Dissection of gene function at clonal level using mosaic analysis with double markers

Abstract

MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato — and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools.

Keywords

MADM / genetic mosaic / clonal analysis / lineage tracing / neural development / genomic imprinting

References

[1] Armakolas A, Klar A J (2006). Cell type regulates selective segregation of mouse chromosome 7 DNA strands in mitosis. Science, 311(5764): 1146-1149

[2] Ayala R, Shu T, Tsai L H (2007). Trekking across the brain: the journey of neuronal migration. Cell, 128(1): 29-43

[3] Badea T C, Wang Y, Nathans J (2003). A noninvasive genetic/pharmacologic strategy for visualizing cell morphology and clonal relationships in the mouse. J Neurosci, 23(6): 2314-2322

[4] Barlow D P (2011). Genomic imprinting: a mammalian epigenetic discovery model. Annu Rev Genet, 45(1): 379-403

[5] Bartolomei M S, Ferguson-Smith A C (2011). Mammalian genomic imprinting. Cold Spring Harb Perspect Biol, 3(7): 3

[6] Bi W, Yan J, Stankiewicz P, Park S S, Walz K, Boerkoel C F, Potocki L, Shaffer L G, Devriendt K, Nowaczyk M J, Inoue K, Lupski J R (2002). Genes in a refined Smith-Magenis syndrome critical deletion interval on chromosome 17p11.2 and the syntenic region of the mouse. Genome Res, 12(5): 713-728

[7] Blair S S (2003). Genetic mosaic techniques for studying Drosophila development. Development, 130(21): 5065-5072

[8] Bonaguidi M A, Wheeler M A, Shapiro J S, Stadel R P, Sun G J, Ming G L, Song H (2011). In vivo clonal analysis reveals self-renewing and multipotent adult neural stem cell characteristics. Cell, 145(7): 1142-1155

[9] Branda C S, Dymecki S M (2004). Talking about a revolution: The impact of site-specific recombinases on genetic analyses in mice. Dev Cell, 6(1): 7-28

[10] Brennand K, Huangfu D, Melton D (2007). All beta cells contribute equally to islet growth and maintenance. PLoS Biol, 5(7): e163

[11] Buckingham M E, Meilhac S M (2011). Tracing cells for tracking cell lineage and clonal behavior. Dev Cell, 21(3): 394-409

[12] Cajal S R y (1911). Histology of the Nervous System of Man and Vertebrates. Oxford University Press, Inc, Oxford 1995 Translation

[13] Cepko C, Ryder E F, Austin C P, Walsh C, Fekete D M (1995). Lineage analysis using retrovirus vectors. Methods Enzymol, 254: 387-419

[14] Chow B Y, Han X, Boyden E S (2012). Genetically encoded molecular tools for light-driven silencing of targeted neurons. Prog Brain Res, 196: 49-61

[15] Cowan W M (1998). The emergence of modern neuroanatomy and developmental neurobiology. Neuron, 20(3): 413-426

[16] De Paola V, Arber S, Caroni P (2003). AMPA receptors regulate dynamic equilibrium of presynaptic terminals in mature hippocampal networks. Nat Neurosci, 6(5): 491-500

[17] Desgraz R, Herrera P L (2009). Pancreatic neurogenin 3-expressing cells are unipotent islet precursors. Development, 136(21): 3567-3574

[18] Dessaud E, Yang L L, Hill K, Cox B, Ulloa F, Ribeiro A, Mynett A, Novitch B G, Briscoe J (2007). Interpretation of the sonic hedgehog morphogen gradient by a temporal adaptation mechanism. Nature, 450(7170): 717-720

[19] Dymecki S M, Kim J C (2007). Molecular neuroanatomy’s “Three Gs”: a primer. Neuron, 54(1): 17-34

[20] Espinosa J S, Luo L (2008). Timing neurogenesis and differentiation: insights from quantitative clonal analyses of cerebellar granule cells. J Neurosci, 28: 2301-2312

[21] Espinosa J S, Wheeler D G, Tsien R W, Luo L (2009). Uncoupling dendrite growth and patterning: single-cell knockout analysis of NMDA receptor 2B. Neuron, 62(2): 205-217

[22] Feil R, Brocard J, Mascrez B, LeMeur M, Metzger D, Chambon P (1996). Ligand-activated site-specific recombination in mice. Proc Natl Acad Sci USA, 93(20): 10887-10890

