Mouse Genetics and Transgenics A Practical Approach

by Jackson, Ian J.; Abbott, Catherine M.

• ISBN13: 9780199637096
• ISBN10: 0199637091
• Format: Hardcover
• Copyright: 2000-03-09
• Publisher: Oxford University Press

Summary

This unique book integrates knowledge from a wide range of expertise, specifically applied to the mouse and addressed at a wide audience from those new to the field to experts who want an update on the state of the art. Mouse Genetics and Transgenics: A Practical Approach covers all aspects of using the mouse as a genetic model organism: care and husbandry; archiving stocks as frozen embryos or sperm; making new mutations by chemical mutagenesis; transgenesis; gene targeting; mapping mutations and polygenic traits by cytogenetic, genetic, and physical means; and disseminating and researching information via the Internet.

Table of Contents

List of Contributors	xxi
Abbreviations	xxiii
Mouse care and husbandry	1	(26)
Colin M. Hetherington
Brendan Doe
Donald Hay
Introduction	1	(1)
Housing	1	(7)
Types of facilities	1	(1)
Conventional accommodation	1	(1)
Barrier accommodation or specified pathogen free	1	(1)
Germ-free (axenic) and gnotobiotic accommodation	2	(1)
Maintenance of pathogen-free animals	2	(1)
Breeding performance and production	2	(1)
Interpretation of data	2	(1)
Collaborative experiments	2	(1)
Health screening	3	(1)
Quarantine	3	(1)
Flexible film isolators	4	(1)
Individually ventilated cage (IVC) racks	4	(1)
Fumigation	5	(3)
Husbandry	8	(3)
Caging	8	(1)
Bedding	9	(1)
Diet	9	(1)
Water	10	(1)
Environmental control	10	(1)
Environmental enhancement	10	(1)
Animal identification	11	(5)
Ear punch	11	(1)
Toe clip	11	(1)
Ear tags	11	(1)
Tail and paw tattooing	11	(3)
Electronic tags	14	(2)
Record keeping	16	(1)
Breeding systems	16	(4)
Timed mating	17	(1)
Pseudopregnancy and vasectomy	18	(1)
Superovulation	19	(1)
Rederivation	20	(4)
Euthanasia	24	(1)
Transportation	24	(1)
Legislation	24	(3)
Acknowledgements	25	(1)
References	25	(1)
Further reading	25	(2)
Cryopreservation and rederivation of embryos and gametes	27	(34)
Peter H. Glenister
William F. Rall
Introduction	27	(1)
Proliferation of mouse models	27	(2)
Long-term maintenance of mouse models	28	(1)
Cryopreservation and banking of mouse germplasm: resources for future research	28	(1)
Principles of cryopreservation	29	(4)
Controlled freezing	30	(2)
Vitrification	32	(1)
Skills required for embryo and gamete cryopreservation	33	(1)
Special equipment required for cryopreservation	34	(1)
Cryopreservation and recovery of mouse embryos	34	(12)
Source of embryos and preferred developmental stages	35	(1)
Freezing embryos using propylene glycol as cryoprotectant	36	(3)
Recovery of embryos and live mice from embryos frozen according to Protocol 2	39	(1)
Freezing embryos using glycerol as cryoprotectant	40	(2)
Vitrification of embryos in vitrification solution VS3a	42	(2)
Recovery of embryos and live mice from embryos cryopreserved according to Protocols 4 and 5	44	(2)
Cryopreservation and recovery of mouse gametes	46	(7)
Cryopreservation of mouse metaphase II oocytes	47	(1)
Recovery of oocytes frozen using Protocol 7	48	(1)
Cryopreservation of mouse sperm	49	(2)
In vitro fertilization of mouse oocytes	51	(2)
Hints and tips	53	(2)
Embryo cryopreservation	53	(1)
Sperm cryopreservation and in vitro fertilization	54	(1)
Long-term storage of embryos and gametes	55	(2)
Expected overall survival of cryopreserved embryos and gametes	55	(2)
Genetic resource banks	57	(4)
Acknowledgements	58	(1)
References	58	(3)
Spatial analysis of gene expression	61	(26)
Stefan G. Nonchev
Mark K. Maconochie
Introduction	61	(1)
