Methods in Cell Biology - GBV · Methods in Cell Biology VOLUME 77 The Zebrafish: Genetics,...
Transcript of Methods in Cell Biology - GBV · Methods in Cell Biology VOLUME 77 The Zebrafish: Genetics,...
Methods in Cell Biology
VOLUME 7 7
The Zebrafish : Genetics, Genomics, and Informatics
H. William Detrich, III
Monte Westerfield
Leonard I . Zon
Contributors
xv
Preface
Dedication
-cv
PART I Forward and Reverse Genetics
1 . Retroviral-Mediated Insertional Mutagenesis in Zebrafish
Adam Amsterdam and Nancy Hopkins
I. Introduction
3
II. Mutagenesis
5
III. Cloning the Mutated Genes
8
IV. Future Directions
1 4
References
1 8
2 . Genetic Screens for Maternal-Effect Mutations
Francisco Pelegri and Mary C . Mullins
I. Introduction
22
II. Strategies for Maternal-Effect Screens
23
III. Selection of Lines for Genetic Screens
3 3
IV. Recovery and Maintenance of Maternal-Effect Mutations
3 7
V. Mapping Maternal-Effect Mutations
4 1
VI. Solutions, Materials, and Protocols
44
VII. Conclusions
48
References
49
3 . Behavioral Screening Assays in Zebrafis h
Michael B . Orger, Ethan Gahtan, Akira Muto, Patrick Page-McCaw, Matthew C . Smear,
and Herwig Baier
I . Introduction
53
IL General Considerations
54
III. Behavioral Assays
5 6IV. Conclusions
6 6
References
6 6
4 . Target-Selected Gene Inactivation in Zebrafish
Erno Wienholds and Ronald H . A . Plasterk
I. Introduction
7 0II. Gene Targeting Strategies
7 1III. Target-Selected Mutagenesis in Zebrafish
7 5IV. Discussion
83V. Materials and Methods
8 5
References
87
5 . A High-Throughput Method for Identifying N-Ethyl-N-Nitrosourea (ENU)-Induce dPoint Mutations in Zebrafish
Bruce W. Draper, Claire M . McCallum, Jennifer L . Stout, Ann J. Slade, and Cecilia B . Moens
I. Introduction
92II. Rationale for Reverse Genetics in Zebrafish
95III. Rationale for Using the CEL1 Assay to Detect Induced Mutations
9 6IV. Rationale for Generating a Cryopreserved Mutant Library
9 8V. Method of N-Ethyl-N-Nitrosourea (ENU) Mutagenesis and Rearing of F l
Founder Fish
9 8VI. Generating a Cryopreserved Mutant Library
99VII. Isolating Genomic DNA
102VIII. Choosing Fragments to Screen
104IX. CEL1 Endonuclease Assay
104X. Recovery of Mutations from Cryopreserved Sperm
109XI. Materials Cost Estimate
11 0
References
11 1
6 . Production of Zebrafish Germline Chimeras by Using Cultured Embryoni cStern (ES) Cells
Lianchun Fan, Jennifer Crodian, and Paul Collodi
I. Introduction
11 3II. Methods
11 4III. Reagents
11 7IV. Future Directions
11 8
References
118
7 . Nonconventional Antisense in Zebrafish for Functional Genomics Applications
Stephen C . Ekker
I. Introduction
12 1
II. General Use of Nonconventional Antisense Tools in Zebrafish
12 3
III. Use of Morpholinos (MOs) as Antisense Tools in Zebrafish
12 5
IV. Comparison of MO-Based Screening Success to Mutational Methods
13 3
References
13 4
8 . Downregulation of Gene Expression with Negatively Charged Peptide Nucleic Acid s
(PNAs) in Zebrafish Embryo s
Eric Wickstrom, Karen A . Urtishak, Michael Choob, Xiaobing Tian, Nitzan Sternheim ,
Laura M . Cross, Amy Rubinstein, and Steven A . Farber
I. Introduction
13 8
II. Materials and Methods
143
III. Results
14 6
IV. Discussion
15 5
V. Summary
15 6
References
15 6
9 . Photo-Mediated Gene Activation by Using Caged mRNA in Zebrafish Embryo s
Hideki Ando, Toshiaki Furuta, and Hitoshi Okamot o
I. Introduction
160
II. Synthesis of Bhc-Caged mRNA
