EEB 600A Lecture 26: Mobile Genetic Elements and Other Families of Repetitive DNA

Lecture 26: Mobile Genetic Elements and Other Families of Repetitive DNA

(version 22 April 2003)

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Families of Repetitive DNAs

The genome is littered with large families of repetitive sequences that have no apparent function in the cell.

Mobile Genetic Elements

Also called Transposons or Transposable elements (TEs) these are sequences that move around the genome

Three different mechanisms for transposition:

As the above figures show, a very common feature of mobile elements is duplication of a short sequence at the target site. This generates short direct repeats flanking the newly inserted element. This results for a staggered cut being made in the DNA strands at the site of insertion.

DNA-Immediate Mobile Genetic Elements

The typical mobile genetic element that uses a strictly DNA immediate has the following canonical structure:

The Short inverted repeats at the ends of the element are acted on by the transposase gene encoded for by the element. These inverted repeats act as the substrates for recombination reactions mediated by the transposase.

An important variation of this canonical structure are Autonomous vs. Non-autonomous elements. If one has an element with inverted repeats, this element can still move, provided the transposase is supplied from some other (active) element. This is a common theme for families of mobile elements, where very often a large number of members require the presence of a functional transposase that the non-autonomous elements themselves do not encoded.

Examples of DNA-intermediate mobile elements

DNA transposons tend to have short life spans within a species.

Retrotransposons

There are a large number of variants of mobile elements that reply in reverse transcriptase for their mobility.

  • Retorviruses

    The basic structure is an LTR = long terminal repeat which flanks three genes,

    A complete retroviruses also contains three genes:

    The repeat structure of the LTR follows from how the mRNA is reverse-transcribed into a cDNA, starting with a tRNA primer:

  • LTR retroposons

    Bascially, these are retroviruses without the env protein. Current thinking is that retroviruses evolved from retropsons. They have the LTR and (usually) gag genes. LTR retroposons are often simple called retrotransposons.

  • Non-LTR retroposons

    Also called retroposons. Again, have the pol and gag-related gene, but now also lack the LTRs,

    Example: LINEs (Long interspersed elements)

    Parasites upon parasites: SINEs (Short interspersed elements)

  • Processed pseudogenes (retropseudogenes)

    cDNA copies of reverse-transcribed mRNAs. Because the mRNA does not contain the Pol II promoter (it is external to the coding sequence), these are almost always inactivate upon formation.

    Age and Number of Mobile elements

    Evolutionary Implications of Mobile Elements

    Simple Sequence Repeats (SSR)

    Families of Simple Sequence repeats make up over 3% of the human genome.

    Mechanisms of simple sequence amplification and homogenization

    Replication slippage, polymerase stuttering

    Rolling circle replication is commonly seen on viruses with circular chromosomes, wherein the polymerase just goes round and round the circle, generating concatenated repeats of the origin sequence:

    Likewise, if a short piece of DNA forms a circle and this includes an origin of replication, a very long tandem repeat of the sequence can be generated. Reinsertion of this sequence into a chromosome has thus generated in one event a large block of tandemly-repeated sequences.

    Large blocks of tandem-repeated DNA tend to accumualte in regions of low recombination.

    Concerted evolution can occur either through a birth and death model, wherein amplification events (like rolling circles) generate large blocks de nova. Likewise, it can also occur via cycles of unequal crossing over. Given that even closely related species can have very different repeats forming their large blocks of satellite DNA, a birth and death model seems more likely.