molecular genetics (분자유전학 -...
TRANSCRIPT
Molecular genetics (분자유전학)
담당교수 : 최제용
2010년 2학기
Mouse mutagenesis
Mouse mutagenesis
Mouse mutagenesis
Reverse genetics approach
• Gene-driven approach
• well known sequence and structure of a target gene
• Tools
- Gene targeting
- gene-trap mutagenesis
- RNAi mediated knockdown
- ENU in vitro
Generation of KO mouse mutants by gene targeting in ES cells
- Establishment of ES cell line
- Germline transmission in chimeric mice
- Homologous recombination
Establishment of ES cells
- Establishment of ES cell line
- Germline transmission in chimeric mice
- Homologous recombination
ES cell mutagenesis and chimera production
Target vector construction
- Establishment of ES cell line- Germline transmission in chimeric mice
- Homologous recombination
- ET- Recombineering
Web-based resources for mouse mutagenesis
Web-based resources for mouse mutagenesis
Conditional knockout
Cre-loxP system
Chromosomal engineering
Principle of conditional gene targeting using the Cre/loxP recombination system.
Establishment of ES cells
- Establishment of ES cell line
- Germline transmission in chimeric mice
- Homologous recombination
ES cell mutagenesis and chimera production
Target vector construction
- Establishment of ES cell line- Germline transmission in chimeric mice
- Homologous recombination
- ET- Recombineering
Screen genomic library for genomic clone
Select for insertion event
Isolate surviving clones and screen DNA
Blastocyst Injection
Chimeric mice
Breed heterozygous mice to produce homozygous mouses
Transfection by electroporation
Prepare Primary Embryonic Fibroblasts
Grow ES cells on fibroblast feeder layer
Construction of targeting vector
Cre recombinase- consists of 4 subunits and two domains
- larger carboxyl (C-terminal) domain catalytic site
: similar in structure to the domain in the Integrase family of enzymes isolated
from l phage
- smaller amino (N-terminal) domain
- recombination of DNA between specific sites in a DNA molecule (LoxP)
Lox P site (from phage 1)
13bp 8bp 13bp
ATAACTTCGTATA -GCATACAT-TATACGAAGTTAT
Cre-Lox recombination
A.
Cre
LoxP LoxPGene Insert
+
Insert
Excision
Integration
LoxP LoxPGene Insert
LoxP LoxPGene Insert
B.
inverstion Cre
FLP-Frt recombination
- Site-directed recombination technology used to manipulate an organism's DNA under
controlled conditions in vivo and in vitro.
34bp long FRT site sequence
: derived from the S. cerevisiae 2mm DNA plasmid,
a selfish genetic elements present in about 60 copies/cell
Flipase(FLP) binding site
5'-GAAGTTCCTATTCtctagaaaGTATAGGAACTTC-3'.
FRT FRT
FRT FRT
FRT FRT
+
A. Inversion B. Excision/Integration
Recombineering
Utilizes the efficient homologous recombination functions encoded by λphage or cryptic phage Rac to perform DNA manipulation in E. coli.
Bacteriophage λengages in homologous recombination during its lyticcycle, even in a recombination-deficient host, through expression of its red genes (1968)
E. Coli has multiple recombination pathways.
• RecBCD pathway
• RecE pathway
• RecF pathway
Bacteriophage λ
• Red recombination system
IntegrationExcision
HomologousRecombination
Early Regulation
DNAReplication
?
LateRegulation
Lysis
Head
Tail
Int, xis
Red system:Exo, bet, gam
N, cI, cro, cII
O, P
Nin region:orf, rap
Q
S,R
NuJ-FII
Z-J
λ genes
Recombineering
Three λ phage Red proteins
Gam
• inhibits RecBCD and SbcCD exonuclease activities of E. Coli
• preserving linear dsDNA and allowing it to be used as a substrate for R
Beta
• a single-stranded DNA binding protein that promotes annealing of cDNA strands
• bind to ssDNA longer than 35 bp, and can protect ssDNA overhangs fromsingle-strand nuclease degradationmake it possible to use only about 50 nt of homology for efficient
recombination
Exo
• dsDNA-dependent 5’-3’ exonuclease that processes linear dsDNA and generate a 3’ ssDNA overhang at each end, the substrate that Beta binds.