[23] Feinberg A P (2007). Phenotypic plasticity and the epigenetics of human disease. Nature, 447(7143): 433-440

[24] Feng G, Mellor R H, Bernstein M, Keller-Peck C, Nguyen Q T, Wallace M, Nerbonne J M, Lichtman J W, Sanes J R (2000). Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron, 28(1): 41-51

[25] Foo L C, Allen N J, Bushong E A, Ventura P B, Chung W S, Zhou L, Cahoy J D, Daneman R, Zong H, Ellisman M H, Barres B A (2011). Development of a method for the purification and culture of rodent astrocytes. Neuron, 71(5): 799-811

[26] Franco S J, Müller U (2013). Shaping our minds: stem and progenitor cell diversity in the mammalian neocortex. Neuron, 77(1): 19-34

[27] Gao P, Sultan K T, Zhang X J, Shi S H (2013). Lineage-dependent circuit assembly in the neocortex. Development, 140(13): 2645-2655

[28] Gorski J A, Talley T, Qiu M, Puelles L, Rubenstein J L, Jones K R (2002). Cortical excitatory neurons and glia, but not GABAergic neurons, are produced in the Emx1-expressing lineage. J Neurosci, 22: 6309-6314

[29] Hallonet M E, Le Douarin N M (1993). Tracing neuroepithelial cells of the mesencephalic and metencephalic alar plates during cerebellar ontogeny in quail-chick chimaeras. Eur J Neurosci, 5(9): 1145-1155

[30] Hayashi S, McMahon A P (2002). Efficient recombination in diverse tissues by a tamoxifen-inducible form of Cre: a tool for temporally regulated gene activation/inactivation in the mouse. Dev Biol, 244(2): 305-318

[31] Hegemann P, Möglich A (2011). Channelrhodopsin engineering and exploration of new optogenetic tools. Nat Methods, 8(1): 39-42

[32] Hippenmeyer S, Johnson R L, Luo L (2013). Mosaic analysis with double markers reveals cell-type-specific paternal growth dominance. Cell Rep, 3: 960-967

[33] Hippenmeyer S, Vrieseling E, Sigrist M, Portmann T, Laengle C, Ladle D R, Arber S (2005). A developmental switch in the response of DRG neurons to ETS transcription factor signaling. PLoS Biol, 3(5): e159

[34] Hippenmeyer S, Youn Y H, Moon H M, Miyamichi K, Zong H, Wynshaw-Boris A, Luo L (2010). Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration. Neuron, 68(4): 695-709

[35] Imayoshi I, Ohtsuka T, Metzger D, Chambon P, Kageyama R (2006). Temporal regulation of Cre recombinase activity in neural stem cells. Genesis, 44(5): 233-238

[36] Indra A K, Warot X, Brocard J, Bornert J M, Xiao J H, Chambon P, Metzger D (1999). Temporally-controlled site-specific mutagenesis in the basal layer of the epidermis: comparison of the recombinase activity of the tamoxifen-inducible Cre-ER(T) and Cre-ER(T2) recombinases. Nucleic Acids Res, 27(22): 4324-4327

[37] Jefferis G S, Livet J (2012). Sparse and combinatorial neuron labelling. Curr Opin Neurobiol, 22(1): 101-110

[38] Lao Z, Raju G P, Bai C B, Joyner A L (2012). MASTR: a technique for mosaic mutant analysis with spatial and temporal control of recombination using conditional floxed alleles in mice. Cell Rep, 2: 386-396

[39] Lee T, Luo L (1999). Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron, 22(3): 451-461

[40] Legué E, Joyner A L (2010). Genetic fate mapping using site-specific recombinases. Methods Enzymol, 477: 153-181

[41] Lehtinen M K, Walsh C A (2011). Neurogenesis at the brain-cerebrospinal fluid interface. Annu Rev Cell Dev Biol, 27(1): 653-679

[42] Lewandoski M (2001). Conditional control of gene expression in the mouse. Nat Rev Genet, 2(10): 743-755

[43] Liang H, Xiao G, Yin H, Hippenmeyer S, Horowitz J M, Ghashghaei H T (2013). Neural development is dependent on the function of specificity protein 2 in cell cycle progression. Development, 140(3): 552-561

[44] Liu C, Sage J C, Miller M R, Verhaak R G, Hippenmeyer S, Vogel H, Foreman O, Bronson R T, Nishiyama A, Luo L, Zong H (2011). Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell, 146(2): 209-221

