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
- Tandemly repeated simple sequence DNAs
- Satellite DNAs
- Short simple repeats (microsatellites)
Mobile Genetic Elements
Also called Transposons or Transposable elements (TEs) these are sequences that move around the genome
Three different mechanisms for transposition:
- Conservative transposition: The element itself moves from the donor site into the target site.
- Replicative transposition: The element moves a copy of itself to a new site via a DNA intermediate.
- Retrotransposition: The element makes an RNA copy of itself which is reversed-transcribed into a DNA copy which is then inserted.
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
- Insertion Sequences (IS) elements in bacteria
P elements in Drosophila
AC/DS elements in maize
- AC is a full-length autonomous copy
- DS is a truncated copy of AC that is non-autonomous, requiring AC in order to transpose.
- At least seven major classes of DNA
transposons in the human genome (3% of total genome)
DNA transposons tend to have short life spans within a species.
DNA transposons cannot exercise a cis-preference: the encoded transposase is produced in the cytoplasm and, when it returns to the nucleus, it
cannot distinguish active from inactive elements.
- As inactive copies accumulate in the genome, transposition becomes less efficient.
checks the expansion of any DNA transposon family and in due course causes it to die out.
- To survive, DNA transposons must eventually
move by horizontal transfer to virgin genomes, and there is considerable evidence for such transfer
There are a large number of variants of mobile elements that reply in reverse transcriptase for their mobility.
The basic structure
is an LTR = long terminal repeat which flanks three genes,
A complete retroviruses also contains three genes:
- gag = structural gene for capsid
- Pol = reverse transcriptase plus other stuff.
- env = envelope gene for the virus
The repeat structure of the LTR follows from how the mRNA is reverse-transcribed into a cDNA, starting with a tRNA primer:
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.
Also called retroposons. Again, have the pol and gag-related gene, but now also lack the LTRs,
Example: LINEs (Long interspersed elements)
- LINEs are one of the most ancient and successful inventions in eukaryotic genomes.
- In humans, are about 6 kb long, harbour an internal polymerase II promoter and encode two open reading frames (ORFs).
- Upon translation, a LINE RNA assembles with its
own encoded proteins and moves to the nucleus, where an endonuclease activity makes a single-stranded nick and the reverse transcriptase
uses the nicked DNA to prime reverse transcription from the 3' end of the LINE RNA.
- Reverse transcription frequently fails to proceed to
the 5' end, resulting in many truncated, nonfunctional insertions.
- Most LINE-derived repeats are short, with an average size of 900
bp for all LINE1 copies, and a median size of 1,070 bp for copies of the currently active LINE1 element (L1Hs).
- The LINE machinery is believed to be responsible for most reverse transcription in the
genome, including the retrotransposition of the non-autonomous SINEs and the creation of processed pseudogenes
distantly related LINE families are found in the human genome: LINE1, LINE2 and LINE3.
- Only LINE1 is still active.
Parasites upon parasites: SINEs (Short interspersed elements)
- SINEs are freeloaders on the backs of LINE elements.
- short (about 100Ð400 bp), harbour an internal polymerase
III promoter and encode no proteins.
- non-autonomous transposons use the LINE machinery for transposition.
- most SINEs 'live' by sharing the 3' end with a resident LINE element.
- Most promoter regions of known SINEs are derived from
- A single monophyletic family of SINEs (ALU) derived from the signal recognition particle component 7SL
- This family is the only active SINE in the human genome
- The human genome contains three distinct monophyletic families of
SINEs: the active Alu, and the inactive MIR and Ther2/MIR3.
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
Humans contain a higher percentage of mobile elements (active and incactive) relative to three other fully-sequenced genes (Fly, worm, mustard):
- However, human elements are older.
- Even when compared to mice, again human elements are older.
- Hence, relative to certain "model" organisms, humans have a higher percentage of their genome from mobile elements, but the vast majority of these are old, no longer functional, elements.
Evolutionary Implications of Mobile Elements
- Huge generators of new mutations
- Regulatory changes from strong promoters in TEs
- Insertion mutation
- excision mutations
- Hybrid dysgenesis
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.