RecombineeringRecBCD nuclease
Gam
MC1-TK Amp Ori
Exon 3
BAC
Retrieve of genomic DNA of interst into vector
PCR
MC1-TKAmpOri
Electrophoration into SW102
Containing retrieved exon 3
PL452
MC1-TKAmpOri
Electrophoration
into SW102
Insertion of 1st loxP site into retrieved vector
MC1-TKAmpOri
Electrophoration into SW106
expressing Cre recombinase
MC1-TKAmpOri
Re-electrophoration into SW102
: LoxP
MC1-TKAmpOri
NEO
MC1-TKAmpOri
NEO
Insertion of 2nd loxP site into retrieved vector
: LoxP
: Frt
neo
Amp
Runx2 conditional knockout vector
Electrophoration
Embryo transfer
LoxP
Frt
Runx2Exon3
ES cell
Blastocyst
Runx2 Conditional Knockout mouse
105002 3
121100127100137100143100
22500
BstXI
121864122910135750139494140445
Not1
137100
SpeI
122368128474142610 140945
BamHI
128616134616
XbaI
131100 125100140100 134100
Sep 29’ 06
129100 123100
Procedure
1. Transformation of Bac DNA into SW102
2. Retrieving genomic DNA from SW102 containing Bac clone- PCR with long primers- Temp: PL253- Electroporation of linear gap repair plasmid- Selection in Amp LB plate and plasmid DNA extraction- Retransformation of gap repaired plasmid (1ng) into SW102- Confirmation of retrieved gDNA by restriction mapping
3. Targeting the first loxP site into the subcloned plasmid DNA- mini-targeting cassettes for inserting loxP (loxP cassette)
5’ 42bp-hm_RE(6)_loxP(34)_cgacctgcagcctgttga-3’
5’ 48bp-hm(rv)_rv-loxP(34)_gtcgaggctgatcagcga-3’
PCR; 1-2 ng template (PL452), 25 cycles, 1-2 ul DpnI 1h at 37 and gel puri O/N- electroporation of mini-loxP cassette into SW102 containing retrieved gDNA- kanamycin (due to Neo) plate and DNA confirmation- Cre-mediated “pop-out” of this cassette after electroporation into SW106
4. Targeting the second loxP site - mini-targeting cassettes for inserting Frt-Neo-Frt-loxP (2-loxP cassette)
5’ 48bp-hm_gaagttcctattctctagaaagtataggaacttcaggtctgaagaggagttt-3’
5’ 50bp-hm_ataacttcgtatagcatacattatacgaagttatattatgtacctgactg-3’
PCR; 1-2 ng template (PL451), 25 cycles, 1-2 ul DpnI 1h at 37 and gel puri O/N- electroporation of 2-loxP cassette into SW102 containing 1st loxP inserted gDNA
1칸=5kb
3’-6-10kb 정도downstream
T7
SP6
Display
View Evidence
View Evidence
Restriction Mapping of BAC
0 100 200 239 Kb120 140 160 18020 40 60 80 220
BH1
SalI
XhoI
NotI
SacII
MluI
ClaI
Recombineering
Bac DNA Confirm
Retrieving of gDNA
Plate test
Bac DNA Prep
The first loxP site
Pop-out floxed neo
The 2nd loxP site
20 30 10 20 30
Primers
1. Targeting the first loxP site into the subcloned plasmid DNAupper: 42bp(hm)_NdeI(6)_loxP(34)_cgacctgcagcctgttga-3’
lower: 48bp(rvhm)_rvloxP(34)_gtcgaggctgatcagcga-3’
(1st-LoxP-Upp)5’-ccggcgggcggcggcagcggctgcgatccgcaggctccagat_catatg_
ataacttcgtataatgtatgctatacgaagttat_cgacctgcagcctgttga-3’
(1st-LoxP-Low)5’-tgccgggaggtaagtgggggcggggggagagcggatctcggggcgacag_
ataacttcgtatagcatacattatacgaagttat_gtcgaggctgatcagcga-3’