16 1
III. Microinjection of the Bhc-Caged mRNA
165
IV. Uncaging by Illumination of UV Light
167
V. Titration of Caging Efficiency
168
VI. Injection of Dimethyl Sulfoxide (DMSO) Solution of Caged mRNA
170
References
170
10 . Current Status of Medaka Genetics and Genomic sThe Medaka Genome Initiative (MGI)
Manfred Schartl, Indrajit Nanda, Manko Kondo, Michael Schmid, Shuichi Asakawa ,
Takashi Sasaki, Nobuyoshi Shimizu, Thorsten Henrich, Joachim Wittbrodt ,
Makoto Furutani-Seiki, Hisato Kondoh, Heinz Himmelbauer, Yunhan Hong,
Akihiko Koga, Masaru Nonaka, Hiroshi Mitani, and Akihiro Shim a
I. Introduction
17 4II. Current Status of Medaka Genetics
17 5
III. Current Status of Medaka Genomics
18 6
IV. Other Progress
193
V. Internet Web Sites Relevant to Medaka Resources and Databases
193References
194
11 . Transgenesis and Gene Trap Methods in Zebrafish by Using the To12Transposable Elemen t
Koichi Kawakami
I. Introduction
20 1II. Transgenesis by Using the To12 Transposable Element in Zebrafish
20 3III. A Gene Trap Approach that Uses the To12 Transposon System in Zebrafish 21 0IV. Summary and Perspectives
21 9References
22 0
PART II The Zebrafish Genome and Mapping Technologie s
12 . The Zebrafish Genome Project : Sequence Analysis and Annotation
Kerstin Jekosch
I. Introduction
22 5II. Automated Annotation of Whole Genome Shotgun (WGS) Assemblies
22 7III. Clone-by-Clone Analysis and Annotation
23 0IV. The Sanger Zebrafish Web Services
23 4V. Future Releases
23 8References
23 8
13 . Molecular Cytogenetic Methodologies and a Bacterial Artificial Chromosome (BAC )Probe Panel Resource for Genomic Analyses in Zebrafish
Charles Lee and Amanda Smith
I. Introduction
24 1II. Methods
24 2III. First-Generation Zebrafish BAC Probe Panel
24 8References
25 4
14 . Automated Analysis of Conserved Syntenies for the Zebrafish Genom e
John Postlethwait, Victor Ruotti, Michael J . Carvan, and Peter" Tonellato
I. Introduction
25 6II. The Conservation of Zebrafish and Mammalian Genomes
25 6III. Using Genome Conservation in Zebrafish Research
258
IV. Genomic Connections Between Zebrafish and Tetrapods Facilitat eDisease Research
260
V. Bioinformatic Approaches to Automating Zebrafish Connectionsand Comparative Maps
264
VI. A Conserved Syntenic Map for Zebrafish : Preliminary Results
266
VII. Conclusion
267References
268
15 . Update of the Expressed Sequence Tag (EST) and Radiation Hybrid Panel Projects
Yi Zho u
I. Expressed Sequence Tag (EST) Projects
27 4
II. Radiation Hybrid (RH) Panel Project
277
III. Future Directions
29 1
References
29 2
16 . Bacterial Artificial Chromosome (BAC) Clones and the Current Clone Map of the
Zebrafish Genome
Romke Koch, Gerd-Jörg Rauch, Sean Humphray, Robert Geisler, and Ronald Plasterk
I. Introduction
29 6
II. Physical Map of Fingerprinted Clones
29 6
III. Screening Methods and Utilization of the Current Zebrafish Clone Map
300
IV. Example : Discovery of the Zebrafish dicerl Gene
302
References
304
17 . The Zon Laboratory Guide tö Positional Cloning in Zebrafis h
Nathan Bahary, Alan Davidson, David Ransom, Jennifer Shepard, Howard Stern ,
Nikolaus Trede, Yi Zhou, Bruce Barut, and Leonard I . Zo n
I. Introduction
30 6
II. Mapping Strains
30 6
III. Families and Genetic Markers
307
IV. Crosses for Line Maintenance and Mapping
307
V. Preparation of the DNA
30 9
VI. Mapping Genes
31 0
VII. Overgo Strategy for Rapidly Doing Chromosomal Walks an d
