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Volumn 10, Issue 1, 2016, Pages

Site-specific recombinatorics: In situ cellular barcoding with the Cre Lox system

Author keywords

Cell fate tracking; Cellular barcoding; Combinatorial explosion; Cre lox system; DNA stochastic programme

Indexed keywords

CRE RECOMBINASE; INTEGRASE;

EID: 84976878537     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/s12918-016-0290-3     Document Type: Article
Times cited : (14)

References (58)
  • 3
    • 84886924368 scopus 로고    scopus 로고
    • Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding
    • Verovskaya E, Broekhuis MJ, Zwart E, Ritsema M, van Os R, de Haan G, Bystrykh LV. Heterogeneity of young and aged murine hematopoietic stem cells revealed by quantitative clonal analysis using cellular barcoding. Blood. 2013; 122(4):523-32.
    • (2013) Blood , vol.122 , Issue.4 , pp. 523-532
    • Verovskaya, E.1    Broekhuis, M.J.2    Zwart, E.3    Ritsema, M.4    van Os, R.5    de Haan, G.6    Bystrykh, L.V.7
  • 4
    • 84896727582 scopus 로고    scopus 로고
    • Heterogeneity and hierarchy of hematopoietic stem cells
    • Ema H, Morita Y, Suda T. Heterogeneity and hierarchy of hematopoietic stem cells. Exp Hematol. 2014; 42(2):74-82.
    • (2014) Exp Hematol , vol.42 , Issue.2 , pp. 74-82
    • Ema, H.1    Morita, Y.2    Suda, T.3
  • 5
    • 84928706022 scopus 로고    scopus 로고
    • Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex
    • Johnson MB, Wang PP, Atabay KD, Murphy EA, Doan RN, Hecht JL, Walsh CA. Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex. Nat Neurosci. 2015; 18(5):637-46. doi: 10.1038/nn.3980.
    • (2015) Nat Neurosci , vol.18 , Issue.5 , pp. 637-646
    • Johnson, M.B.1    Wang, P.P.2    Atabay, K.D.3    Murphy, E.A.4    Doan, R.N.5    Hecht, J.L.6    Walsh, C.A.7
  • 6
    • 84883580414 scopus 로고    scopus 로고
    • Genetic basis of neuronal individuality in the mammalian brain,
    • Yagi T. Genetic basis of neuronal individuality in the mammalian brain,. J Neurogenet. 2013; 27(3):97-105. doi: 10.3109/01677063.2013.801969.
    • (2013) J Neurogenet , vol.27 , Issue.3 , pp. 97-105
    • Yagi, T.1
  • 8
    • 84879467613 scopus 로고    scopus 로고
    • Measurement of cancer cell growth heterogeneity through lentiviral barcoding identifies clonal dominance as a characteristic of in vivo ttmor engraftment
    • Nolan-Stevaux O, Tedesco D, Ragan S, Makhanov M, Chenchik A, Ruefli-Brasse A, Quon K, Kassner PD. Measurement of cancer cell growth heterogeneity through lentiviral barcoding identifies clonal dominance as a characteristic of in vivo ttmor engraftment. PLoS ONE. 2013; 8(6):67316.
    • (2013) PLoS ONE , vol.8 , Issue.6 , pp. 67316
    • Nolan-Stevaux, O.1    Tedesco, D.2    Ragan, S.3    Makhanov, M.4    Chenchik, A.5    Ruefli-Brasse, A.6    Quon, K.7    Kassner, P.D.8
  • 12
    • 84921817567 scopus 로고    scopus 로고
    • Lymphocyte fate specification as a deterministic but highly plastic process
    • Reiner SL, Adams WC. Lymphocyte fate specification as a deterministic but highly plastic process. Nat Rev Immunol. 2014; 14(10):699-704.
    • (2014) Nat Rev Immunol , vol.14 , Issue.10 , pp. 699-704
    • Reiner, S.L.1    Adams, W.C.2
  • 13
    • 84865607726 scopus 로고    scopus 로고
