1. Xuhua Xia xxia@uottawa.ca http://dambe.bio.uottawa.ca
Transposition
Xuhua Xia

2. Causes of genomic evolution
Variation in genome size and gene content
sequence duplication (genome, segmental, gene)
horizontal gene transfer
transposition (Barbara McClintock)
Genomic mutation
replication fidelity
DNA repair
strand bias
DNA modification
functional constraints

3. Barbara McClintock and the jumping genes
Double fertilization in plants
aleurone layer
The color of seeds we see is that of endosperm (triploid: one sperm and two polar nuclei) surrounding the embryo
Somatic mutations pigment genes in endosperm cells result in changes in color
Color more variegated under stress
Pray and Zhaurova 2008 Nature Education 1:169

4. CCbzbz-- C'C'BzBzDsDs C'CCBzbzbzDs--
Table 1: Maize Genes Studied by Barbara McClintock
Gene
Description C'
Dominant allele on the short arm of chromosome 9 that prevents color from being expressed in the aleurone layer of the maize kernel, causing a so-called "colorless" phenotype (which is actually white or yellow in color). This is also known as the inhibitor allele. C
Recessive allele on the short arm of chromosome 9 that leads to color development. Bz
Dominant allele on the short arm of chromosome 9 that leads to a purple phenotype. bz
Recessive allele on the short arm of chromosome 9 that leads to a dark brown phenotype. Ds
Genetic location on the short arm of chromosome 9 at which chromosomal breakage occurs. Ac
A factor of unknown location (at least when McClintock was conducting her research) that impacts the expression of Ds.
CCbzbz--
C'C'BzBzDsDs
C'CCBzbzbzDs--
Mostly colorless, but some have dark brown or purple spots
Inferences:
C'??Ds genotype has colors: C' is disabled by Ds
CCCBzbzbzDs is dark brown instead of purple: Bz disabled by Ds, allowing bz to express
The genotype regains purple: Ds has moved away from Ds
Ds effect depends on Ac, both defying mapping: they are jumping genes, and Ds needs As to jump
Further observations:
CCCBzbzbzDs-- may be dark brown instead of purple
The genotype above may regain the purple color
Ds effect depends on Ac, both defying mapping
Pray and Zhaurova 2008 Nature Education 1:169

5. Activator (Ac) and Dissociation (Ds) gene structure
The 4.6-kb autonomous Ac element makes a single 3.8-kb transcript encoding an 807-AA transposase
Ds elements can capture fragments of other genes, and transpose new exon combinations to other parts of the genome
They can be used to create mutants
They are not good genetic markers
Du et al BMC Genomics. 12: 588.

6. In plants: “The ups and downs of genome size evolution” due to transposable elements, DNA segment duplications…
Haploid genome size (Mbp)
% repetitive elements
Arabidopsis ~ ~ 15%
rice ~420 ~ 35%
wheat ~ ~ 80%
rye ~ ~ 90%
South side (hot & dry)
~ 22,000 copies BARE-1 (TE) in barley
North side ~ 8000 BARE-1 copies
Within grasses,
> 30-fold range in genome size
“Evolution canyon”, Israel
Environmental stress conditions (hot & dry) trigger retrotransposon copy number increase in barley
Kellogg & Bennetzen Am J Bot 91:1709, 2004
Kalendar PNAS 97: 6603 (2000)

7. Contribution of repetitive sequences to genome expansion
Composition of human genome
Repeated sequences comprise about half the human genome !!
Transposable elements - “selfish DNA”
Microsatellites
This categorization is not correct because transposable elements often contain protein-coding genes.
Protein-coding sequences
NB: Gene = exons + introns
“Unique” likely also includes very degenerate (unrecognizable) transposable elements
Long introns & short exons in human genes
De Koning PLoS Genet 7:e , 2011
Gregory Nature Rev. Genet. 6:699, 2005 & textbooks

8. Classification of transposons
DNA transposons
cut-and-paste DNA transposons (e.g., Ac)
rolling-circle DNA transposons (Helitrons)
self-synthesizing DNA transposons (Polintons)
Retrotransposons
long terminal repeat (LTR) retrotransposons: Ty1-copia, Ty3-gypsy, BEL-Pao-like and DIRS; ERV1, ERV2 and ERV3 (of endogenous retroviruses)
non-LTR retrotransposons:
LINEs (Long INterspersed Elements): with genes encoding all functions for transposition (autonomous retroelements)
SINEs (Short INterspersed Elements): nonautonomous retroelements
Polinton: DNA polymerase and a retroviral-like integrase
Wicker et al Nature Reviews Genetics 8:973–982
Kapitonov & Jurka Nature Reviews Genetics 9:411–412 (used here)