Dissection of post-implantation embryos	62	(1)
Whole-mount non-radioactive in situ hybridization	63	(9)
Precautions for RNA work	63	(1)
Theory of in situ hybridization	64	(1)
Generation of riboprobe	65	(2)
Fixation and pre-treatment of embryos	67	(1)
Hybridization and removal of non-specific hybrids	68	(1)
Immunodetection of signals	69	(2)
Troubleshooting	71	(1)
Reporter transgenes	72	(5)
General considerations	72	(1)
Introduction and uses of reporter genes	72	(1)
Detection of β-galactosidase activity	73	(1)
Detection of alkaline phosphatase activity	74	(1)
Use of the green fluorescent protein (GFP) in transgenesis	75	(2)
Multiple and combined detection systems	77	(6)
Whole-mount staining of early (8.0--12.5 dpc) embryos	77	(1)
Multiple detection on cryostat and paraffin sections	78	(5)
Whole-mount skeletal analysis	83	(4)
Acknowledgements	85	(1)
References	85	(2)
Mapping phenotypic trait loci	87	(34)
Benjamin A. Taylor
Introduction	87	(1)
Rationale for mapping	87	(1)
Genetic definition of trait locus	87	(1)
Identification of candidate genes	87	(1)
Genetic manipulation	87	(1)
Background information for mapping phenotypic trait loci of the mouse	88	(1)
Definitions	88	(1)
Mouse genome	89	(1)
Mapping basics	89	(1)
A backcross mapping experiment: a model for simple mapping experiments	89	(11)
Identifying the phenotypic variant	89	(1)
Choosing a tester strain	90	(2)
Mating mutant and tester stock to produce F1 progeny	92	(1)
Producing backcross progeny	92	(1)
Classifying progeny for the target locus	93	(1)
Extracting a DNA sample	93	(1)
A linkage testing plan	93	(2)
Genotyping a subset of backcross progeny for selected markers	95	(1)
Recording data	96	(1)
Scanning data for linkage	96	(1)
Finding markers that flank the target	97	(1)
Finding closer markers	97	(1)
Analysing the complete data set to determine gene order and distance	97	(1)
Reporting linkage data	98	(1)
Size of cross	99	(1)
Markers for fine mapping	100	(1)
Incomplete penetrance, phenocopies and reduced viability	100	(1)
Mapping by intercross	101	(1)
QTL mapping, including the use of derivitive strains	102	(10)
General nature of QTL mapping	102	(1)
QTL mapping using strain crosses	103	(1)
Strain selection	103	(1)
Backcross versus intercross	103	(1)
Number of progeny	104	(1)
Marker spacing	104	(1)
Selective genotyping	105	(1)
Significance thresholds	106	(1)
Confidence intervals	107	(1)
Fine mapping QTLs	107	(1)
Selective phenotyping	107	(1)
Progeny testing	108	(1)
Congenic strain construction	108	(1)
Advanced intercross populations	108	(1)
Derivative inbred strains for QTL mapping	109	(1)
Recombinant inbred strains	109	(2)
Congenic strains	111	(1)
Recombinant congenic strains	111	(1)
Consomic strains	112	(1)
Markers	112	(2)
DNA pooling	114	(7)
Acknowledgements	118	(1)
References	118	(3)
Mapping genomes	121	(22)
Paul Denny
Stephen D. M. Brown
Introduction	121	(1)
Applications of genetic and physical mapping	122	(2)
Genetic mapping	124	(7)
Types of genetic marker	124	(1)
Genotyping using silver-staining of SSCP gels	124	(2)
Genotyping using fluorescently-labelled dCTP incorporation into PCR products from SSLP markers, for analysis on ABI sequencers	126	(2)
Linking different maps together	128	(1)
Generating new genetic markers in specific genomic regions	129	(2)
Criteria for making the decision to construct physical maps	131	(1)
Physical mapping	131	(12)
Introduction to physical mapping	131	(1)
Primary contig generation	132	(2)
Clone identification using hybridization assay	134	(2)
Chromosome walking/gap filling	136	(1)
Isolating insert end sequences	136	(2)
Validation of clone contigs	138	(2)
Acknowledgements	140	(1)
