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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). Page 1194. A model for the generation of direct repeats of the target sequence by transposon insertion. Page 1195. - PowerPoint PPT Presentation
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Structure of IS elements.
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These and other transposons have inverted terminal repeats (numerals) and are flanked by direct repeats of host DNA target sequences (letters).
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.
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Total size 4957 bp. Inverted terminal repeats 38 bp each
A composite transposon.
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The IS-like modules may have either (a) direct or (b) inverted relative orientations.
Electron micrograph of a single-stranded circular DNA containing
a transposon.
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The cut-and-paste transposition mechanism catalyzed by Tn5
transposase.
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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
X-Ray structure of Tn5 transposase.
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in complex with a 20-bp DNA containing the OE sequence
Replicative transposition.
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This type of transposition inserts a copy of the transposon at the target site while another copy remains at the donor site.
A cointegrate.
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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.
Chromosomal rearrangement via recombination.
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(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.
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hin codes for Hin DNA invertase
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
Iinterspersedinterspersed in tandemin tandem
Moderately Repetitive Sequences in the Human Genomea
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Klasser av intersperserte repetisjoner i det humane genom
Elementer i det humane genom som kan transposeres på en RNA-formidlet måte
Alu elementsLength = ~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 The subfamilies are distinguished by distinguished by ~16 diagnostic ~16 diagnostic positions.positions.
Transposisjonering av et typisk humant Alu-element
Alu-elementer hos primater
Alu sequences in the globin gene cluster
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Gene sequences of (a) retroviruses and(b) the Ty1 retrotransposon from yeast.
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Naturally occuring methylated bases in DNA
The catalytic mechanism of 5-methylcytosine methyltransferases
(m5C-MTases).
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X-Ray structure of M.HhaIP
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in complex with S-adenosylhomocysteine and a duplex 13-mer DNA containing a methylated f5C residue at the enzyme’s target site.
Maintenance methylation.
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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 CpG-rich 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
Tme
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 diseasesTABLE 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
Dentatorubral-pallidoluysian 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
The loop-out mechanism for the alteration of the number of consecutive triplet
repeats in DNA through its replication.
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