9. DNA-mediated transposition
element encodes transposase enzyme enabling integration into host genome
Conservative
Replicative
element flanked by direct repeats
increase in copy number
Fig. 7.1
Most DNA transposons are conservative

10. Some "conservative" transposition may not be conservativeG1 G2 G3
Species 1
Missing link G1 G2 G3 G1 G2 G3
Species 2

11. Generation of direct repeat
GAC
CTG
GAC
CTG
GAC
GAC
CTG
CTG
Transposon DNA

12. RNA-mediated transposition
- mobile retroelement encodes reverse transcriptase
Fig. 7.1
RNA intermediate
MIR: Mammalian-wide interspersed repeat.
Retrotransposons are always replicative.

13. LINE transposition

14. SINES, LINES: (Short & Long INterspersed Elements)
SINEs use the machinery of LINES for their propagation and can have impact on human gene structure/expression
- eg. can be recruited as exons (“Alu-exonization”)
in human genome, Alu repeats (~282 nt) have > 1,000,000 copies dispersed in genome. It is derived from 7SL RNA gene which is ancient (present in invertebrate and even bacterial lineages), but Alu is primate-specific.
tRNA-derived Mammalian-wide interspersed repeat (MIR), ~260 nt, ~400,000 copies in human genome
MIR: Mammalian-wide interspersed repeat.
Nature. 1984 Nov 8-14;312(5990):171-2.
Alu sequences are processed 7SL RNA genes.
Ullu E, Tschudi C.
Abstract
7SL RNA is an abundant cytoplasmic RNA which functions in protein secretion as a component of the signal recognition particle. Alu sequences are the most abundant family of human and rodent middle repetitive DNA sequences (reviewed in ref. 2). The primary structure of human 7SL RNA consists of an Alu sequence interrupted by a 155-base pair (bp) sequence that is unique to 7SL RNA. In order to obtain information about the evolution of the Alu domain of 7SL RNA, we have determined the nucleotide sequence of a cDNA copy of Xenopus laevis 7SL RNA and of the 7SL RNA gene of Drosophila melanogaster. We find that the Xenopus sequence is 87% homologous with its human counterpart and the Drosophila 7SL RNA is 64% homologous to both the human and amphibian molecules. Despite the evolutionary distance between the species, significant blocks of homology to both the Alu and 7SL-specific portions of mammalian 7SL RNA can be found in the insect sequence. These results clearly demonstrate that the Alu sequence in 7SL RNA appeared in evolution before the mammalian radiation. We suggest that mammalian Alu sequences were derived from 7SL RNA (or DNA) by a deletion of the central 7SL-specific sequence, and are therefore processed 7SL RNA genes.
The subfamily active in humans is represented by a typical 282 bp Alu element. Alu is a dimmer composed from two nearly identical monomers (light and intermediate grey). The left monomer has a deletion of the dark grey box. The monomer is derived from 7SL RNA gene, coding for the RNA subunit of SRP (signal recognition particle). SRP is a complex recognising signal peptide of the Sproteins that are to be transported into endoplasmic reticulum lumen or membrane. Note that the 7SL gene is drawn in 50% scale! PolyA region of Alu is not part of the 7SL gene, but is important for success of Alu in retrotransposition. 
Figure 3. Presentation of the 5' end of the putative MIR transcript in a tRNA secondary structure. Imperfect stem symmetries are also predicted in other tRNA-derived SINE transcripts (4-6). The only inconsistency with a tRNA structure is the presence of six instead of seven residues in the anticodon loop.

15. Because transposons are not under functional constraint, they accumulate inactivating mutations over time
Tasmanian devil
“Old” TEs
“Young” TEs
Very few DNA transposons in animal genomes
Intact, functional TE
Can calculate divergence from an intact transposon sequence
“Repeat landscape of the Tasmanian devil genome showing expansion and decline of transposable elements.”
Gallus Mol Biol Evol. 32:1268, 2015