Transposable elements

"The genome is dynamic!"

"Retro is in"

I. Transposable elements - Overview

A. Transposable elements (a.k.a. "jumping genes", "mobile elements") are discrete elements of DNA with the capacity to excise and insert themselves into other sites in their host’s DNA.

Transposable elements are well-characterized in prokaryotes, where they are of particular concern becuse of their role in transferring antibiotic resistance genes.

B. Where the element inserts (i.e. in an exon, in an intron, near a gene, or outside of a gene) will dictate what, if any, effect there will be on a phenotype. 

C. Elements have primary responsibility for the C-value paradox (enigma) __________________.

No correlation between genome size and complexity

• Transposable elements are a principal component of the "junk" DNA that accounts for differences in genome size.
  
  
• But is the "junk" really junk?

D. Transposable elements are "selfish DNA" since they are "parasitic" - they make copies of themselves. If they produce a phenotype, it is by "commandeering" the host genome.

• Perhaps they are not really parasitic - maybe symbiotic?

II. A new appreciation for elements - they play key roles in three aspects of genome evolution: variation, expansion, and architecture.

A. creating genetic variation

• structural

 

• regulatory

 

B. genome expansion - elements are a "one way ticket to genome obesity" (?)

C. changing genome architecture

III. Classification

A. Class I - "Retroelements" remain in the DNA and transpose via a duplicative mechanism involving a mRNA intermediate. The mRNA is then converted to a DNA by reverse transcriptase. Proteins encoded by these retroelements mediate the copy-and-paste transposition. 

• More detail on Retrotransposons and Retroposons

A. Retrotransposons with Long Terminal Repeats (LTRs)

Examples - gypsy, copia

LTR retrotransposon structure

LTR-Gag-Ap-In-Rt-Rh-LTR. 

The order of genes matters and distinguishes copia from gypsy.  Found in animals, plants, fungi.

Gag: encodes a protein important for maturation of RNA genome

Ap: encodes a proteinase

In: integrase inserts cDNA copy back into genome

Rt: reverse transcriptase


LTRs are conserved but within the elements, there can be many mutations in one or more of the components. This can lead to premature stop codons or frameshifts.  

Some elements are lacking most or all of the component ORFs – these are parasitic on the autonomous retrotransposons, which are parasitic on the host genome….

Inactive elements with point mutations or small INDELs can be mobilized in cis.

B. Retroposons, without LTRs

SINES: short interspersed elements (SINES) - can be hundreds of thousands of copies between genes and in introns.

LINES: long interspersed elements. 1 – 5 kb in length and occur in 20,000 – 40,000 copies (in the human genome). 

 

B. Class II - DNA elements that move by excision and reinsertion of DNA via a cut-and-paste mechanism.

• Elements with Terminal Inverted Repeats (TIR): Mu, Ac, Ds

IV. Effects of elements

A. Creating genetic variation

Structural example: kernel color variants in maize

The elements: Ac, Ds and Barbara McClintock

Ac (Activator) is an autonomous element. ___________

• 4563  bp long
• 11-bp inverted repeats at each end. The inverted repeats are essential for transposition. 
• Ac includes DNA coding for a protein (transposase).
  • The transposase is “transacting” in that it also allows Ds elements to transpose. 

Ds (Disassociator) is a non-autonomous (dependent) element. _________________

• It lacks transposase and therefore can only transpose when Ac is present.
• There are Ds elements of varying sizes: aAll are Ac-like, but with deletions.
• 11 bp inverted repeats at each end 

 

How Ac and Ds can cause genetic variation:

Mutation in a gene can result from insertion of the element, which alters the reading frame, and from the excision of the element - an 8 bp target repeat sequence (the "footprint") remains.

• if insertion into an exon: get no expression in all cells descending from the insertion event (i.e. a white sector in a colored kernel)

 

• if insertion into an intron: perhaps altered expression in all cells descending from the insertion event (i.e. change in intensity of a sector in a colored kernel)

 

• if insertion into 5' end: may alter transcription or  if insertion into non-coding DNA, the event may go undetected

 

Other considerations

• Elements tend to transpose within 5 – 10 cM of  their starting point
  
  
• The presence of nested  Ds elements can also provide a site for chromosome breakage
  
• Elements in introns and in intergenic spaces may provide target sites for transcription factors

 

B. Genome expansion

The big picture

In plants, Class I LTR retrotransposons are the principal agents of genome expansion. 

90% of some Triticeae and Liliaceae

~ 50% in diploid Gossypium (cotton)

20% of the Arabidopsis genome

90,000 retrotransposon copies in a wild Oryza (relative of cultivated rice) - 975 Mb vs. 57 Mb in smallest genome Oryza

These changes are on evolutionary time scales (5 million years).....and more recent (500,000)

A microcosm example - Hordeum spontaneum (wild barley) in Evolution Canyon, Mr. Carmel, Israel

BARE elements - Class I LTR type

~ 14,000 copies ~ 4% of the genome

Parasitize each other: neither is autonomous but together, in cis, may achieve functionality

Higher BARE-1 copy number in wild barley on dry south slopes (and increasing with elevation on these slopes) – due to increase in copy number and lower rates of loss.

~8,000 copies on North slopes

~20,000 copies on South slopes

Speculation -

Selection for large genome size more likely in Mediterranean Basin than in tropics. 

Growth mostly during cool wet winter rather than in dry summer.

Growth is due to increases in cell volume rather than cell number since cell division rates are reduced by lower temperatures. 

Larger cell sized correlated with larger genome size.

The BARE-1 promoter has abscissic acid response element, as do water stress induced genes.

There is a balance of retention vs. elimination - Elements can be "cleansed" from a genome by recombination between their LTRs, followed by deletion.

 

 

C. Changing genome architecture - Helitrons of maize

The Helitron

No terminal repeats

No target site duplications

Pick up pieces of genes as they move

May lead to assembly of new genes by combining exons from different genes. 

Lead to a lack of absolute colinearity in genomes of different accessions of the same species

Much to be revealed by comparative sequencing of different genotypes of the same species.

In 2.3 Mb of aligned sequence, less than 50% shared sequence between two inbreds of maize

In japonica vs. indica rice: less than 25% shared sequence.

Not just intergenic content differences. Even gene content. Up to 10,000 gene differences - a basis for hybrid vigor??

 

 

V. Using elements - transposon tagging

The principle:

Insertion/excision of the element can lead to a change in phenotype

The sequences for transposable elements are known and can thus be tracked with PCR or probes

Therefore transposons can be used for insertional mutagenesis to discover genes 

The Ac/Ds system has been transferred to a range of dicot and monocot plants via transgenic technologies.

Example - The barley TNP story

Text  Readings: Chapter 14

Journal articles (FYI):

• Feschotte et al. (general review)
• Hawkins et al. (Gossypium genome expansion)
• Kalendar et al. (BARE elements in Evolution Canyon)
• Lai et al. (Helitrons)
• Morgante (general review)
• Piegu et al.(Oryza genome expansion)
• Tanskanen et al. (More on BARE elements)

On the Web:

Alan Schulman - Master of BAREs and LARDs

Animation of prokaryotic transposition

Kimball's take on transposons

Waynesword on DNA elements in maize