A brief introduction and explanation of plant transposable elements with some article reference for a better understanding of plant genetics

1. PLANT TRANSPOSABLE ELEMENTS-
WHERE GENETICS MEETS
GENOMICS
Chairman
Dr. B.SELVI
Professor,
Department of
Millets,
CPBG,TNAU.
Members
Dr. D. KAVITHAMANI
Assistant Professor,
Department of
Millets,
CPBG,TNAU.
Dr. N.VADIVEL,
Assistant Professor,
Department of
Agronomy,
TNAU.
Student:
S.SUBHASHINI
2017600818
II M.Sc (Ag) GPB

2. • INTRODUCTION
Maize kernel study
• CLASSIFICATION
• CLASS I-CASE STUDY
• CLASS II-CASE STUDY
• EPIGENETIC SILENCING OF TRANSPOSABLE ELEMENTS
• FUTURE DIRECTIONS
• CONCLUSION

3. Transposable
elements (TEs)
Segments of
DNA
Make
duplicate
copies
“Jumping
genes"
Increase (or
decrease) the
amount of DNA
in the genome
of the cell
Cause
mutations
Move
around to
different
positions in
the genome

4. TRANSPOSABLE ELEMENTS
• Maize geneticist Barbara
McClintock discovered TEs in
the 1940s
• McClintock, the first
researcher to suggest that
these genes are turned on
when activation takes place
(McClintock, 1965).

5. TEs play role in
• regulating gene expression
• generating different cell,
based on where in the
genome they insert
themselves (Britten &
Davidson, 1969)

6. JUNKS ARE NOT JUNKS
• Scientists dismissed transposons as useless or "junk"
DNA
• The early speculations of both McClintock and Britten
and Davidson were largely dismissed by the scientific
community
• Only recently have biologists begun to entertain the
possibility that this so-called "junk" DNA might not be
junk after all

7. Maize by Barbara
McClintock
Drosophila, yeast ,
E. coli
C.elegans
Nobel
Prize
in
1983
Humans

8. Using kernel phenotypes to study
Transposon behaviour
TE-induced genes in the anthocyanin
(pigment) biosynthetic pathway give rise to
distinct patterns with respect to the
• Size
• Frequency
• Intensity of sectors

9. • Insertions in promoters or other regulatory
sequences can alter tissue-specific patterns
of expression
• Regulatory regions sustain insertions of
transposon footprints as introns
TE now becomes
introns here

10. • Interplay between a Transposable Element (TE) and a
gene that encodes an enzyme in the anthocyanin
(pigment) biosynthetic pathway
( Macmillan Magazines Ltd.,2002)

11. MAIZE TE FAMILY
Dissociation (Ds) Activator (Ac)
Only in the presence of
Ac
Promote its own
transposition
Non-autonomous (Ds)
elements able to
transpose have no
significant coding
capacity
Autonomous (Ac) have
open reading frames
(ORF)that encode the
products required for
transposition

12. TE
CLASS 2
MITES
CLASS 1
NON-LTR
LINEs-L1
SINEs-Alu
LTR
(Miniature Inverted-Repeat
Transposable Elements)
(Long Terminal Repeat
Retrotransposons)

13. Class 1( Retrotransposons )
• DNA RNA
• Copied DNA is then inserted at a new position
into the genome.
• The reverse transcription step is catalyzed by a
reverse transcriptase, which is often encoded
by the TE itself.
Eg: Retroviruses-HIV
Transcription
Reverse Transcription

14. Retrotransposons

15. Class 1-LTR(Long Terminal Repeats)
• LTR retrotransposons in direct
orientation
• Autonomous elements
contain
1. gag gene (encode capsid-like
protein)
2.pol gene(encodes a reverse
transcriptase)

16. Class 1-LTRs
• LTR retro-transposons were first discovered in
plants as source of both spontaneous and
induced mutations in Maize and Tobacco

17. DNA mRNA
(Reverse transcriptase)
Insertion of copied DNA
If substitution /year is
known,then
sequence divergence
between the LTRs
provides an estimate
of when insertion
occurred
‘smoking guns’
of
transposition
(Millions of years)

18. Transcriptional activation of LTR
Retrotransposons
• Transpose under conditions
of biotic and abiotic stress
• The first active plant
retrotransposon, Tnt1, was
isolated from Tobacco by
wounding, oxidative stress,
pathogen infection and
microbial elicitors

19. Article
www.plantphysiol.org on March 8, 2015 - Published by
www.plant.org 213
Copyright © 2001 American Society of Plant Biologists.