References	140	(3)
Mouse cytogenetics and FISH	143	(1)
Introduction	143	(1)
Analysing mouse chromosomal rearrangements with G-banded chromosomes	144	(10)
Ellen C. Akeson
Muriel T. Davisson
Introduction	144	(1)
Metaphase chromosomes	144	(4)
Stimulation of peripheral mouse lymphyocytes by phytohaemagglutinin and lipopolysaccharide	148	(1)
Phytohaemagglutinin	148	(1)
Lipopolysaccharide	149	(1)
G-bands	149	(2)
Identifying and karyotyping mouse chromosomes	151	(1)
Recognizing aberrant chromosomes	152	(2)
Acknowledgement	153	(1)
References	153	(1)
Fluorescent in situ hybridization (FISH) to mouse chromosomes	154	(17)
Margaret Fox
Sue Povey
Introduction	154	(1)
FISH and chromosome identification	154	(1)
Repeat DNA	154	(1)
Mouse chromosome paints	155	(1)
P1 probes	155	(1)
Obtaining mouse chromosomes	155	(3)
Probes and labelling	158	(2)
DNA	158	(1)
Labelling by nick translation	158	(1)
Chromosome paints and direct labelling	159	(1)
FISH	160	(7)
Probe preparation	160	(2)
Hybridization	162	(5)
Analysis and microscopy	167	(4)
References	169	(2)
Electronic tools for accessing the mouse genome	171	(14)
Janan T. Eppig
Introduction	171	(1)
Databases of genomic information for the mouse	171	(4)
The Mouse Genome Database (MGD)	171	(4)
The MRC Mammalian Genetics Unit	175	(1)
Specific data sets for genetic, radiation hybrid and physical mapping	175	(3)
Genetic data	175	(1)
The Whitehead Institute/MIT map	175	(1)
EUCIB	175	(1)
Jackson Laboratory backcross	176	(1)
Copeland-Jenkins interspecific backcross	176	(1)
M. Seldin interspecific backcross	176	(1)
Radiation hybrid data	176	(1)
The Jackson Laboratory mouse radiation hybrid database	177	(1)
The EBI radiation hybrid database	177	(1)
Physical mapping data	177	(1)
Genome-wide physical map	177	(1)
X-Chromosome physical map	177	(1)
Gene expression data	178	(1)
The Gene Expression Database (GXD)	178	(1)
The mouse 3D atlas	178	(1)
Databases of transgenics, knock-outs and other induced mutations	179	(1)
The transgenic/targeted mutation database (TBASE)	179	(1)
Mouse Knockout and Mutation Database (MKMD)	179	(1)
Induced mutant resource (IMR)	179	(1)
Animal resources lists	180	(1)
International mouse strain resource (IMSR)	180	(1)
The Jackson Laboratory: JAX mice IMR, MMR, DNA resource	180	(1)
European Mouse Mutant Archive (EMMA)	181	(1)
mgi-list, an electronic bulletin board for the mouse community	181	(1)
Summary	181	(4)
References	182	(3)
Mutagenesis of the mouse germline	185	(32)
Monica J. Justice
Introduction	185	(1)
Mouse mutagenesis	185	(6)
Spontaneous mutations	185	(1)
Systems for assessing mutation rate	186	(1)
Reporter genes	186	(1)
Specific locus test	187	(1)
Dominant phenotype assays	188	(1)
Other assays	188	(1)
Developing a mouse mutant resource	188	(1)
Determining functional complexity of genomic regions	189	(1)
Human disease models	189	(1)
Allelic series	190	(1)
Unravelling biochemical or developmental pathways	190	(1)
High-efficiency mutagenesis with N-ethyl-N-nitrosourea	191	(10)
Mode of action	191	(1)
ENU: chemical properties, stability and half-life	191	(1)
Types of DNA lesion caused by ENU	191	(1)
Effects on protein products	192	(1)
Induction of mutations in the mouse germline	192	(1)
Doses and treatment protocols	192	(4)
Genetic screens to isolate mutations	196	(1)
Dominant mutations	196	(1)
Single-locus screens for recessive mutations	197	(1)
Three-generation breeding scheme for recessive mutations	197	(2)
Two-generation breeding scheme using deletions	199	(1)
Modifiers and sensitized pathways	200	(1)
Practical considerations for ENU mutagenesis	201	(8)
Breeding considerations	201	(1)
Male rotations	201	(2)