    • Intracellular competition for fates in the immune system
    • Duffy KR, Hodgkin PD. Intracellular competition for fates in the immune system. Trends Cell Biol. 2012; 22(9):457-64. doi: 10.1016/j.tcb.2012.05.004.
    • (2012) Trends Cell Biol , vol.22 , Issue.9 , pp. 457-464
    • Duffy, K.R.1    Hodgkin, P.D.2
  • 16
    • 77954466035 scopus 로고    scopus 로고
    • A minimum of two distinct heritable factors are required to explain correlation structures in proliferating lymphocytes
    • Markham JF, Wellard CJ, Hawkins ED, Duffy KR, Hodgkin PD. A minimum of two distinct heritable factors are required to explain correlation structures in proliferating lymphocytes. J R Soc Interface. 2010; 7(48):1049-59.
    • (2010) J R Soc Interface , vol.7 , Issue.48 , pp. 1049-1059
    • Markham, J.F.1    Wellard, C.J.2    Hawkins, E.D.3    Duffy, K.R.4    Hodgkin, P.D.5
  • 18
    • 78751510046 scopus 로고    scopus 로고
    • Reconstruction of rat retinal progenitor cell lineages in vitro reveals a surprising degree of stochasticity in cell fate decisions
    • Gomes FL, Zhang G, Carbonell F, Correa JA, Harris WA, Simons BD, Cayouette M. Reconstruction of rat retinal progenitor cell lineages in vitro reveals a surprising degree of stochasticity in cell fate decisions. Development. 2011; 138(2):227-35.
    • (2011) Development , vol.138 , Issue.2 , pp. 227-235
    • Gomes, F.L.1    Zhang, G.2    Carbonell, F.3    Correa, J.A.4    Harris, W.A.5    Simons, B.D.6    Cayouette, M.7
  • 20
    • 84872396644 scopus 로고    scopus 로고
    • A quantitative model of normal caenorhabditis elegans embryogenesis and its disruption after stress
    • Richards JL, Zacharias AL, Walton T, Burdick JT, Murray JI. A quantitative model of normal caenorhabditis elegans embryogenesis and its disruption after stress. Dev Biol. 2013; 374(1):12-23.
    • (2013) Dev Biol , vol.374 , Issue.1 , pp. 12-23
    • Richards, J.L.1    Zacharias, A.L.2    Walton, T.3    Burdick, J.T.4    Murray, J.I.5
  • 22
    • 84922629832 scopus 로고    scopus 로고
    • Quantitative single-cell approaches to stem cell research
    • Etzrodt M, Endele M, Schroeder T. Quantitative single-cell approaches to stem cell research. Cell Stem Cell. 2014; 15(5):546-58.
    • (2014) Cell Stem Cell , vol.15 , Issue.5 , pp. 546-558
    • Etzrodt, M.1    Endele, M.2    Schroeder, T.3
  • 23
    • 84908583870 scopus 로고    scopus 로고
    • Extracting meaning from biological imaging data
    • Cohen AR. Extracting meaning from biological imaging data. Mol Biol Cell. 2014; 25(22):3470-3.
    • (2014) Mol Biol Cell , vol.25 , Issue.22 , pp. 3470-3473
    • Cohen, A.R.1
  • 25
    • 80054719497 scopus 로고    scopus 로고
    • Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding
    • Lu R, Neff NF, Quake SR, Weissman IL. Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nat Biotech. 2011; 29(10):928-33. doi: 10.1038/nbt.1977.
    • (2011) Nat Biotech , vol.29 , Issue.10 , pp. 928-933
    • Lu, R.1    Neff, N.F.2    Quake, S.R.3    Weissman, I.L.4
  • 26
    • 84905190838 scopus 로고    scopus 로고
    • Cellular barcoding: a technical appraisal
    • Naik SH, Schumacher TN, Perié L. Cellular barcoding: a technical appraisal. Exp Hematol. 2014; 42(8):598-608. doi: 10.1016/j.exphem.2014.05.003.
