Transposable Elements Presented by Anne Sternberger, Yingnan Zhang & Yuxi Zhou

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” 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).

Transposable 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 TEs Class 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).

Transposable elements have common characteristics Flanking repeats on each points of insertion into target DNA DNA transposons (Class 2 TEs) have inverted terminal repeats (ITRs)

Transposons vs. Retrotransposons Retrotransposons (Class 1 TEs) RNA intermediate Transposons (Class 2 TEs) DNA intermediate (cut-and-paste mechanism) Transposons vs. Retrotransposons Duplicate → integrate into new site Excise → move to another location From Fedoroff et al., Science. 338, 758-767 (2012).

DNA Transposons and Retrotransposons in Eukaryotes Transpositions in germ cells are passed down to progeny → accumulation in genome

Autonomous vs. Non-autonomous TEs are further classified as autonomous or non-autonomous Autonomous TEs contain ORFs that encode proteins needed for retrotransposition Non-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.

DNA Transposons Have ITRs Single ORF encodes a transposase Flanked by short direct repeats (DR)

Retrotransposons LTR retrotransposons: have direct LTRs Non-LTR retrotransposons: LINEs and SINEs LTR Retrotransposon LINE SINE

Roles of TEs: Are they really selfish junk Roles of TEs: Are they really selfish junk? (talk about a bad reputation) 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 From Fedoroff et al., Science. 338, 758-767 (2012).

Roles 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.

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 Inverted 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, 7th ed.

Transposition of IS element in E. coli Transposition 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, 7th ed.

Prokaryotic Transposon Transposon (Tn) more complex mobile DNA segment contains genes for the insertion of the DNA segment into the chromosome 2 types of prokaryotic transposons: Composite transposons Non-composite transposons. From Griffiths et al. An Introduction to Genetic Analysis. 7th edition.

Composite 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. Bischerour et al. Base Flipping in Tn10 Transposition: An Active Flip and Capture Mechanism. PLOS ONE 4(7): e6201 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.

Non-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. From Griffiths, et al. Modern Genetic Analysis. 7th edition http://www.biologydiscussion.com/cell/prokaryotes/transposable-genetic-elements-in-prokaryotes-2/12001

Prokaryotic Summary E. coli mutations caused by the spontaneous insertion of DNA sequence: insertion sequence/ IS element Transposition of IS element is rare: 1 per 105-107 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, 7th ed.

Eukaryotic 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]

Helitrons 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

Mechanism of rolling-circle transposition Thomas, Jainy; Pritham, Ellen (2014). "Helitrons, the Eukaryotic Rolling-circle Transposable Elements". Microbiology Spectrum. 3 (4): 893–926.

Impact 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.

Genome-wide identification Thomas, Jainy; Pritham, Ellen (2014). "Helitrons, the Eukaryotic Rolling-circle Transposable Elements". Microbiology Spectrum. 3 (4): 893–926.

Evolutionary 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.