Transposable Elements TEs Jumping genes Sequences of DNA that jump from one genome location to another Discovered in 1940s by maize geneticist Barbara McClintock Initially dismissed as junk DNA ID: 810575
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Slide1
Transposable Elements
Presented by Anne Sternberger, Yingnan Zhang & Yuxi Zhou
Slide2Transposable Elements (TEs)
“Jumping genes”Sequences of DNA that “jump” from one genome location to another
Discovered in 1940s by maize geneticist Barbara McClintock
Initially dismissed as “junk DNA”Functional roles that can be both beneficial and pathological
Barbara McClintock, the “
illuminator of transposons”
From Hosaka and Kakutani, Curr Opin Genetics Dev. 49, 43-48 (2018).
Slide3Transposable Elements (transposons, TE)
Found in almost all organisms (prokaryotes and eukaryotes) and typically in large numbers.
E.g. comprise ~50% of human genome and ~90% of maize genome
Two classes of TEsClass 1 TEs: Retrotransposons
Class 2 TEs: DNA transposons
Retrotransposons transpose via
RNA intermediate
Transposons transpose via DNA intermediate (cut-and-paste)
From Hosaka and Kakutani, Curr Opin Genetics Dev. 49, 43-48 (2018).
Slide4Transposable elements have common characteristics
Flanking repeats on each points of insertion into target DNA
DNA transposons (Class 2 TEs) have inverted terminal repeats (ITRs)
Slide5Transposons vs. Retrotransposons
From Fedoroff et al., Science. 338, 758-767 (2012).
Transposons (Class 2 TEs)
DNA intermediate (cut-and-paste mechanism)
Retrotransposons (Class 1 TEs)
RNA intermediate
Excise → move to another location
Duplicate → integrate into new site
Slide6DNA Transposons and Retrotransposons in Eukaryotes
Transpositions in germ cells are passed down to progeny → accumulation in genome
Slide7Autonomous vs. Non-autonomous
TEs are further classified as autonomous or non-autonomous
Autonomous TEs
contain ORFs that encode proteins needed for retrotranspositionNon-autonomous TEs lack reverse transcriptase (class 1) or transposase (Class 2) gene needed for transposition
“Borrow” proteins from other TEs (e.g. Ac/Ds elements)
From Munoz-Lopez and Garcia-Perez. Curr Genomics. 11(2), 115-128.
Slide8DNA Transposons
Have ITRs
Single ORF encodes a transposase
Flanked by short direct repeats (DR)
Slide9Retrotransposons
LTR retrotransposons: have direct LTRs
Non-LTR retrotransposons
: LINEs and SINEs
LTR Retrotransposon
LINE
SINE
Slide10Roles of TEs: Are they really selfish junk? (talk about a bad reputation)
From Fedoroff et al., Science. 338, 758-767 (2012).
C-value paradox
: organisms of similar complexity differ greatly in DNA content
Arabidopsis genome contains 27,000 genes and ~20 Mb of retrotransposons
Maize genomone contains 40,000 genes and > 1800 Mb of retrotransposons
Slide11Roles of TEs: Effects depend on transposition location
Can inactivate or alter gene expression (insertion)
Can participate in genome reorganization (mobilization of non-TE DNA; recombination of substrates)
Loss of genomic DNA (deletions)
From Munoz-Lopez and Garcia-Perez. Curr Genomics. 11(2), 115-128.
Slide12Inverted repeat of 10-40 bp is present at each end of IS element
5’ to 3’ sequence on one strand is repeated on the other strand
From Lodish
et al
., Molecular Cell Biology, 7
th ed.
Insertion Sequences or Insertion-Sequence (IS) Elements
Segments of
bacterial
DNA
Interrupt the coding sequence and inactivate the expression of that gene
IS elements were first found in
E. coli
Slide13Transposition of an IS element occurs by a “cut-and-paste” mechanism.
(1) Excises the IS element from the donor DNA
(2) Makes staggered cuts in a short sequence in the target DNA
(3) Ligates the 3′ termini of the IS element to the 5′ ends of the cut donor DNA.