Positional Cloning
317
VIII. Protocol for Overgo Probing of High-Density Filters
31 8
IX. General Flow of Information from the Radiation Hybrid Panel Maps ,
the Sanger Institute Sequencing Project, and Fingerprinting the BACs
32 1
X. Synteny Between Human, Zebrafish, and Fugu Genomes
325
XI. Proving a Candidate Gene Is Responsible for the Mutant Phenotype
326
XII. Morpholinos
327References
32 8
PART III Transgenesi s
18 . Lessons from Transgenic Zebrafish Expressing the Green Fluorescent Protein (GFP )
in the Myeloid Lineag e
Karl Hsu, A . Thomas Look, and John P. Kank i
I. Introduction
33 4
II. Myeloid Cells in Zebrafish
33 4
III. Expression of pu .1 in Myeloid Development
33 5
IV. Analysis of the Zebrafish pu .1 Locus
33 6
V. Germline Expression of Enhanced Green Fluorescent Protein (EGFP)
Under Control of the Zebrafish pu .1 Promoter
33 8
VI. Conclusions
345
References
346
19 . Sleeping Beauty Transposon for Efficient Gene Deliver y
Spencer Hermanson, Ann E . Davidson, Sridhar Sivasubbu, Darius Balciunas, an d
Stephen C . Ekke r
I. Introduction
34 9
II. Transgenesis Constructs
35 0
III. Microinjection of the Zebrafish Embryo
35 1
IV. Raising Injected Embryos
35 5
V. Identifying Transgenic Founders
35 6
VI. Visualizing Fluorescent Reporters
35 7
VII. Molecular Characterization of the Transposon Integration Site
35 8
References
36 1
20 . Transgene Manipulation in Zebrafish by Using Recombinases
Jie Dong and Gary W. Stuart
I. Introduction
36 3
II. Recombinase-Mediated Transgene Exchange, and Mobilization
36 7
III. Summary and Conclusion
37 5
References
376
21 . Highly Efficient Zebrafish Transgenesis Mediated by the Meganuclease I-Sce l
Clemens Grabher, Jean-Stephane Joly, and Joachim Wittbrodt
I. Introduction
38 1
II. Transgenesis by Meganucleases
38 6
References
39 8
22 . Cloning Zebrafish by Nuclear Transfer
Bensheng Ju, Haigen Huang, Ki-Young Lee, and Shuo Lin
I. Introduction
403
II. Recipes for Cell Culture and Nuclear Transfer
404
III. Cell Culture
404
IV. Nuclear Transfer
405
V. Summary of Nuclear Transfer
40 8
VI. Potential Applications of Zebrafish Cloning
409
References
410
PART IV Informatics and Comparative Genomics
23 . Data Mining the Zebrafish Genome
Lynn M. Schriml and Judy Sprague
I. Introduction
41 5
II. National Center for Biotechnology Information (NCBI) Tools ,
Resources, and Data Sets ,
41 6
III. Zebrafish Information Network (ZFIN)
42 8
IV. Tutorial
43 3
References
437
24 . The Zebrafish DVD Exchange Project: A Bioinformatics Initiative
Mark S . Cooper, Greg Sommers-Herivel, Cara T. Poage, Matthew B . McCarthy,
Bryan D . Crawford, and Carey Phillips
I. Introduction
440
II. Economic Aspects of Visual Bioinformatics
440
III. Building Infrastructures to Access Images
442
IV. Prior Experiences with Visual Data Dissemination (Mark Cooper)
443
V. Goals of the Zebrafish DVD Exchange Project
445
VI. Production of the Compact Disc (CD) Set : :"Zebrafish: The Livin g
Laboratory" (Greg Sommers-Herivel)
447
VII. Visual Bioinformatics and Databases
451
VIII. Internet2
45 2IX. Hyper Text Markup Language (HTML) and eXtensible Markup Languag e
XML (Bryan Crawford)
45 3X. Virtual Reality and Data Visualization Tools (Carey Phillips)
45 4XI. Summary
45 6References
45 7
25 . Comparative Genomics-An Application for Positional Cloning of th eweissherbst Mutan t
Anhua Song and Yi Zho u
I. Introduction
