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Jackson Crouse
Dr. Ely
Biology 303: Fundamental Genetics
1 November 2013
Transposable Elements: The Next Great Genetic Tool
In the vastly changing world of genetics, scientists continue to look for ways to make
their own marks in their respective fields. Many geneticists concern themselves with solving
various cancers, curing pesky diseases, and modifying the human genotype. So perhaps it is
preposterous to think that one of the most useful tools in genetics rested in the DNA of mere
soybeans and rice. These crops are staples in the world’s food supply, and have been proven to
contain heritable insertions of transposable elements. Transposable elements, or “jumping genes”
are DNA fragments that have the ability to move from one chromosomal location to another
(Yasuda, et al. 2013). With the ability to jump from one spot on a chromosome to another, TEs
present geneticists with endless possibilities for modification. The graphic below illustrates the
jumping action of TEs (Board Institute, 2013).
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Recently researched TEs are present in the Gimbozu rice genome, Drosophila melanogaster, or
in mutated soybeans, and were used as genetic tools for inserting DNA segments into desirable
chromosomal locations. The natural occurrence of these elements, coupled with their ability to
serve as genetic tools, “insert” transposable elements into the forefront of genetic sciences.
Though various research seems to possess the same message regarding the existence of
transposable elements, the same research states many varying roles for TEs. Transposable
elements are involved in the formation of novel gene structures as well as genome reconstructing
(Petrov, et al. 2010). Other sources say that these elements are responsible for the regulation of
neighboring genes, due to their “jumping” capabilities (Yasuda, et al. 2013). In addition to these
functions, TEs are also known to produce heritable mutations in the genes that they affect
(Hancock, et al. 2011). Only through experimentation are scientists able to examine these
functions and assess the true genetic value of which TEs provide.
Going in chronological order, in 2010, scientists from Stanford University wished to
explore the population dynamics of TE families in the Drosophila melanogaster species. These
researchers believed that understanding the role of TEs in population genomics was critical in
understanding the eukaryotic evolution and function of the entire species. They studied the
population genomics of 755 euchromatic TEs from 55 families in order to determine if any
difference in order, level, length, or strength of the TEs would be evident (Petrov, et al. 2010).
Using a pooled Polymerase Chain Reaction (PCR) to estimate population frequencies of the TEs,
researchers found that of the 755 TEs, frequencies were as follows: 114 fixed, 72 common, 159
rare, and 410 very rare (Petrov, et al. 2010). Petrov goes on to say that, overall, TEs of D.
melanogaster appear deleterious and will disrupt the function of the gene, exerting local
deleterious effects (2010).
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Genomic
compartments
CDS
Amount of DNA
Very Rare
Rare
Common
Fixed
19%
22.46
0%
0
0%
0
0%
0
0%
0
Intron
41%
49.12
48%
196
43%
68
44%
32
37%
42
Intergenic
38%
45.08
52%
212
57%
91
56%
40
61%
70
The above results, alone, do not mean much, but researchers then went on to test why this
mass deletion had occurred, by separating the TEs into three categories: 1) TEs inside proteincoding regions (CDS), 2) TEs within introns, and 3) TEs in intergenic regions. The following
table displays the results of TE location within the study, demonstrating where, and at what
frequencies, TEs are present in the D. melanogaster species. It can also be said that TE
frequency is due to varying strength of purifying selections acting on TEs, in part because
recombination within the same family may cause a lethal chromosomal rearrangement (Petrov, et
al. 2010). Petrov et al. found that TE insertions into the CDS regions were almost universally
strongly deleterious since they were not detected (2010). This detail is not vastly important, but it
does show that researchers are able to use PCR analysis to test for the presence of transposable
elements.
Researchers in the Drosophila melanogaster experiment focused largely on population
genomics, whereas a different group of scientists focused specifically on an individual
transposable element, mPing, and its effect on a specific species. To test for the effectiveness of
mPing as a mutagenesis tool; that is, the effect created by a mutated insertion of the TE, Hancock
and his team used PCR based on primers that flank the mPing to detect transposition (2011).