2. Targeting the second loxP siteUp:48bp(hm)_gaagttcctattctctagaaagtataggaacttcaggtctgaagaggagttt-3’
Lo:50bp(hm)_ataacttcgtatagcatacattatacgaagttatattatgtacctgactg-3’
(2nd-LoxP-Upp)5’-cattttgcctgggaggaaaagggaatcctgtggagcaacttcggttgg_
gaagttcctattctctagaaagtataggaacttcaggtctgaagaggagttt-3(2nd-LoxP-Low)5’-agttctggctctttcaaggcaaataaagttttcacctctgtttattctga_
ataacttcgtatagcatacattatacgaagttatattatgtacctgactg-3’
5’ probe
RV RV
gDNAfrom Bac
Neo
7.1 kb
8.1 kb
7.1 kb
MC1 TK
MC1 TK
6.0 kb
MC1 TK
Neo
MC1 TK
MC1 TK
RV RV
3.1 kb
4.1
6.0 kb
1.1
MC1 TK
4.0 kb
3.1kb
3.1 kb
3.1 kb
3.1 kb
3.1 kb
MC1 TK
NeoSpeI
SalI
pSK+
SalI
NeoSpeI
5’ probe 3’probe
Conditional target vector
Genomic locus
Targeted allele
BamHI
gDNAfrom Bac
Neo
11 kb
MC1 TK
MC1 TK
5.8 kb
MC1 TK
Neo
MC1 TK
MC1 TK
BamHI
MC1 TK
6.6 kb
7.2 kb
10 kb
10 kb
5.8 kb
4.2 kb
NdeI
NdeI
NdeI
NdeI
NdeI
MC1 TK
NeoNdeI
SalI
pSK+
SalI
NeoNdeI
5’ probe 3’probe
Conditional target vector
Genomic locus
Targeted allele
16.5 kb
NdeI NdeI
4.6 kb
BamHI
12.5 kb
BamHI
1kb
3260 bp
2511bp
5.8 kb
BamHI BamHI
3.0 kb
ZMCTK
2
SpeI/BamHI/XbaIBstXI/NotI Hind3
5’-NotI-homology-Hind3-3’ 5’-Hind3-homology-SpeI-3’
5’ 3’
Plasmid: PL253
Primers:
Cloning of Runx2-Ex2-Retriving vector via three-way ligation
Fragements elusion, restriction digestion and three-way ligation
Sep 29’ 06
Primer A:NotIRunx2-Ex2-Ret-5’-15’-ATAAGCGGCCGCGTCGACGGGAAAGCAAGGAGAGAGAG-3’
Primer B:H3Runx2-Ex2-Ret-5’-2----- 939bp (39+900)5’-GTCAAGCTTACTGCTGCCATGAAATGCTAAGTCTCTTAG-3’
Primer Y:H3Runx2-Ex2-Ret-3’-15’-GATAAACATGGTTGGGAATATTCAAAGGAGA-3’
Primer Z:SpeIRunx2-Ex2-Ret-3’-2----702bp(40+660+2)5’-ACTACTAGTGGTAAGCATCCGTTAAGAGTG-3’
A B Y
2
SalI
BstXI/Not1I
Cloning of Retrieved E3 Vector (RE3 vector) via long primers
R2-Ex2-Ret-5’-Upper (Hm50-NotI-template24)795’-AATCACAAGTATATAAAATAATGTGGAAGGAGTTAGGACGGGAAAGCAAG-CGGCCGC-TCTAGCCTCGAGGCTAGAACTA-3
R2-Ex2-Ret-3’-Lower (rvHm50-SalI-rvtemplate 24)805’-AGTGGTAAGCATCCGTTAAGAGTGTCACTGTGTATGTGATGCCTCACAGC-GTCGAC-tcgtattacaattcactggccgtc-3’
Mc1-TKAmp
BAC
NarI-NheI-ClaI-SalI-KpnI
McTK Amp 5350 bp
Ori
/SpeI/BamHI/Xba
Mini-targeting cassettes for inserting loxP and Frt-neo-Frt-loxP
1st targeting and 2nd targeting step
Primer C:SalIRunx2-Ex2-Mini-5’L-1 (PL452)5’-GTCGTCGACTCAAAGGGGGAGGGCACAGGAGTG-3’ 33mersPrimer D:RIRunx2-Ex2-Mini-5’L-2 (PL452)---323bp(40+240+43)5’-GTCGAATTCAGCAAGGGACCTGTCATGACCCT-3’ 32mersPrimer E:BamHRunx2-Ex2-Mini-5’R-1 (PL452)5’-ATAGGATCCGGCGGATTTCCCGGCTTCTGTGGG-3’ 33mersPrimer F:NotIRunx2-Ex2-Mini-5’R-2 (PL452)---343bp(58+240+45)5’-ATAAGCGGCCGCGTTATGGGGGGAGGCGATTTTGG-3’ 35mersPrimer G:SalRunx2-Ex2-3’L-1 (PL451)5’-GTCGTCGACTCACCCTAATAGTTTCATCTCTCTG-3’ 34mersPrimer H:RIRVRunx2-Ex2-3’L-2 (PL451)---332bp(27+240+65)5’-GTCGAATTCGATATCCTGCTTTCCACCTGACAA-3’ 33mersPrimer I:BamHRunx2-Ex2-3’R-1 (PL451)5’-ATAGGATCCAAAAATACAAGACAGCTAGTAGTCTTCA-3’ 37mersPrimer J:NotRunx2-Ex2-3’R-2 (PL451)---334bp(52+240+42)5’-TAAAGCGGCCGCTACTAGATGCAGGGTCAATGTG-3’ 34mers
MC1-TKAmpOri
PL253
