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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). Page 1195 A model for the generation of direct repeats of the target sequence by transposon insertion. Page 1194 Properties of Some Insertion Elements. Page 1195 A map of transposon Tn3. Total size 4957 bp. Inverted terminal repeats 38 bp each Page 1195 A composite transposon. The IS-like modules may have either (a) direct or (b) inverted relative orientations. Page 1215 Electron micrograph of a singlestranded circular DNA containing a transposon. Page 1195 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 Page 1196 X-Ray structure of Tn5 transposase. in complex with a 20-bp DNA containing the OE sequence Page 1197 Replicative transposition. This type of transposition inserts a copy of the transposon at the target site while another copy remains at the donor site. Page 1197 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. Page 1197 Here more lightly shaded bars represent newly synthesized DNA. Page 1199 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 Page 1200 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 Page 1437 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 Page 1444 Alu sequences in the globin gene cluster Page 1203 Gene sequences of (a) retroviruses and (b) the Ty1 retrotransposon from yeast. Naturally occuring methylated bases in DNA Page 1205 The catalytic mechanism of 5methylcytosine methyltransferases (m5C-MTases). Page 1206 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. Page 1207 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 Page 1209 The loop-out mechanism for the alteration of the number of consecutive triplet repeats in DNA through its replication.