Mapping cell fate and function using recombinase-based intersectional strategies

Methods in Enzymology

Volumn 477, Issue C, 2010, Pages 183-213

  Dymecki, Susan M ^a   Ray, Russell S ^a   Kim, Jun C ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRE RECOMBINASE; REAGENT; RECOMBINASE; TRACER;

ARTICLE; CELL FATE; CELL LINEAGE; CELL SUBPOPULATION; CELL TYPE; FRT GENE; GENE; GENE ACTIVATION; GENE CASSETTE; GENE EXPRESSION; GENE MAPPING; GENE TARGETING; GENETIC MANIPULATION; LOXP SITE; NONHUMAN; PRIORITY JOURNAL; SENSOR; TRANSGENE;

EID: 77955352376     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)77011-7     Document Type: Chapter

References (80)

1. Airan R., Hu E., Vijaykumar R., Roy M., Meltzer L., Deisseroth K. Integration of light-controlled neuronal firing and fast circuit imaging. Curr. Opin. Neurobiol. 2007, 17:587-592.
2. Akagi K., Sandig V., Vooijs M., Van der Valk M., Giovannini M., Strauss M., Berns A. Cre-mediated somatic site-specific recombination in mice. Nucleic Acids Res. 1997, 25:1766-1773.
3. Alexander G.M., Rogan S.C., Abbas A.I., Armbruster B.N., Pei Y., Allen J.A., Nonneman R.J., Hartmann J., Moy S.S., Nicolelis M.A., McNamara J.O., Roth B.L. Remote control of neuronal activity in transgenic mice expressing evolved G protein-coupled receptors. Neuron 2009, 63:27-39.
4. Arenkiel B.R., Klein M.E., Davison I.G., Katz L.C., Ehlers M.D. Genetic control of neuronal activity in mice conditionally expressing TRPV1. Nat. Methods 2008, 5:299-302.
5. Armbruster B.N., Li X., Pausch M.H., Herlitze S., Roth B.L. Evolving the lock to fit the key to create a family of G protein-coupled receptors potently activated by an inert ligand. Proc. Natl. Acad. Sci. USA 2007, 104:5163-5168.
6. Awatramani R., Soriano P., Mai J.J., Dymecki S.M. A FLP indicator strain, R26::FRAP, driving alkaline phosphatase expression from the ROSA26 locus. Nat. Genet. 2001, 29:257-259.
7. Awatramani R., Soriano P., Rodriguez C., Mai J.J., Dymecki S.M. Cryptic boundaries in roof plate and choroid plexus identified by intersectional gene activation. Nat. Genet. 2003, 35:70-75.
8. Bai C.B., Auerbach W., Lee J.S., Stephen D., Joyner A.L. Gli2, but not Gli1, is required for initial Shh signaling and ectopic activation of the Shh pathway. Development 2002, 129:4753-4761.
9. Beard C., Hochedlinger K., Plath K., Wutz A., Jaenisch R. Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis 2006, 44:23-28.
10. Branda C., Dymecki S.M. Talking about a revolution: The impact of site-specific recombinases on genetic analyses in mice. Dev. Cell 2004, 6:7-28.
11. Buchholz F., Ringrose L., Angrand P.-O., Rossi F., Stewart A.F. Different thermostabilities of FLP and Cre recombinases: Implications for applied site-specific recombination. Nucleic Acids Res. 1996, 24:4256-4262.
12. Buchholz F., Angrand P.O., Stewart A.F. Improved properties of FLP recombinase evolved by cycling mutagenesis. Nat. Biotechnol. 1998, 16:657-662.
13. Cepko C.L., Austin C.P., Walsh C., Ryder E.F., Halliday A., Fields-Berry S. Studies of cortical development using retrovirus vectors. Cold Spring Harb. Symp. Quant. Biol. 1990, 55:265-278.
14. Conklin B.R., Hsiao E.C., Claeysen S., Dumuis A., Srinivasan S., Forsayeth J.R., Guettier J.M., Chang W.C., Pei Y., McCarthy K.D., Nissenson R.A., Wess J., et al. Engineering GPCR signaling pathways with RASSLs. Nat. Methods 2008, 5:673-678.
15. Dymecki S.M. Site-specific recombination in cells and mice. Gene Targeting: A Practical Approach 2000, 37-99. Oxford University Press, Oxford. A.L. Joyner (Ed.).
16. Dymecki S.M., Kim J.C. Molecular neuroanatomy's "Three Gs": A primer. Neuron 2007, 54:17-34.
