Transposable elements Transposons

1
Transposable elements (Transposons)

• Mobile genetic elements - they move from one
  location in the genome to another
• Requires no homology between donor and recipient
  DNAs.
• Found in all organisms (so far studied)
• Effects
• Insertion near or within a gene can inactivate or
  activate the target gene.
• Cause deletions, inversions, and translocations
  of DNA
• Lead to chromosome breaks

2
Effects of transposable elements depends on their
location
Transposition is a potentially dangerous process.
It must be tightly regulated. 10-5 to 10-7 events
per element per generation
3
Prokaryotic Transposons(DNA-mediated)

• Simplest transposons (IS)
• More complex transposons (Tn)
• Composite transposons

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Simplest transposons

• Insertion sequences or IS elements
• IS followed by an identifying number (Table
  30-6)
• Length lt 2,000 bp, common E. coli strain has 8
  copies of IS1 and 5 copies of IS2.
• see Fig. 30-81 for the generation of direct
  repeats of the target sequence by insertion.

Transposase gene, some regulatory gene
short inverted terminal repeats
directly repeated segment of host DNA
Figure 30-80
5
More complex transposons (Tn)

• Carry genes not involved in the transposition
  process, e.g. antibiotics resistance genes
• Length gt 2,000 bp

Figure 30-82
6
Composite transposons

• Gene in central region plus two identical or
  nearly identical IS-like modules (same or
  inverted relative orientation)
• Composite transposons can transpose any sequence
  of DNA in their central region

Figure 30-83
7
Non-replicative (cut and past) vs. Replicative
transposition
Non-replicative transposition (Direct
transposition)
Donor replicon is lost unless the break is
repaired


Donor
Recipient
Replicative transposition
resolution


Relicon B
Replicon A with a transposable element TE
Cointegrate
fusion of replicons during replication of the TE
8
Direct (Simple) transposition

• Physically moves form one DNA site to another
• Cut-and-Paste Mechanism

Figure 30-84
9
Replicative transposition from the crossover
structure

• The 3 ends of each strand from the staggered
  break (at the target) serve as primers for repair
  synthesis.
• Copying through the transposon followed by
  ligation leads to formation of a cointegrate
  structure.
• Copying also generates the flanking direct
  repeats.
• The cointegrate is resolved by recombination.
• Model for transposition (Fig. 30-88) and
  resolution (Fig. 30-89)

10
Recombination between two nearly identical
sequences (e.g transposons) will lead to
rearrangements of the host DNA

• Inversion if the repeats are in the opposite
  orientation (Fig. 30-91a)
• Deletion if the repeats are in the same
  orientation (Fig. 30-91b)

11
Transposones in Eukaryote

• 3 of human genome consists of DNA-based
  transposons. Their sequences have mutated so as
  to render them inactive
• Most eukaryotic transposons exhibit little
  similarity to those of prokaryotes
• Base sequences resemble those of retroviruses.
  Retrotransposons
• 20 of the human genome is retrotransposons

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Figure 30-96 Gene sequences of (a) retroviruses
and (b) the Ty1 retrotransposon.
13
Transposable elements that move by RNA
intermediates

• Called retrotransposons
• Common in eukaryotic organisms
• Some have long terminal repeats (LTRs) that
  regulate expression
• Yeast Ty-1
• Retroviral proviruses in vertebrates
• Non-LTR retrotransposons
• Mammalian LINE repeats ( long interspersed
  repetitive elements, L1s)
• Similar elements are found even in fungi
• Mammalian SINE repeats (short interspersed
  repetitive elements, e.g. human Alu repeats)
• Drosophila jockey repeats
• Processed genes (have lost their introns). Many
  are pseudogenes.

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Figure 30-97 Proposed mechanism for the
transposition of nonviral retrotransposons.
15
Mechanism of retrotransposition

• The RNA encoded by the retrotransposon is copied
  by reverse transcriptase into DNA
• Primer for this synthesis can be generated by
  endonucleolytic cleavage at the target
• Both reverse transcriptase and endonuclease are
  encoded by SOME (not all) retrotransposons
• The 3 end of the DNA strand at the target that
  is not used for priming reverse transcriptase can
  be used to prime 2nd strand synthesis

16
DNA Methylation

• N6-methyladenine (m6A)
• N4-methylcytosine (m4C)
• 5-methylcytosine (m5C)
• Dam methyltransferase (Dam MTase)
• methylate A residue in GATC
• Dcm methyltransferase (Dcm MTase)
• methylate C residue (C5 position) in CCA/TGG

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Mechanism of Methylation reaction

• Chemical reaction scheme (Fig. 30-98, p1205)
• Base flipped out mechanism
• Base flipping is a common mechanism through which
  enzymes gain access to the bases in dsDNA on
  which they perform chemistry

Figure 30-99 X-Ray structure of M.HhaI in complex
with S-adenosylhomocysteine and a duplex 13-mer
DNA con-taining a methylated f5C residue at the
enzymes target site.
18
DNA methylation in eukaryotes functions in gene
regulation

• 5-methylcytosine is the only methylated base in
  most eukaryotic DNA
• CG dinucleotide of various palindromic sequences
• CpG islands The upstream regions of many genes
  have normal CG frequencies
• DNA methylation can be analyzed by Southern blots

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DNA methylation varies

• Species, Tissue and Position along a chromosome
• DNA methylation switches off eukaryotic gene
  expression
• One model of repression
• DNA methylation is recognized by a family of
  proteins contain methyl-CpG binding domain (MBD)
• It recruits protein complex that induce the
  alternation of the local chromosome structure