell is a convenient way to abolish the expression of a gene 2. It can be used to clone a particular gene in an approach known as transposon tagging

An early example of transposon tagging involved an X-linked gene in Drosophila that affects eye color Wild-type = red ; Mutant = white In 1981, Paul Bingham, Robert Levis and Gerald Rubin use transposon tagging to clone this gene They started with a wild-type population of Drosophila that carried a transposon called copia From this red-eyed strain, a white-eyed strain was obtained The copia element transposed into the X-linked eye color gene, thereby inactivating it