17. Dymecki S.M., Rodriguez C.I., Awatramani R.B. Switching on lineage tracers using site-specific recombination. Embryoni Stem Cells: Methods and Protocols 2002, Humana Press, New Jersey. K. Turksen (Ed.).
18. Farago A.F., Awatramani R.B., Dymecki S.M. Assembly of the brainstem cochlear nuclear complex is revealed by intersectional and subtractive genetic fate maps. Neuron 2006, 50:205-218.
19. Farley F.W., Soriano P., Steffen L.S., Dymecki S.M. Widespread recombinase expression using FLPeR (flipper) mice. Genesis 2000, 28:106-110.
20. Galileo D.S., Gray G.E., Owens G.C., Majors J., Sanes J.R. Neurons and glia arise from a common progenitor in chicken optic tectum: Demonstration with two retroviruses and cell type-specific antibodies. Proc. Natl. Acad. Sci. USA 1990, 87:458-462.
21. Gong S., Doughty M., Harbaugh C.R., Cummins A., Hatten M.E., Heintz N., Gerfen C.R. Targeting Cre recombinase to specific neuron populations with bacterial artifical chromosome constructs. J. Neurosci. 2007, 27:9817-9823.
22. Han X., Boyden E.S. Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution. PLoS One 2007, 2:e299.
23. Han X., Qian X., Bernstein J.G., Zhou H.H., Franzesi G.T., Stern P., Bronson R.T., Graybiel A.M., Desimone R., Boyden E.S. Millisecond-timescale optical control of neural dynamics in the nonhuman primate brain. Neuron 2009, 62:191-198.
24. Heintz N. BAC to the future: The use of bac transgenic mice for neuroscience research. Nat. Rev. Neurosci. 2001, 2:861-870.
25. Jensen P., Farago A.F., Awatramani R.B., Scott M.M., Deneris E.S., Dymecki S.M. Redefining the serotonergic system by genetic lineage. Nat. Neurosci. 2008, 11:417-419.
26. Johansson T., Broll I., Frenz T., Hemmers S., Becher B., Zeilhofer H.U., Buch T. Building a zoo of mice for genetic analyses: A comprehensive protocol for the rapid generation of BAC transgenic mice. Genesis 2010, 48:264-280.
27. Joyner A., Zervas M. Genetic inducible fate mapping in mouse: Establishing genetic lineages and defining genetic neuroanatomy in the nervous system. Dev. Dyn. 2006, 235:2376-2385.
28. Kanki H., Suzuki H., Itohara S. High-efficiency CAG-FLPe deleter mice in C57BL/6J background. Exp. Anim. 2006, 55:137-141.
29. Keller R.E. Vital dye mapping of the gastrula and neuraula of Xenopus laevis. I. Prospective areas and morphogenetic movements of the superficial layer. Dev. Biol. 1975, 42:222-241.
30. Kim J.C., Cook M.N., Carey M.R., Shen C., Regehr W.G., Dymecki S.M. Linking genetically defined neurons to behavior through a broadly applicable silencing allele. Neuron 2009, 63:305-315.
31. Kramer I., Sigrist M., de Nooij J.C., Taniuchi I., Jessell T.M., Arber S. A role for Runx transcription factor signaling in dorsal root ganglion sensory neuron diversification. Neuron 2006, 49:379-393.
32. Kranz A., Fu J., Duerschke K., Weidlich S., Naumann R., Stewart A.F., Anastassiadis K. An Improved Flp Deleter Mouse in C57Bl/6 Based on Flpo Recombinase 2010, Genesis. May 4. [Epub ahead of print].
33. Landsberg R.L., Awatramani R.B., Hunter N.L., Farago A.F., DiPietrantonio H.J., Rodriguez C.I., Dymecki S.M. Hindbrain rhombic lip is comprised of discrete progenitor cell populations allocated by Pax6. Neuron 2005, 48:933-947.
34. Lechner H.A., Lein E.S., Callaway E.M. A genetic method for selective and quickly reversible silencing of Mammalian neurons. J. Neurosci. 2002, 22:5287-5290.
35. Le Douarin N. The Neural Crest 1982, Cambridge University Press, Cambridge.
36. Lee E.C., Yu D., Martinez de Velasco J., Tessarollo L., Swing D.A., Court D.L., Jenkins N.A., Copeland N.G. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 2001, 73:56-65.
37. Lerchner W., Xiao C., Nashmi R., Slimko E.M., van Trigt L., Lester H.A., Anderson D.J. Reversible silencing of neuronal excitability in behaving mice by a genetically targeted, ivermectin-gated Cl- channel. Neuron 2007, 54:35-49.