20. Induction by the
binding of a
transcriptional
activator to a cis-motif
(yellow box)
Some Tnt1-encoded
mRNAs are converted
into cDNAs that
integrate into the
Tobacco genome. cDNA

21. Digestion of restriction enzyme (EcoRI)

22. CLASS 1-NON-LTR
LINEs (Long INterspersed
Elements)
SINEs (Short INterspersed
Elements)
6,500 base pairs in length 100–400 base pairs in length
Over 5 lakh copies Over one million copies in the
human genome
The human genome 19% of
LINEs
Representing 9% of our total
DNA
50 L1 elements are functional
genes
The most abundant SINEs are
the Alu elements

23. https://www.nature.com/articles/nrg793

24. Class 2 Transposons(1000-40,000 bp)
• “cut and paste” mechanism
• Transposase
• Endonucleases,Ligases
1.cleave transposan from its initial
location in the genome
2.cleaves target sites where the
element is to be inserted
Once the transposon is
ligated (bound) into its new
position, gaps are filled through
the synthesis of nucleotides.

25. ARTICLE

26. Transposase
• DDE motif(Aspartate-97, Aspartate-188, and
Glutamate-326) catalyzes the movement of the
transposon
• Mn,Mg-catalytic reaction
Transposase highly inactive
DDE region is mutated
Transposase becomes hyperactive
Catalyzes the movement of the transposon

27. UNCERTAINITY
• In in vitro- SDS heat treatment denatures the
transposase
• However, it is still uncertain what happens to
the transposase in vivo

28. ARTICLE

29. CLASS 2
• P elements first
appeared in
Drosophila about
50 years ago
• They get activated
in germline cells
• THAP9 genes -
active P element
“transposase”
proteins.

30. Miniature Inverted-repeat
Transposable Elements (MITEs)
•Short lengths, (400 to 600 base pairs)
•Present in Oryza sativa,Caenorhabditis elegans,
miRNAs which play a role in RNA interference
are derived from MITEs
https://www.nature.com/articles/nrg793

31. • Have Terminal inverted-
repeat (black triangles)
mirror sequences -15bp
duplications of conserved
length in super-families
• Non-autonomous family
members are usually
derived from an
autonomous family
member by internal
deletion.

32. Numerous related, but distinct, Autonomous elements
only share sequence similarity in their terminal inverted repeats (TIRs; black triangles)
Transposase
Same transposase (‘trans’)
By a close relative (‘cross-mobilization’)

33. MITEs Approaches
• ‘Top-down’ connects an
active source of
transposase to a MITE
family.
• ‘Bottom-up’ uses the
MITE sequence to
identify the partner
transposase

34. MITE insertion are homologous genes that
originated through
• Orthologous gene(speciation)
• Paralogous genes(duplication)
• MITEs are important factor in creating
structural allelic diversity
• One challenge for the future will be to
determine how MITE insertions has altered
gene expression or gene products

35. https://www.nature.com/articles/nrg793

36. Epigenetic silencing of Transposable
elements
• TGS seems to be the principal pathway to
silence plant TEs
• PTGS has been well documented in plants,
most notably as a defence against viral
replication

37. •CMT3,
Chromomethylase 3
•DDM1, Decreased DNA
Methylation 1
•LTR, Long Terminal Repeat
•MET1, Methyltransferase 1
•MOM1, Morpheus’ molecule
•Spn-E, Spindle E

38. ARTICLE
www.nature.com/reviews/genetics
2007 Nature Publishing Group

39. TEs have served as building blocks for epigenetic
phenomena
PTGS(Post Transcriptional Gene Silencing)

40. (Histone H3 lysine 9)
TGS-
Transcriptional
Gene Silencing
RNA-directed
Methylation

41. In Morning glory flowers, DNA methylation of a non-
autonomous MuLE transposon can spread to the
promoter of a flower-colour gene (Dfr-B), creating
petal-colour streaks
In Maize –activity of one TE family MuT transposan
generating single sectors of pale green (hcf106 mutant)

42. Future directions:
waking the sleeping
giant
• TEs were first discovered and studied as the
causative agents of genetically unstable
mutations in Maize
• Activated quiescent Elements-breakage–
fusion–bridge Cycle

43. Isolated mutagenized plants or strains
undergoing the BREAKAGE–FUSION–BRIDGE
CYCLE

45. CONCLUSION
• Modern assays to detect new TE insertions that are
still able to transpose and re-structure plant genomes
• Computer-assisted analysis to design family-specific
primers for analysis of TE expression
• In this way, it should be possible to isolate active TEs
from a variety of plant species
Knowledge of these elements facilitate studies of the
continuing co-evolution of TEs with their hosts.

46. Insertional mutagenesis
Signature-tagging mutagenesis(STM)
Tagged transposons- insertion(bacterium)
Randomly integration-host genome
Host’s altered phenotype
Tagged transposons identified by genome
sequencing
Locus expressing the phenotypes

47. Sleeping Beauty Transposon
• Genetic researchers
Zsuzsanna Izsvák
discovered a fish
transposon sequence,
dormant for 15 million
years
• Described in 1997-
artificially reactivated into
a functioning transposon
for inserting foreign genes
- experimented in 2010.

48. REFERENCES
• Steimer, A. et al. Endogenous targets of
transcriptional gene silencing in Arabidopsis. Plant
Cell 12, 1165–1178(2000).
• http://depa.fquim.unam.mx/amyd/archivero/Articul
o1_24946.pdf
• https://www.nature.com/articles/nrg793

49. THANK YOU