Two samples, each from different stages of somatic embryo development, were taken and tested
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for mPing excision (Hancock, et al. 2011). The two stages of soybean that were used can be seen
in the picture below.
Seven out of ten globular stage lines had mPing in the original position. In the other three
lines mPing had excised from its original position (Hancock, et al. 2011). In the cotyledonary
stage, however, eight of the ten lines had excised from their original position, which indicates a
higher frequency for mPing excision later on in embryonic development (Hancock, et al. 2011).
They determined that transposition of mPing occurred over at least two generations of
plants, under normal growth conditions, suggesting that the best way to use transposable
elements in this case was to grow plants with high mPing activity to saturate the genome with the
mPing insertions (Hancock, et al. 2011). This idea of saturating a genome with TEs has been
present in rice for several years prior to Hancock’s research, yet this experiment was the first to
detect heritable insertions in a species other than rice (Hancock, et al. 2011). Since transposition
occurred at different developmental stages of the soybeans, Hancock hinted that understanding
these regulations may be the best way to control transposition (2011).
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The objective of the above experiment was to determine whether TE insertions, of
mPing, could be used to regulate the soybean genome expression. The study concluded with
several key points that relate to modern views of transposable elements in general:
1) mPing produced heritable insertions in soybeans over multiple generations (Hancock, et
al. 2011).
2) Since mPing is heritable, it retains the transposition characteristics that are favorable for
TE tagging (Hancock, et al. 2011).
3) mPing and other transposable elements with similar characteristics will facilitate gene
identification in soybean, or other related crops (Hancock, et al. 2011).
These observations regarding specific TE insertions, coupled with the factors affecting TE
insertion, have established TEs as realistic genetic tools. While the primary function of TEs
might be a regulatory one, further experimentation is needed to verify this (Pray, 2008). As
previously alluded to, TEs have been prominent features in certain rice DNA, and in May of
2013, a team of researchers out of Kyoto University in Japan wished to examine the alteration of
gene expression under different physical conditions, such as stress.
In the Kyoto research, the transposable element mPing was used in a study of a Gimbuzo
rice species, since mPing has an exceptionally active transposition frequency (Yasuda, et al.
2013). Additionally, previous research (Naito, et al. 2009) had suggested that the stress response
through gene expression could be analyzed under stressful conditions given to the rice crop. If
the insertion of this particular TE would affect the stress response, for example, researchers
would be able to say that they had modified the expression of a target gene (Yasuda, et al. 2013).
Yasuda et al. chose to work with 11,520 Gimbozu plants grown in Kyoto University
fields to establish both a DNA and a seed pool (2013). Eight-plant bulked samples were used,
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and after centrifugation and an ethanol washing, 1440 DNA pools and their corresponding 1400
seed pools were established (Yasuda, et al. 2013). Following this, a PCR treatment was
administered in hopes of amplifying all target regions within each gene, with the concluding step
of the PCR technique involving basic gel electrophoresis. Furthermore, stress treatments had to
be administered to the DNA and seed pools. Seeds were placed in dark environments, cold
environments, (4˚C) and salt conditions (medium containing 250 mM NaCl). The last step taken
to enact stress conditions was that of a real-time PCR. Denaturation of the samples, as well as
annealing (a heat treatment that alters the microstructure of material, causing changes in
properties) allowed researchers to analyze the expression of the target genes. These results were
then compared to the control lines of seeds.
Yasuda et al. looked first at mutation screening of stress tolerance genes with the
Gimbozu population. They found that mPing-inserted promoters were found in six different
genes, with two of the promoters being found in two different bulked-DNA samples (2013). This
led to the conclusion that a “hotspot” had been identified, due to the independent nature of each
insertion event (Yasuda, et al. 2013).