38. Lewandoski M. Conditional control of gene expression in the mouse. Nat. Rev. Genet. 2001, 2:743-755.
39. Lobe C.G., Koop K.E., Kreppner W., Lomeli H., Gertsenstein M., Nagy A. Z/AP, a double reporter for Cre-mediated recombination. Dev. Biol. 1999, 208:281-292.
40. Luo L., Callaway E.M., Svoboda K. Genetic dissection of neural circuits. Neuron 2008, 57:634-660.
41. Madisen L., Zwingman T.A., Sunkin S.M., Oh S.W., Zariwala H.A., Gu H., Ng L.L., Palmiter R.D., Hawrylycz M.J., Jones A.R., Lein E.S., Zeng H. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 2010, 13:133-140.
42. Martin J.R., Keller A., Sweeney S.T. Targeted expression of tetanus toxin: A new tool to study the neurobiology of behavior. Adv. Genet. 2002, 47:1-47.
43. Meyers E.N., Lewandoski M., Martin G.R. An Fgf8 mutant allelic series generated by Cre- and Flp-mediated recombination. Nat. Genet. 1998, 18:136-141.
44. Miyoshi G., Hjerling-Leffler J., Karayannis T., Sousa V.H., Butt S.J., Battiste J., Johnson J.E., Machold R.P., Fishell G. Genetic fate mapping reveals that the caudal ganglionic eminence produces a large and diverse population of superficial cortical interneurons. J. Neurosci. 2010, 30:1582-1594.
45. Muyrers J.P., Zhang Y., Stewart A.F. Techniques: Recombinogenic engineering-New options for cloning and manipulating DNA. Trends Biochem. Sci. 2001, 26:325-331.
46. Nagy A. Cre recombinase: The universal reagent for genome tailoring. Genesis 2000, 26:99-109.
47. Nagy A., Gertsenstein M., Vintersten K., Behringer R. Manipulating the Mouse Embryo: A Laboratory Manual 2003, Cold Spring Harbor Laboratory Press, New York.
48. Nakashiba T., Young J.Z., McHugh T.J., Buhl D.L., Tonegawa S. Transgenic inhibition on synaptic transmission reveals role of CA3 output in hippocampal learning. Science 2008, 319:1260-1264.
49. Nichols C.D., Roth B.L. Engineered G-protein coupled receptors are powerful tools to investigate biological processes and behaviors. Front. Mol. Neurosci. 2009, 2:16.
50. Niwa H., Yamamura K., Miyazaki J. Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene 1991, 108:193-200.
51. Novak A., Guo C., Yang W., Nagy A., Lobe C.G. Z/EG, a double reporter mouse line that expresses enhanced green fluorescent protein upon Cre-mediated excision. Genesis 2000, 28:147-155.
52. Pei Y., Rogan S.C., Yan F., Roth B.L. Engineered GPCRs as tools to modulate signal transduction. Physiology (Bethesda) 2008, 23:313-321.
53. Ray R.S., Dymecki S.M. Rautenlippe Redux-Toward a unified view of the precerebellar rhombic lip. Curr. Opin. Cell Biol. 2009, 21:741-747.
54. Raymond C.S., Soriano P. High-efficiency FLP and PhiC31 site-specific recombination in mammalian cells. PLoS One 2007, 2:e162.
55. Rodriguez C.I., Dymecki S.M. Origin of the precerebellar system. Neuron 2000, 27:475-486.
56. Rodriguez C.I., Buchholz F., Galloway J., Sequerra R., Kasper J., Ayala R., Stewart A.F., Dymecki S.M. High-efficiency deleter mice show that FLPe is an alternative to Cre-loxP. Nat. Genet. 2000, 25:139-140.
57. Sauer B. Manipulation of transgenes by site-specific recombination: Use of Cre recombinase. Methods in Enzymology-Guide to Techniques in Mouse Development 1993, Vol. 225:890-900. Academic Press, Inc., San Diego.
58. Schaft J., Ashery-Padan R., van der Hoeven F., Gruss P., Stewart A.F. Efficient FLP recombination in mouse ES cells and oocytes. Genesis 2001, 31:6-10.
59. Schiavo G., Matteoli M., Montecucco C. Neurotoxins affecting neuroexocytosis. Physiol. Rev. 2000, 80:717-766.
60. Schneider M.B., Gradinaru V., Zhang F., Deisseroth K. Controlling neuronal activity. Am. J. Psychiatry 2008, 165:562.
