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| SINE: |
Short inter-spread nuclear element
-nonautonomous
-poly-A retrotransposons, Alu, no integrase and no reverse transcriptase
-LINE-encoded proteins bind immediately to their own RNA during translation
-represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into tRNA, rRNA, and other small nuclear RNAs. |
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mcs5109 Fri, 26 Sep 2008 04:32:10 GMT |
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| LINE: |
Long inter-spread nuclear element, autonomous poly-A retrotransposons, ~20% human genome, L1, integrase and reverse transcriptase
-represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase II into mRNA |
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mcs5109 Fri, 26 Sep 2008 04:32:39 GMT |
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| Yeast Ty Elements |
Transpose into Safe Havens in the Genome
-Transposons in Yeast
- viral-like retrotransposons
-preferentially integrate into specific chromosomal regions
Mechanism: formation of specific protein-protein complexes between the integrase and host specific proteins bound to these chromosomal sites (Sir4 for Ty5). Try to integrate a site away from important genes for host. This is specially important with small, gene-rich genomes (e.g., yeast) |
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mcs5109 Fri, 26 Sep 2008 04:03:54 GMT |
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| Tcl/Mariner Elements |
-DNA elements in Eukaryotes
-simplest autonomous transposons -only a pair of terminal inverted repeat sequences and a gene encoding a transposase protein
-move by a cut-and-paste transposition mechanism
Artificially hyperactivated
-Sleeping beauty
-promising as a tool for mutagenesis and DNA insertion in many eukaryotic organisms |
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mcs5109 Fri, 26 Sep 2008 04:03:54 GMT |
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| MuB: |
ATPase that stimulates MuA activity and controls the choice of the DNA target site |
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mcs5109 Fri, 26 Sep 2008 03:59:41 GMT |
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| MuA: |
transposase, member of the DDE protein superfamily |
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mcs5109 Fri, 26 Sep 2008 03:59:41 GMT |
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| Tn10 Transposition |
-Coupled to Cellular DNA Replication
DNA methylation regulates Tn10 transposition
Limit the overall frequency of transposition
It also restricts transposition specifically to actively dividing cells
Two copies of the chromosome present to heal the double-stranded DNA break left in the old target site |
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mcs5109 Fri, 26 Sep 2008 03:59:41 GMT |
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| IS4-Family Transposons |
Are Compact Elements with Multiple Mechanisms for Copy
Number Control
Antisense RNA controls the expression of the transposase gene to regulate copy number |
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mcs5109 Fri, 26 Sep 2008 03:59:41 GMT |
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| Poly-A Retrotransposons |
Example: human LINE elements.
The poly-A retrotransposons also move by using an RNA intermediate
Many of the poly-A retrotransposons that have been detected by genomic sequencing.
Most of these elements are truncated therefore have lost the ability to transpose. |
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mcs5109 Fri, 26 Sep 2008 03:54:26 GMT |
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| Viral-like Retrotransposons and Retroviruses |
-transposon transcribed into mRNA
-reverse transcriptase
-interase-catalyzed 3' end cleavage
-this RNA does not carry the entire LTR sequence |
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mcs5109 Fri, 26 Sep 2008 03:54:26 GMT |
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| Replicative transposition . |
frequently causes chromosomal inversions and deletion (disadvantage for a selection) |
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mcs5109 Fri, 26 Sep 2008 03:54:26 GMT |
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| DNA transposition |
-cut and paste
-replicative |
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mcs5109 Fri, 26 Sep 2008 03:54:26 GMT |
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| There Are Multiple Mechanisms for Cleaving the Nontransferred Strand during DNA Transposition ( |
-transposons cleave 3' end of eement DNA
-different ways to cleave 5' end |
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mcs5109 Fri, 26 Sep 2008 03:47:25 GMT |
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| cut and paste |
Transposase recognizes terminal inverted repeats at the end of transposon and brings the two ends together to generate stable protein-DNA complex (synaptic complex or transpososome) |
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mcs5109 Fri, 26 Sep 2008 03:47:25 GMT |
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| Elements of DNA transposons |
terminal inverted repeat (recombinase sites)
transposase (integrase)
additional genes like AB resistance |
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mcs5109 Fri, 26 Sep 2008 03:47:25 GMT |
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| transposon frequency |
More than 50 % of both the human and maize genomes are composed of transposon-related DNA sequence |
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mcs5109 Fri, 26 Sep 2008 03:47:25 GMT |
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| Ftks |
-cell division protein
-if FTKs unavailable, only 2 XerC active and cleave
-can't fully separate
-goes back to original position a lot
-when FTKs is available, 2nd pair of XerD cleaves and separates |
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mcs5109 Fri, 26 Sep 2008 03:31:41 GMT |
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| Xer |
-tyrosine kinase
-cell division protein: Ftsk
-XerC and XerD
-XerC always cleaves
-need FTKs for XerD to work |
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mcs5109 Fri, 26 Sep 2008 03:31:41 GMT |
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| Resolvases (site-specific recombinases) |
generate monomeric DNA molecule from dimer.
How resolvases carry out directional selectivity (coupled with cell division) of the recombination reaction? |
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mcs5109 Fri, 26 Sep 2008 03:31:41 GMT |
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| Site-specific DNA bending protein, Fis |
stimulates the rate of recombination ~1,000-fold (When Fis protein is present, the three-segment complex “invertasome” can form, Fig. 11-14). |
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mcs5109 Fri, 26 Sep 2008 03:23:12 GMT |
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| Salmonella Hin recombinase |
is common in bacteria, known as programmed rearrangement. It changes expression of two alternative form of flagellin (H1 and H2 forms). |
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mcs5109 Fri, 26 Sep 2008 03:23:12 GMT |
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| Phage l Excision Requires a New DNA-Bending Protein |
(called architectural protein) |
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mcs5109 Fri, 26 Sep 2008 03:23:12 GMT |
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| Tyrosine Recombinases |
requires four subunits of Cre, each subunit bound to one binding site on the substrate DNA molecules
-Two fold symmetry instead of four (“one strand at a time” exchange mechanism).
-active sites switch thing |
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mcs5109 Fri, 26 Sep 2008 03:23:12 GMT |
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| Tyrosine Recombinases |
-makes 2 breaks
-Cleave and rejoin two DNA strands first and then cleave and region the other two strands
Four molecules of recombinase are needed
-Holiday junction intermediate |
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mcs5109 Fri, 26 Sep 2008 03:18:10 GMT |
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| Serine Recombinases |
-DSBs in both DNAs
-cleave all four strands
A minimum of four subunits (that is a tetramer) of the recombinase is required
-just flip the DNA after cleavage |
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mcs5109 Fri, 26 Sep 2008 03:18:10 GMT |
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| serine recombinase; and 2) tyrosine recombinases. |
-covalent protein-DNA intermediate
-site specific
-no external energy (e.g. ATP-hydrolysis) is needed for DNA cleavage and rejoining. |
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mcs5109 Fri, 26 Sep 2008 03:18:10 GMT |
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| Site-Specific Recombination |
insertion, delietion, inversion |
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mcs5109 Fri, 26 Sep 2008 03:18:10 GMT |
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