Next, mPing’s effect on the stress response in neighboring gene expression was
examined. Using four of the genes in which TE promoters were found, Yasuda et al. found that
the stress tolerance of plants in salt conditions was strengthened in the ZFP252 gene (2013). To
contrast this, Yasuda also observed that stress conditions of mfDREB+ and mrDREB+ were not
affected by the mPing insertions, regardless of the mPing orientation (2013). The remainder of
the results can be found in the graphs below:
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In the above graph, the expression levels of target genes were exhibited as relative values
to those in the control condition. In chart C, the relative mRNA levels in the salt condition are
much higher than those of the control or cold condition, indicating a stronger expression of the
ZFP252 gene during salt stress. Charts A and B show a high amount of mRNA in the cold
conditions, indicating increased expression of the mfDREB and mrDREB genes during cold
stress.
The larger point behind all of this is that the use of these inducible mPing promoters has
the potential to improve plant growth by increasing their stress tolerance (Yasuda, et al. 2013).
Most importantly, this can/will occur through natural mutation, and therefore will not be subject
to any restrictions that apply to GMOs (Yasuda, et al. 2013). Lastly, on a global scale, the
resistance to stress conditions in a rice species will eventually help to eliminate certain problems
within the world food supply, seeing as the promotion of transposable elements will allow plants
to grow in unfavorable conditions.
Overall, several experiments have revealed numerous truths about transposable elements,
most notably in the past three years or so. On a very basic level, it is determined that TE
efficiency can be affected by such factors as length of the TE, recombination frequency of the
gene, or even copy number of the TE (Petrov, et al. 2010). Additionally, TEs could produce
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tagged insertions of heritable DNA across multiple generations (Hancock, et al. 2011). And to
bring everything together, the Kyoto research team with Yasuda found that different stress levels
could be modified to increase a rice crop’s tolerance to extreme cold or extreme salt conditions
(2013). As TEs continue to naturally impose themselves within neighboring genes, a regulatory
pattern can be seen (Broad Institute, 2013). Once a pattern is detected, modification involving
the promotion of TEs into favorable genomic locations can occur shortly thereafter. As with
everything in modern science, transposable elements must first be understood before they can be
acted upon. The Drosophila, the soybean, and the rice experiments all contributed to the
understanding of individual TEs. As society steps further into the 21st century, it is essential for
humans to understand a deeper biological function for the elements that can have such a huge
influence on the genome (Pray, 2008). Nature has made the first move. Now, it is our move.
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Literature Cited
Broad Institute. "Transposon." Broad Institute of MIT and Harvard. N.p., 2013. Web. 01 Nov.
2013.
Available from: http://www.broadinstitute.org/education/glossary/transposable-elements
Hancock NC, Zhang F, Floyd K, Richardson AO, LaFayette P, Tucker D, Wessler SR, Parrott
WA. The Rice Miniature Inverted Repeat Transposable Element mPing Is an Effective
Insertional Mutagen in Soybean. Plant Physiology. Volume 157. pp 552-562. August
2011.
Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192579/pdf/552.pdf
Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka
T, Wessler SR (2009)Unexpected consequences of a sudden and massive transposon
amplification on rice gene expression. Nature 461:1130–1134
Petrov DA, Fiston-Lavier AS, Lipatov M, Lenkov K, Gonzalez J. Population Genomics of
Transposable Elements in Drosophila melanogaster. Stanford University. Mol. Bio. Evol.
Volume 28. Issue 5. pp 1633-1644. Decmeber 2010.
Available from: http://petrov.stanford.edu/pdfs/76.pdf
Pray, Leslie. Transposons, or Jumping Genes: Not Junk DNA?. Nature Education. Volume 1
2008.
Available from: http://www.nature.com/scitable/topicpage/transposons-or-jumpinggenes-not-junk-dna-1211
Tompkins, Jeffrey. Transposable Elements Are Key to Genome Regulation. Institute for Creation
Research. Published Online. March 2013.
Available from: http://www.icr.org/article/7388/
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Yasuda K, Ito M, Sugita T, Tsukiyama T, Saito H, Naito K, Teraishi M, Tanisaka T, Okumoto
Y. Utilization of transposable element mPing as a novel genetic tool for modification of
the stress response in rice. Molecular Breeding. Volume 32. Issue 3. Pp 505-516. 2013.
Available from: http://link.springer.com/article/10.1007%2Fs11032-013-9885-1#page-1