61. Schwenk F., Baron U., Rajewsky K. A cre-transgenic mouse strain for the ubiquitous deletion of loxP-flanked gene segments including deletion in germ cells. Nucleic Acids Res. 1995, 23:5080-5081.
62. Slimko E.M., McKinney S., Anderson D.J., Davidson N., Lester H.A. Selective electrical silencing of mammalian neurons in vitro by the use of invertebrate ligand-gated chloride channels. J. Neurosci. 2002, 22:7373-7379.
63. Soriano P. Generalized lacZ expression with ROSA26 Cre reporter strain. Nat. Genet. 1999, 21:70-71.
64. Srinivas S., Watanabe T., Lin C.-S., William C.M., Tanabe Y., Jessell T.M., Costantini F. Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus. BMC Dev. Biol. 2001, 1:4.
65. Stark W.M., Boocock M.R., Sherratt D.J. Catalysis by site-specific recombinases. Trends Genet. 1992, 8:432-439.
66. Sweeney S.T., Broadie K., Keane J., Niemann H., O'Kane C.J. Targeted expression of tetanus toxin light chain in Drosophila specifically eliminates synaptic transmission and causes behavioral defects. Neuron 1995, 14:341-351.
67. Tan E.M., Yamaguchi Y., Horwitz G.D., Gosgnach S., Lein E.S., Goulding M., Albright T.D., Callaway E.M. Selective and quickly reversible inactivation of mammalian neurons in vivo using the Drosophila allatostatin receptor. Neuron 2006, 51:157-170.
68. Tan W., Janczewski W.A., Yang P., Shao X.M., Callaway E.M., Feldman J.L. Silencing preBotzinger complex somatostatin-expressing neurons induces persistent apnea in awake rat. Nat. Neurosci. 2008, 11:538-540.
69. Tsien J.Z., Chen D.F., Gerber D., Tom C., Mercer E.H., Anderson D.J., Mayford M., Kandel E.R., Tonegawa S. Subregion- and cell type-restricted gene knockout in mouse brain. Cell 1996, 87:1317-1326.
70. Walsh C., Cepko C.L. Clonally related cortical cells show several migration patterns. Science 1988, 241:1342-1345.
71. Wehr M., Hostick U., Kyweriga M., Tan A., Weible A.P., Wu H., Wu W., Callaway E.M., Kentros C. Transgenic silencing of neurons in the mammalian brain by expression of the allatostatin receptor (AlstR). J. Neurophysiol. 2009, 102:2554-2562.
72. Wetts R.F., Fraser S.E. Multipotent precursors can give rise to all major cell types of the frog retina. Science 1988, 239:1142-1145.
73. Wu Y., Wang C., Sun H., LeRoith D., Yakar S. High-efficient FLPo deleter mice in C57BL/6J background. PLoS One 2009, 4:e8054.
74. Yamamoto M., Wada N., Kitabatake Y., Watanabe D., Anzai M., Yokoyama M., Teranishi Y., Nakanishi S. Reversible suppression of glutamatergic neurotransmission of cerebellar granule cells in vivo by genetically manipulated expression of tetanus neurotoxin light chain. J. Neurosci. 2003, 23:6759-6767.
75. Yamamoto M., Shook N.A., Kanisicak O., Yamamoto S., Wosczyna M.N., Camp J.R., Goldhamer D.J. A multifunctional reporter mouse line for Cre- and FLP-dependent lineage analysis. Genesis 2009, 47:107-114.
76. Zambrowicz B.P., Imamoto A., Fiering S., Herzenberg L.A., Kerr W.G., Soriano P. Disruption of overlapping transcripts in the ROSA ßgeo 26 gene trap strain leads to widespread expression of β-galactosidase in mouse embryos and hematopoietic cells. Proc. Natl. Acad. Sci. USA 1997, 94:3789-3794.
77. Zhang F., Wang L.P., Boyden E., Deisseroth K. Channelrhodopsin-2 and optical control of excitable cells. Nat. Methods 2006, 10:785-792.
78. Zhang F., Aravanis A.M., Adamantidis A., de Lecea L., Deisseroth K. Circuit-breakers: Optical technologies for probing neural signals and systems. Nat. Rev. Neurosci. 2007, 8:577-581.
79. Zinyk D., Mercer E.H., Harris E., Anderson D.J., Joyner A.L. Fate mapping of the mouse midbrain-hindbrain constriction using a site-specific recombination system. Curr. Biol. 1998, 8:665-668.
80. Zong H., Espinosa J.S., Su H.H., Muzumdar M.D., Luo L. Mosaic analysis with double markers in mice. Cell 2005, 121:479-492.