From Lodish
et al
., Molecular Cell Biology, 7
th
ed.
Transposition of IS element in
E. coli
Slide14Transposon (Tn)
more complex mobile DNA segment contains genes for the insertion of the DNA segment into the chromosome
2 types of prokaryotic transposons:
Composite transposonsNon-composite transposons.
Prokaryotic Transposon
From Griffiths et al. An Introduction to Genetic Analysis. 7th edition.
Slide15Composite Transposons
Central region containing genes, e.g., drug resistance genes
IS-L and IS-R
IS-L and IS-R may be in the same/ inverted orientation relative to each other. Because the ISs themselves have terminal inverted repeats, the composite transposons also have terminal inverted repeats.
Weinreich, et al. Characterization of the Tn5 transposase and inhibitor proteins: a model for the inhibition of transposition.
Journal of bacteriology
,
175
(21), 6932-8.
Bischerour et al. Base Flipping in Tn
10
Transposition: An Active Flip and Capture Mechanism. PLOS ONE 4(7): e6201
Slide16Non-composite Transposons
Containing genes such as those for drug resistance.
Do not terminate with IS elements.
Have the repeated sequences at their ends that are required for transposition.
http://www.biologydiscussion.com/cell/prokaryotes/transposable-genetic-elements-in-prokaryotes-2/12001
From Griffiths, et al. Modern Genetic Analysis. 7th edition
Slide17Prokaryotic Summary
E. coli mutations caused by the spontaneous insertion of DNA sequence: insertion sequence/ IS element
Transposition of IS element is rare: 1 per 10
5-107 cells per generation
Transpositions can inactivate essential genes, killing the host cell and IS elements it carries
Higher rates of transposition would result in too much mutation rate
IS elements transpose can enter nonessential regions and into plasmids or lysogenic viruses
Lodish
et al
., Molecular Cell Biology, 7
th
ed.
Slide18Eukaryotic transposons:
Transposable elements(TEs) occur in almost all eukaryotic genomes.
In most situations, the transposons in a genome are epigenetically silenced(for example, silenced by histone modification).
Helitrons are a group of Transposable elements. They are described as eukaryotic class 2 transposable element.Wang, Zhenxing, and Kunze, Reinhard(Jun 2015) Transposons in Eukaryotes (Part A): Structures, Mechanisms and Applications. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0026264]
Slide19Helitrons
A unique group of eukaryotic DNA transposons that have generated unusually extensive genome variation
Discovered by analysis of whole genome sequences.
https://upload.wikimedia.org/wikipedia/commons/d/d6/Structure_and_coding_capacity_of_canonical_animal_and_plant_Helitrons.PNG
Slide20Mechanism of rolling-circle transposition
Thomas, Jainy; Pritham, Ellen (2014). "Helitrons, the Eukaryotic Rolling-circle Transposable Elements". Microbiology Spectrum. 3 (4): 893–926.
Slide21Impact on gene expression
Like other transposable elements, helitrons may cause genetic mutation
Helitron insertions can modify the expression of nearby genes.
Thomas, Jainy; Pritham, Ellen (2014). "Helitrons, the Eukaryotic Rolling-circle Transposable Elements". Microbiology Spectrum. 3 (4): 893–926.Thomas, Jainy; et al. (2014). "Rolling-Circle Transposons Catalyze Genomic Innovation in a Mammalian Lineage". Genome Biology and Evolution. 6 (10): 2595–2610.
Slide22Genome-wide identification
Thomas, Jainy; Pritham, Ellen (2014). "Helitrons, the Eukaryotic Rolling-circle Transposable Elements". Microbiology Spectrum. 3 (4): 893–926.
Slide23Evolutionary implication
The captured gene would be destroyed by multiple mutations if it did not provide any selective advantage to the transposon.
It would be kept as a gene related to the original host gene if its capture is beneficial for the transposon, which is tolerated by the host
.
Thomas, Jainy; Pritham, Ellen (2014). "Helitrons, the Eukaryotic Rolling-circle Transposable Elements". Microbiology Spectrum. 3 (4): 893–926.