Gamete sampling for spermatogonial stem-cell mutagenesis	203	(3)
Strain background effects	206	(1)
Inbred strains to use for mutagenesis	206	(1)
F1 hybrids	207	(1)
Other observations	208	(1)
Rate of recovery to fertility	208	(1)
Mutation rates for different loci	208	(1)
Cancer susceptibility and lifespan	208	(1)
Other mutagens	209	(2)
Radiation mutagenesis	209	(1)
X-rays: treatment and mutations recovered	209	(1)
Other types of radiation	210	(1)
Chlorambucil	210	(1)
Future prospects	211	(6)
DNA repair	211	(1)
Sequence-based screening for lesions	211	(1)
The future of mutagenesis	211	(1)
References	212	(5)
Generation of transgenic mice from plasmids, BACs and YACs	217	(30)
Annette Hammes
Andreas Schedl
Introduction	217	(4)
Principles and general considerations	217	(1)
Difficulties and limitations	218	(1)
Construct design	219	(1)
Perspectives	220	(1)
Factors influencing the efficiency of transgenesis	220	(1)
Choice of mouse strains	221	(1)
DNA isolation	221	(7)
Plasmid DNA	221	(2)
YAC DNA	223	(3)
BAC DNA	226	(1)
Testing the DNA concentration and quality	227	(1)
The microinjection set-up	228	(4)
Location and design of the injection table	229	(1)
Microscope	230	(1)
Micromanipulators	230	(1)
The holding pipette	231	(1)
Microinjection needles	231	(1)
The microinjection experiment	232	(8)
Superovulation and isolation of fertilized oocytes	232	(2)
Microinjections	234	(1)
Timing of injections	234	(1)
Injections	234	(2)
Oviduct transfer	236	(1)
Pseudopregnant females	236	(1)
Preparation of the transfer pipette	237	(1)
Oviduct transfer	238	(2)
Analysis of transgenic founders	240	(7)
Tail tipping and ear punching	243	(1)
Isolation of genomic DNA from tail biopsies	243	(2)
Southern blot analysis	245	(1)
References	245	(2)
Directed mutagenesis in embryonic stem cells	247	(38)
Antonius Plagge
Gavin Kelsey
Nicholas D. Allen
Introduction	247	(2)
Basic elements of construct design	249	(5)
Replacement versus insertion	249	(1)
Regions of homology	250	(1)
The mutation	251	(1)
Components of the targeting cassette	251	(1)
Enrichment for targeted events	252	(1)
Screening strategies	253	(1)
Alternative approaches for construct design	254	(1)
The use of site-specific recombinases in targeting	254	(9)
Excision of heterologous DNA from a targeted locus	255	(1)
Excision from ES-cell clones with recombinase expression plasmids	256	(1)
Excision in mice using transgenic mice expressing recombinase	257	(1)
Oocyte microinjection of recombinase	257	(1)
Use of recombinases to generate conditional somatic knock-outs	257	(1)
Spatially restricted knock-outs using tissue specific promoters to drive recombinase expression	258	(1)
Temporally regulated knock-outs using inducible recombinases	259	(3)
Knocking-in: recombinase mediated integration into chromosomally positioned target sites	262	(1)
Subtle mutations without site-specific recombinases	263	(2)
Double replacement	264	(1)
`Hit-and-run'	265	(1)
Chromosome engineering in ES cells	265	(3)
Deletions, inversions and duplications	265	(3)
Translocations	268	(1)
Generating, analysing and maintaining knock-out mice	268	(17)
ES-cell culture and pluripotency	268	(1)
Analysis of ES-cell potency in chimeras with tetraploid embryos	269	(1)
Equipment for injection of ES cells into embryos	269	(2)
Host embryos	271	(1)
Blastocyst injection	272	(3)
Morula injection	275	(2)
Morula aggregation	277	(1)
Transfer of embryos to the uterus	278	(1)
Genetic background	279	(1)
Maintenance of mutations as co-isogenic and congenic lines and mutant analysis in a hybrid background	280	(1)
Chimera analysis	281	(1)
Acknowledgements	282	(1)
References	282	(3)
List of suppliers	285	(5)
Index	290