[45] Liu P, Jenkins N A, Copeland N G (2002). Efficient Cre-loxP-induced mitotic recombination in mouse embryonic stem cells. Nat Genet, 30(1): 66-72

[46] Lui J H, Hansen D V, Kriegstein A R (2011). Development and evolution of the human neocortex. Cell, 146(1): 18-36

[47] Luo L (2007). Fly MARCM and mouse MADM: genetic methods of labeling and manipulating single neurons. Brain Res Brain Res Rev, 55(2): 220-227

[48] Mabb A M, Judson M C, Zylka M J, Philpot B D (2011). Angelman syndrome: insights into genomic imprinting and neurodevelopmental phenotypes. Trends Neurosci, 34(6): 293-303

[49] 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 (2010). A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat Neurosci, 13(1): 133-140

[50] Marín O, Valiente M, Ge X, Tsai L H (2010). Guiding neuronal cell migrations. Cold Spring Harb Perspect Biol, 2(2): a001834

[51] McConnell S K (1988). Fates of visual cortical neurons in the ferret after isochronic and heterochronic transplantation. J Neurosci, 8: 945-974

[52] Merkle F T, Mirzadeh Z, Alvarez-Buylla A (2007). Mosaic organization of neural stem cells in the adult brain. Science, 317(5836): 381-384

[53] Metzger D, Chambon P (2001). Site- and time-specific gene targeting in the mouse. Methods, 24(1): 71-80

[54] Ming G L, Song H (2011). Adult neurogenesis in the mammalian brain: significant answers and significant questions. Neuron, 70(4): 687-702

[55] Miyoshi G, Hjerling-Leffler J, Karayannis T, Sousa V H, Butt S J, Battiste J, Johnson J E, Machold R P, Fishell G (2010). Genetic fate mapping reveals that the caudal ganglionic eminence produces a large and diverse population of superficial cortical interneurons. J Neurosci, 30: 1582-1594

[56] Morgan T H (1914). Mosaics and gynandromorphs in Drosophila. Proc Soc Exp Biol Med, 11(6): 171-172

[57] Muzumdar M D, Luo L, Zong H (2007). Modeling sporadic loss of heterozygosity in mice by using mosaic analysis with double markers (MADM). Proc Natl Acad Sci USA, 104(11): 4495-4500

[58] Nelson S B, Sugino K, Hempel C M (2006). The problem of neuronal cell types: a physiological genomics approach. Trends Neurosci, 29(6): 339-345

[59] Nicholls R D, Knepper J L (2001). Genome organization, function, and imprinting in Prader-Willi and Angelman syndromes. Annu Rev Genomics Hum Genet, 2(1): 153-175

[60] Ninkovic J, Gotz M (2013). Fate specification in the adult brain-lessons for eliciting neurogenesis from glial cells. BioEssays, 35: 242-252

[61] Novak A, Guo C, Yang W, Nagy A, Lobe C G (2000). Z/EG, a double reporter mouse line that expresses enhanced green fluorescent protein upon Cre-mediated excision. Genesis, 28(3-4): 147-155

[62] Petersen P H, Zou K, Hwang J K, Jan Y N, Zhong W (2002). Progenitor cell maintenance requires numb and numblike during mouse neurogenesis. Nature, 419(6910): 929-934

[63] Reiner O, Carrozzo R, Shen Y, Wehnert M, Faustinella F, Dobyns W B, Caskey C T, Ledbetter D H (1993). Isolation of a Miller-Dieker lissencephaly gene containing G protein beta-subunit-like repeats. Nature, 364(6439): 717-721

[64] Ross M E, Walsh C A (2001). Human brain malformations and their lessons for neuronal migration. Annu Rev Neurosci, 24(1): 1041-1070

[65] Sanes J R (1989). Analysing cell lineage with a recombinant retrovirus. Trends Neurosci, 12(1): 21-28

[66] Schnütgen F, Doerflinger N, Calléja C, Wendling O, Chambon P, Ghyselinck N B (2003). A directional strategy for monitoring Cre-mediated recombination at the cellular level in the mouse. Nat Biotechnol, 21(5): 562-565

[67] Shaner N C, Campbell R E, Steinbach P A, Giepmans B N, Palmer A E, Tsien R Y (2004). Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol, 22(12): 1567-1572

[68] Smith G B, Fitzpatrick D (2012). Specifying cortical circuits: a role for cell lineage. Neuron, 75(1): 4-5