BAC clone
MC1-TKAmpOri
Recombineering
Homologous region 1
Homologous region 2
그림1.
MC1-TKAmpOri
neo
neo
PCR Electrophoration into SW102 containing retrieved gene X
PL452
MC1-TKAmpOri
neo
Electrophoration into SW106expressing Cre recombinase
그림2.
neo Neomycin gene
loxP site
Homologous region 3
Homologous region 4
PCR from PL451neo
그림3.
neo
Electrophoration into SW102 containing first loxP site
neo
neo Neomycin gene
Homologous region 5
Homologous region 6
FRT site
neo pX-FRT
pX-ΔFRT
pX-Δexon
pX-ret : PL253 retrieved vectorpX-neo : PL253 retrieved vector containing 1st neo cassette floxed loxP sitepX-Δneo : PL253 retrieved vector containing 1st loxP sitepX-FRT : PL253 retrieved vector containing 2nd neo cassette franked FRT sitepX-ΔFRT : PL253 retrieved vector deleted 2nd neo cassettepX-Δexon PL253 retrieved vector deleted exon of gene X
A.
B.
그림4.
Chan W et al., NAR 35, e64, 2007
Recombineering of interesting gene
Tools for targeted manipulation of the mouse genome
Van der Weyden, David J Adams and Allan Bradley
Physiol Genomics 11:133-164, 2002
Procedure for the generation of genetically modified mice generated by gene targeting strategies
Examples of some commonly used dominant selectable markers
FIAU, 1(1-2-deoxy-2-fluoro-b-d-arabinofuranosyl)-5-iodouracil
Replacement and insertion type vectors
Replacement vector
Insertion vector
Hit-and-run targeting procedure
“Double replacement” targeting
Tetracycline-responsive regulatory system for transcriptional transactivation
Knock-in strategies
Mechanisms for generating mosaics in vitro and in vivo
Genetic mosaics are individuals that contain cells of more than one genotype,Whereas chimeras refer to individuals that are formed from cells of differentSources.
Genetic mosaic s are generated when mitotic recombination b/w homologousChromosomes occurs during the G2 phase of the cell cycle and the recombinant Chromatids segregate to different daughter cells: (X segregation).
Recombinant chromatids produced in G2 can also segregate to the same daughter cell, (Z segregation). In this case, both daughter cells will be phenotypicallyIndistinguishable from the parent cell or from cells produced by G1 recombination
Z segregation is thus not useful for genetic mosaic analysis.
Mechanisms for generating mosaics in vitro and in vivo
Mechanisms for generating mosaics in vitro and in vivo
Mechanisms for generating mosaics in vitro and in vivo
Mechanisms for generating mosaics in vitro and in vivo
Recombinase target sites
Gene targeting in ES cells
Generation of defined chromosome rearrangements
Nested chromosomal deletions induced with a retroviral vector
Recombineering steps to generate a BAC recombinant
Large-scale dominant and recessive ENU-induced mutation screens
ENU-induced mutagenesis screens for mouse chromosome 11 using
chromosomal engineering technology
The basic trap vectors
Large-scale gene trapping projects