45 9II. Resources for Comparative Genomics Studies
460III. An Example of Using Comparative Genomic Resources in a Positiona l
Cloning Project
46 1References
47 3
26 . Comparative Genomics in Erythropoietic Gene Discovery : Synergisms Between th e
Antarctic Icefishes and the Zebrafish
H. William Detrich, III and Donald A . Yergea u
I. Introduction
47 6II. Representational Difference Analysis (RDA) Protocol
47 7III. Analysis of Unidentified RDA Contigs
48 5
IV. Isolation of Full-Length cDNAs Corresponding to RDA Products
49 3V. Model Hopping: Functional Analysis of the Zebrafish Ortholog of the
Novel Antarctic Fish Gene bloodthirsty
49 8VI. General Considerations
50 0References
50 1
27 . Spatial and Temporal Expression of the Zebrafish Genome by Large-Scale In Sit uHybridization Screenin g
Bernard Thisse, Vincent Heyer, Aline Lux, Violaine Alunni, Agnes Degrave, Iban Seiliez ,Johanne Kirchner, Jean-Paul Parkhill, and Christine Thiss e
I. Introduction and Goals
50 6II. Preparation of Antisense Digoxigenin (DIG)-Labeled RNA Probes
50 6III. Preparation of Embryos
50 8IV. Reagents and Buffers for In Situ Hybridization
50 9V. In Situ Hybridization Protocol
51 0VI. Double In Situ Protocol
514
VII. Recording Results
51 7
VIII. Concluding Remarks
51 7
References
51 9
28 . Design, Normalization, and Analysis of Spotted Microarray Dat a
F. B . Pichler, M. A . Black, L. C. Williams, and D . R . Lov e
I. Introduction
52 2II. Design of Microarray Experiments
52 2III. Array Preprocessing
53 0IV. Analysis of Microarray Experiments
53 5V. Discussion
54 0References
542
29. Comparative Genomics, cis-Regulatory Elements, and Gene Duplicatio n
Allan Force, Cooduvalli Shashikant, Peter Stadler, and Chris T. Amemiy a
I. Introduction
545
II. Comparative Genomics and Identification of cis-RegulatoryElements (CREs)
546III. Duplicated Genomes, Duplicated Genes
55 2References
55 6
PART V Infrastructure
30 . Zebrafish Facilities for Small and Large Laboratorie s
Bill Trevarro w
T . Introduction
566II. Zebrafish Biology
568
III. Fish Housing
569
IV. Quarantining
586V. Injections
587VI. Mutagenesis Room
587VII. Treating Outflow
588
VIII. Disposing of the Dead
588
IX. Disease Prevention
589
X. Cleaning
590XI. Human Safety
590References
591
31 . A Nursery that Improves Zebrafish Fry Surviva l
Peter Cattin and Phil Crosier
I. Introduction
59 3II. General Methods for Raising Embryos and Larvae
59 4III. A Nursery that Improves Fry Survival
59 4References
59 8
32 . Genetic Backgrounds, Standard Lines, and Husbandry of Zebrafis h
Bill Trevarrow and Barrie Robison
I. Introduction
599II. Nomenclature and Definitions
602III. Goals for Line Use
603IV. Breeding Strategies
60 4V. Cryopreservation
61 2VI. Monitoring and Response
61 3VII. Distribution
61 4VIII. Summary and Recommendations
61 4References
61 5
33 . Common Diseases of Laboratory Zebrafis h
Jennifer L . Matthews
I. Introduction
61 7II. Diagnostic Evaluation
61 8III. Common Diseases of Laboratory Zebrafish
61 8IV. Zoonosis
640References
641
34 . Zebrafish Sperm Cryopreservation
Stephane Berghmans, John P. Morris IV, John P. Kanki, and A . Thomas Loo k
I. Introduction : Benefits of Zebrafish Sperm Cryopreservation
64 5II. Critical Variables Affecting Sperm Cryopreservation
64 6III. Zebrafish Sperm Cryopreservation with N,N-Dimethylacetarnide
65 0IV. Future Directions
65 6References
65 8
Index
66 1
Volumes iii Series
679