Download Structure of IS elements.

Page 1194
Structure of IS elements.
These and other transposons have inverted terminal
repeats (numerals) and are flanked by direct repeats of
host DNA target sequences (letters).
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A model for the generation of direct
repeats of the target sequence by
transposon insertion.
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Properties of Some Insertion
Elements.
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A map of transposon Tn3.
Total size 4957 bp. Inverted terminal repeats 38 bp each
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A composite transposon.
The IS-like modules may have either (a) direct or (b) inverted
relative orientations.
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Electron micrograph of a singlestranded circular DNA containing
a transposon.
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The cut-and-paste transposition
mechanism catalyzed by Tn5
transposase.
Cut and paste transposition
How the cut is
performed
Comparison of transposition
pathways.
Grey segments represent transposable DNA elements. Small arrows indicate phosphodiester bond
breakage. Solid and dotted lines represent donor and target DNA, respectively
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X-Ray structure of Tn5
transposase.
in complex with a 20-bp DNA containing the OE sequence
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Replicative transposition.
This type of transposition inserts a copy of the transposon at the
target site while another copy remains at the donor site.
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A cointegrate.
This structure forms by the fusion of two plasmids, one carrying a
transposon, such that both junctions of the original plasmid are
spanned by transposons with the same orientation (arrows).
A model for transposition involving
the intermediacy of a cointegrate.
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Here more lightly
shaded bars
represent newly
synthesized DNA.
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Chromosomal rearrangement
via recombination.
(a) The inversion of a DNA segment between two identical
transposons with inverted orientations.
Chromosomal rearrangement
via recombination..
(b) The deletion of a DNA segment between two identical
transposons with the same orientation
The mechanism of phase
variation in Salmonella.
hin codes for Hin DNA
invertase
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hix : Two sites, closely related,
26 bp (2 x 12 bp imperfect
inverted repeats separated by 2
bp)
H1, H2: Genes for two
antigenically distinct flagellin
proteins
rh1: Gene for H1 gene
repressor
Størrelse av genomer
Sammensetning av genomet
Repetitive DNA
interspersed
I
in tandem
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Moderately Repetitive Sequences in
the Human Genomea
Klasser av intersperserte repetisjoner
i det humane genom
Elementer i det humane genom som kan
transposeres på en RNA-formidlet måte
Alu elements
Length = ~300 bp
Repetitive: > 1,000,000 times in the human genome
Constitute >10% of the human genome
Found mostly in intergenic regions and introns
Propagate in the genome through retroposition (RNA
intermediates).
Evolution of Alu elements
Alu elements can be divided into
subfamilies
The subfamilies are
distinguished by
~16 diagnostic
positions.
Transposisjonering av et typisk
humant Alu-element
Alu-elementer hos primater
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Alu sequences in the globin
gene cluster
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Gene sequences of (a) retroviruses and
(b) the Ty1 retrotransposon from yeast.
Naturally occuring methylated
bases in DNA
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The catalytic mechanism of 5methylcytosine methyltransferases
(m5C-MTases).
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X-Ray structure of M.HhaI
in complex with S-adenosylhomocysteine and a duplex 13-mer DNA containing a
methylated f5C residue at the enzyme’s target site.
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Maintenance
methylation.
CpG-frekvens og CpG-øyer
The typical density of
CpG doublets in
mammalian DNA is
~1/100 bp, as seen for a
-globin gene. In a CpGrich island, the density is
increased to >10
doublets/100 bp. The
island in the APRT gene
starts ~100 bp upstream
of the promoter and
extends ~400 bp into
the gene. Each vertical
line represents a CpG
doublet.
CpG-øyer
Vedlikeholdsmetylering
Ved maintenance-metylering
induserer metyleringsmønsteret i
en parental DNA-tråd det
tilsvarende metyleringsmønster i
den komplementære tråden. Slik
kan et stabilt
metyleringsmønster
opprettholdes i en cellelinje
CpG – underrepresentert i
genomet
The CpG doublet occurs in vertebrate DNA at only ~20%
of the frequency that would be expected from the
proportion of G·C base pairs. (this is because CpG
doublets are methylated on C, and spontaneous
deamination of methyl-C converts it to T, introducing a
mutation that removes the doublet.) In certain regions,
however, the density of CpG doublets reaches the
predicted value; in fact, it is increased by 10× relative to
the rest of the genome. The CpG doublets in these
regions are unmethylated
Cytosin, metylcytosin og tymin
me
T
Evolusjon av CpG-øyer: en
mulig mekanisme
Ancestralt eukaryot genom
med metylering av C i CpG,
bortsett fra i visse
genassosierte områder
Metylerte CpG muteres
gradvis til TpG eller CpA,
mens umetylerte CpG forblir
Microsatellite terminology
Trinucleotide expansion diseases
TABLE 1
DISEASES OF TRINUCLEOTIDE REPEATS
NAME OF THE DISEASE
SEQUENCE OF
THE REPEAT
LOCATION OF
THE REPEAT
Fragile site 11B
Fragile X syndrome
CGG
EXON
Dentatorubralpallidoluysian atrophy
Haw river syndrome
Huntington's disease
Machado-Joseph disease
Spinal and Bulbar
muscular dystrophy
Spinocerebellar ataxia
type 1
CAG
EXON
Myotonic dystrophy
CTG
EXON
Friedrich's ataxia
GAA
INTRON
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The loop-out mechanism for the alteration
of the number of consecutive triplet
repeats in DNA through its replication.