[69] Soriano P (1999). Generalized lacZ expression with the ROSA26 Cre reporter strain. Nat Genet, 21(1): 70-71

[70] Stern C (1936). Somatic Crossing over and Segregation in Drosophila Melanogaster. Genetics, 21(6): 625-730

[71] Tasic B, Miyamichi K, Hippenmeyer S, Dani V S, Zeng H, Joo W, Zong H, Chen-Tsai Y, Luo L (2012). Extensions of MADM (mosaic analysis with double markers) in mice. PLoS ONE, 7(3): e33332

[72] Tronche F, Kellendonk C, Kretz O, Gass P, Anlag K, Orban P C, Bock R, Klein R, Schütz G (1999). Disruption of the glucocorticoid receptor gene in the nervous system results in reduced anxiety. Nat Genet, 23(1): 99-103

[73] Tsai J W, Chen Y, Kriegstein A R, Vallee R B (2005). LIS1 RNA interference blocks neural stem cell division, morphogenesis, and motility at multiple stages. J Cell Biol, 170(6): 935-945

[74] Walsh C, Cepko C L (1992). Widespread dispersion of neuronal clones across functional regions of the cerebral cortex. Science, 255(5043): 434-440

[75] Wingate R J, Hatten M E (1999). The role of the rhombic lip in avian cerebellum development. Development, 126(20): 4395-4404

[76] Woodruff A, Xu Q, Anderson S A, Yuste R (2009). Depolarizing effect of neocortical chandelier neurons. Front Neural Circuits 3: 15.

[77] Wynshaw-Boris A, Pramparo T, Youn Y H, Hirotsune S (2010). Lissencephaly: mechanistic insights from animal models and potential therapeutic strategies. Semin Cell Dev Biol, 21(8): 823-830

[78] Xu Q, Tam M, Anderson S A (2008). Fate mapping Nkx2.1-lineage cells in the mouse telencephalon. J Comp Neurol, 506(1): 16-29

[79] Xu T, Rubin G M (1993). Analysis of genetic mosaics in developing and adult Drosophila tissues. Development, 117(4): 1223-1237

[80] Yang S B, Mclemore K D, Tasic B, Luo L, Jan Y N, Jan L Y (2012). Kv1.1-dependent control of hippocampal neuron number as revealed by mosaic analysis with double markers. J Physiol, 590(Pt 11): 2645-2658

[81] Yingling J, Toyo-Oka K, Wynshaw-Boris A (2003). Miller-Dieker syndrome: analysis of a human contiguous gene syndrome in the mouse. Am J Hum Genet, 73(3): 475-488

[82] Yingling J, Youn Y H, Darling D, Toyo-Oka K, Pramparo T, Hirotsune S, Wynshaw-Boris A (2008). Neuroepithelial stem cell proliferation requires LIS1 for precise spindle orientation and symmetric division. Cell, 132(3): 474-486

[83] Youn Y H, Pramparo T, Hirotsune S, Wynshaw-Boris A (2009). Distinct dose-dependent cortical neuronal migration and neurite extension defects in Lis1 and Ndel1 mutant mice. J Neurosci, 29: 15520-15530

[84] Young P, Qiu L, Wang D, Zhao S, Gross J, Feng G (2008). Single-neuron labeling with inducible Cre-mediated knockout in transgenic mice. Nat Neurosci, 11(6): 721-728

[85] Zhang F, Aravanis A M, Adamantidis A, de Lecea L, Deisseroth K (2007). Circuit-breakers: optical technologies for probing neural signals and systems. Nat Rev Neurosci, 8(8): 577-581

[86] Zhu X, Bergles D E, Nishiyama A (2008). NG2 cells generate both oligodendrocytes and gray matter astrocytes. Development, 135(1): 145-157

[87] Zhuo L, Theis M, Alvarez-Maya I, Brenner M, Willecke K, Messing A (2001). hGFAP-cre transgenic mice for manipulation of glial and neuronal function in vivo. Genesis, 31(2): 85-94

[88] Zong H, Espinosa J S, Su H H, Muzumdar M D, Luo L (2005). Mosaic analysis with double markers in mice. Cell, 121(3): 479-492

Acknowledgements

I thank L. Luo and H. Zong for continued discussions about MADM and G. Arque for helpful comments on the manuscript. This work was supported by IST Austria institutional funds.

Compliance with ethics guidelines

Simon Hippenmeyer declares that he has no conflict of interest and that all IST Austria institutional and national guidelines for the care and use of laboratory animals were followed.

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg