Transposable%20Elements

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Transposable Elements

• ISP-elements
• Human repetitive sequences

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Prokaryotes

• Insertion Sequences (IS elements)
• Composite transposons
• Tn3 elements

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IS element
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IS elements

• IS elements are relatively small transposable
  elements that range in size from 760 to less than
  2,500 base pairs (bp).
• can insert at many different sites in bacterial
  and viral chromosomes and plasmids, and they
  contain genes whose products are involved in
  promoting and regulating transposition.
• One of the genes is a transposase that functions
  in excision of the element from a chromosome,
  plasmid.

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IS elements

• IS elements typically generate unstable mutants
  that revert to wild-type at a detectable
  frequency. For that reason, IS elements
  originally were called "mutable" genes.

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IS elements

• All IS elements contain inverted terminal repeats
  that range in size (length) from 9 to 40 base
  pairs.
• At the site of integration there invariably is a
  target site duplication of from 2-13 base pairs.

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Composite Transposons

• Composite transposons (denoted by symbol Tn)
• Tn elements stem from two IS elements that insert
  near one other. The regions (sequences) between
  the two elements can be "mobilized" by the joint
  action of the two IS elements. This is of
  significance in that many Tn elements possess
  genes that confer resistance to antibiotics
  between the two IS elements.
• Tn transposition is regulated by a "repressor"
  that appears to exist to keep the elements
  somewhat quiescent.

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Tn3

• Tn3 elements are simply large transposable
  elements that are not generated by flanking IS
  elements (as in Tn elements).

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Eukaryotes

• DNA transposable elements
• RNA transposable elements

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Conservative Transposition
http//nitro.biosci.arizona.edu/courses/EEB600A-20
03/lectures/lecture26/lecture26.html
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Replicative Transposition
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Retrotransposition
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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

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Transposable Elements (Transposons)

• DNA elements capable of moving ("transposing")
  about the genome
• Discovered by Barbara McClintock, largely from
  cytogenetic studies in maize, but since found
  in most organisms
• She was studying "variegation" or sectoring in
  leaves and seeds
• She liked to call them "controlling elements
  because they affected gene expression in myriad
  ways

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Mutant Kernel Phenotypes

• Pigmentation mutants
• affect anthocyanin pathway
• elements jump in/out of transcription factor
  genes (C or R)
• sectoring phenotype - somatic mutations
• whole kernel effected - germ line mutation

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Some maize phenotypes caused by transposable
elements excising in somatic tissues.
Start with mutant kernels defective in
anthocyanin synthesis and the element excises
during development.
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Somatic Excision of Ds from C
Wild type
Sectoring
Mutant
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Molecular Analysis of Transposons

• Transposons isolated by first cloning a gene that
  they invaded. A number have been cloned this way,
  via "Transposon trapping.
• Some common molecular features
• Exist as multiple copies in the genome
• Insertion site of element does not have extensive
  homology to the transposon
• Termini are an inverted repeat
• Encode transposases that promote movement
• A short, direct repeat of genomic DNA often
  flanks the transposon Footprint

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Ac and Ds

• Ds is derived from Ac by internal deletions
• Ds is not autonomous, requires Ac to move
• Element termini are an imperfect IR
• Ac encodes a protein that promotes movement -
  Transposase
• Transposase excises element at IR, and also cuts
  the target

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Structure of Ac and Ds deletion derivatives
Ds is not autonomous, requires Ac to move!
Fig. 23.11
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How duplications in the target site probably
occur.
Duplication remains when element excises, thus
the Footprint.
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Hybrid Dysgenesis

• P-elements are transposable elements that carry
  genes for transposase activity that cause the
  elements to move, and repressor activity that
  prevents expression of transposase.
• In a cross between a P-element-carrying female
  and a laboratory male left, repressors in the
  maternally - derived cytoplasm repress expression
  of the maternally - inherited P elements. The
  resulting offspring show the wild-type phenotype.

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Examples P-elements in Drosophila

• P elements were discovered when it was found that
  certain strains of Drosophila exhibited an
  assortment of aberrant phenotypes, including
  elevated mutation (and reversion), chromosome
  breakage, and sterility hybrid dysgenesis
• normally (within populations) the P elements are
  quiescent and do not jump. When hybrids were
  made between individuals from different
  geographic populations, the elements moved and
  promoted the dysgenic phenotypes.

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P-elements

• P elements vary in size (the largest are nearly
  3,000 base pairs in length). Complete (intact) P
  elements possess a gene for a transposase. The
  number of P elements per individual varies from a
  few to up to 50.

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Experimental uses of P-elements

• Transposon tagging, where genes mutated by P
  element insertion can be isolated and
  "discovered" by using the P element sequence as a
  "tag and
• Transformation vectoring, where genes or
  sequences of interest are "vectored" into a
  chromosomal location by putting the gene/sequence
  of interest into an incomplete P element (no
  transposase) and carrying out a mixed infection
  (transformation or electroporation) with a
  complete P element.

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Mariner elements

• Mariner elements appear to be a fairly widespread
  transposon of roughly 1,200 base pairs.

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Retrotransposones

• Retrovirus-like elements
• Retroposons

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LTRlong terminal repeat

• Flanks three genes a complete retrovirus has
  three genes
• gag structural gene for capsid
• Pol reverse transcriptase plus other stuff.
• env envelope gene for the virus

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retrovirus
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Retrovirus like elements

• The basic structure of retrovirus-like elements
  is a central coding region of two genes flanked
  by long terminal repeats LTRs that are oriented
  in the same direction and bounded by short
  inverted repeats.
• The two genes are homologous to two genes in
  retroviruses and encode a structural protein of
  the virus capsule and a reverse
  transcriptase/integrase enzyme.

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Retrovirus like elements

• Active retroviruses carry a third gene that codes
  for a protein of the virus envelope. Active
  retroviruses are capable of exiting cells and
  infecting other cells.
• Transposition involves transcription (RNA
  synthesis) of the DNA sequence integrated in the
  chromosome, reverse transcription of the RNA,
  synthesis of a double-stranded DNA from the RNA,
  and insertion into a new chromosomal location.

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Retroposons

• These are elements that move through an RNA
  intermediary but do not possess direct or
  inverted repeats at their termini (LTR) nor the
  env gene.
• They possess instead a string of AT base pairs
  at one end (of the DNA), and presumably represent
  a copy from reverse transcription of the poly-A
  tail of the mature RNA transcript.
• Some LINE sequences in mammals are retroposons,
  and the LlNE-1 retroposon is the only
  transposable element thus far documented in
  humans.
• Drosophila telomere sequences

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Non-LTR transposition
The LINE is transcribed into mRNA (red). A part
of this mRNA is translated into proteins involved
in the integration complex, which binds to the 3'
end of the mRNA transcript. The target site
(blue) is cleaved followed by reverse
transcription, with the 3' end of the target site
as the primer. Newly synthesized cDNA is shown in
pale green. Ligation of the cDNA occurs at the 5'
end, and the second strand is synthesized using
the first cDNA strand as template and the host
DNA polymerase
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Long term fate of non-LTR

• In an evolving genome, non-LTR elements are
  thought to proliferate by amplification of an
  extremely small number of "master" genes.
• These genes usually give rise to inactive copies
  (truncated at the 5' end) that are incapable of
  further transposition within the genome.
• The defective copies arise because of their mode
  of transposition through reverse transcription
  (see the figure), which in most cases stops
  replication before the 5' end is reached.
• These truncated elements, called DOA ("dead on
  arrival"), can be used as surrogates for
  pseudogenes in species such as Drosophila that
  have few bona fide pseudogenes

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LINEs

• 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.

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LINEs

• 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
• Three distantly related LINE families are found
  in the human genome LINE1, LINE2 and LINE3.
• Only LINE1 is still active.

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SINEs

• SINEs are freeloaders on the backs of LINE
  elements.
• short (about 100-400 bp), harbour an internal
  polymerase III promoter and encode no proteins.
• non-autonomous transposons use the LINE machinery
  for transposition.

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SINEs

• most SINEs 'live' by sharing the 3' end with a
  resident LINE element.
• Most promoter regions of known SINEs are derived
  from tRNA sequences

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Alu

• 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.

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Human Genome
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Comparative
Element Human Fly Worm Arabodopis
LINE/SINE 33.4 0.7 0.4 0.5
LTR 8.1 1.5 0.0 4.8
DNA 2.8 0.7 5.3 5.1
All TEs 44.4 3.1 6.5 10.5
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Direct Repeats

• 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

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LTR retroposons

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

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Simple Sequence Repeat Content of Human Genome
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Human Genome
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Mouse vs Human Genome
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Transposable Elements
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Transposable Elements
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Activity of Transposable Elements
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Evolution of TEs
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LTRs
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Transposons
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LINEs
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LINEs
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SINEs
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LINE/SINE Genomic Distribution
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LINE distribution
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SINE distribution
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CpG Methylation
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CpG Methylation
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CpG Islands
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CpG Islands
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Function
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Methylation and Gene Silencing
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Methylation and CpG Content
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Diseases
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Spontaneous Mutations
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CpG Mutations
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CpG Mutations
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CpG Mutations
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Function of Alu
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Function of Alu