    • (2014) Exp Hematol , vol.42 , Issue.8 , pp. 598-608
    • Naik, S.H.1    Schumacher, T.N.2    Perié, L.3
  • 28
    • 0006761646 scopus 로고
    • Clonal contributions of small numbers of retrovirally marked hematopoietic stem cells engrafted in unirradiated neonatal W/Wv mice
    • Capel B, Hawley R, Covarrubias L, Hawley T, Mintz B. Clonal contributions of small numbers of retrovirally marked hematopoietic stem cells engrafted in unirradiated neonatal W/Wv mice. Proc Natl Acad Sci U S A. 1989; 86(12):4564-8.
    • (1989) Proc Natl Acad Sci U S A , vol.86 , Issue.12 , pp. 4564-4568
    • Capel, B.1    Hawley, R.2    Covarrubias, L.3    Hawley, T.4    Mintz, B.5
  • 29
    • 84876297531 scopus 로고    scopus 로고
    • Diverse and heritable lineage imprinting of early haematopoietic progenitors
    • Naik SH, Perié L, Swart E, Gerlach C, van Rooij N, de Boer RJ, Schumacher TN. Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature. 2013; 496(7444):229-32. doi: 10.1038/nature12013.
    • (2013) Nature , vol.496 , Issue.7444 , pp. 229-232
    • Naik, S.H.1    Perié, L.2    Swart, E.3    Gerlach, C.4    van Rooij, N.5    de Boer, R.J.6    Schumacher, T.N.7
  • 31
    • 84950283224 scopus 로고    scopus 로고
    • The branching point in erythro-myeloid differentiation
    • Perié L, Duffy KR, Kok L, de Boer RJ, Schmacher TN. The branching point in erythro-myeloid differentiation. Cell. 2015; 163(7):1655-62.
    • (2015) Cell , vol.163 , Issue.7 , pp. 1655-1662
    • Perié, L.1    Duffy, K.R.2    Kok, L.3    de Boer, R.J.4    Schmacher, T.N.5
  • 34
    • 84870675684 scopus 로고    scopus 로고
    • An exactly solvable model of random site-specific recombinations
    • Wei Y, Koulakov AA. An exactly solvable model of random site-specific recombinations. Bull Math Biol. 2012; 74(12):2897-916.
    • (2012) Bull Math Biol , vol.74 , Issue.12 , pp. 2897-2916
    • Wei, Y.1    Koulakov, A.A.2
  • 35
    • 84921374973 scopus 로고    scopus 로고
    • In vivo generation of DNA sequence diversity for cellular barcoding
    • Peikon ID, Gizatullina DI, Zador AM. In vivo generation of DNA sequence diversity for cellular barcoding. Nucleic Acids Res. 2014; 42(16):127. doi: 10.1093/nar/gku604.
    • (2014) Nucleic Acids Res , vol.42 , Issue.16 , pp. 127
    • Peikon, I.D.1    Gizatullina, D.I.2    Zador, A.M.3
  • 36
    • 35948992641 scopus 로고    scopus 로고
    • Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system
    • Livet J, Weissman TA, Kang H, Draft RW, Lu J, Bennis RA, Sanes JR, Lichtman JW. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 2007; 450(7166):56-62.
    • (2007) Nature , vol.450 , Issue.7166 , pp. 56-62
    • Livet, J.1    Weissman, T.A.2    Kang, H.3    Draft, R.W.4    Lu, J.5    Bennis, R.A.6    Sanes, J.R.7    Lichtman, J.W.8
  • 38
    • 0022366181 scopus 로고
    • Formation of small circular DNA molecules via an in vitro site-specific recombination system
    • Hoess R, Wierzbicki A, Abremski K. Formation of small circular DNA molecules via an in vitro site-specific recombination system. Gene. 1985; 40(2-3):325-9.
    • (1985) Gene , vol.40 , Issue.2-3 , pp. 325-329
    • Hoess, R.1    Wierzbicki, A.2    Abremski, K.3
  • 39
    • 0033485539 scopus 로고    scopus 로고
    • Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances
    • Ringrose L, Chabanis S, Angrand PO, Woodroofe C, Stewart AF. Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances. EMBO J. 1999; 18(23):6630-41.
    • (1999) EMBO J , vol.18 , Issue.23 , pp. 6630-6641
    • Ringrose, L.1    Chabanis, S.2    Angrand, P.O.3    Woodroofe, C.4    Stewart, A.F.5
  • 41
    • 79251592245 scopus 로고    scopus 로고
    • BAC modification through serial or simultaneous use of CRE/Lox technology
    • Parrish M, Unruh J, Krumlauf R. BAC modification through serial or simultaneous use of CRE/Lox technology. J Biomed Biotechnol. 2011; 2011:1-12. doi: 10.1155/2011/924068.
    • (2011) J Biomed Biotechnol , vol.2011 , pp. 1-12
    • Parrish, M.1    Unruh, J.2    Krumlauf, R.3
  • 42
    • 0034059140 scopus 로고    scopus 로고
    • Cre recombinase: the universal reagent for genome tailoring
    • Nagy A. Cre recombinase: the universal reagent for genome tailoring. Genesis. 2000; 26:99-109.
    • (2000) Genesis , vol.26 , pp. 99-109
    • Nagy, A.1
  • 44
    • 0019888368 scopus 로고
    • Bacteriophage P1 site-specific recombination. II. Recombination between loxP and the bacterial chromosome
    • Sternberg N, Hamilton D, Hoess R. Bacteriophage P1 site-specific recombination. II. Recombination between loxP and the bacterial chromosome. J Mol Biol. 1981; 150(4):487-507.
    • (1981) J Mol Biol , vol.150 , Issue.4 , pp. 487-507
    • Sternberg, N.1    Hamilton, D.2    Hoess, R.3
  • 45
    • 0021764162 scopus 로고
    • Site-specific recombination by the bacteriophage P1 lox-Cre system. Cre-mediated synapsis of two lox sites
    • Hamilton DL, Abremski K. Site-specific recombination by the bacteriophage P1 lox-Cre system. Cre-mediated synapsis of two lox sites. J Mol Biol. 1984; 178(2):481-6.
    • (1984) J Mol Biol , vol.178 , Issue.2 , pp. 481-486
    • Hamilton, D.L.1    Abremski, K.2
  • 46
    • 0030886293 scopus 로고    scopus 로고
    • Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse
    • Guo F, Gopaul DN, Van Duyne GD. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature. 1997; 389(6646):40-6. doi: 10.1038/37925.
    • (1997) Nature , vol.389 , Issue.6646 , pp. 40-46
    • Guo, F.1    Gopaul, D.N.2    Van Duyne, G.D.3
  • 47
    • 2142746976 scopus 로고    scopus 로고
    • Unidirectional Cre-mediated genetic inversion in mice using the mutant loxP pair lox66/lox71
    • Oberdoerffer P, Otipoby KL, Maruyama M, Rajewsky K. Unidirectional Cre-mediated genetic inversion in mice using the mutant loxP pair lox66/lox71. Nucleic Acids Res. 2003; 31(22):e140.
    • (2003) Nucleic Acids Res , vol.31 , Issue.22
    • Oberdoerffer, P.1    Otipoby, K.L.2    Maruyama, M.3    Rajewsky, K.4
  • 48
    • 1542608429 scopus 로고    scopus 로고
    • Murine marrow cellularity and the concept of stem cell competition: geographic and quantitative determinants in stem cell biology
    • Colvin GA, Lambert JF, Abedi M, Hsieh CC, Carlson JE, Stewart FM, Quesenberry PJ. Murine marrow cellularity and the concept of stem cell competition: geographic and quantitative determinants in stem cell biology. Leukemia. 2004; 18(3):575-83. doi: 10.1038/sj.leu.2403268.
    • (2004) Leukemia , vol.18 , Issue.3 , pp. 575-583
    • Colvin, G.A.1    Lambert, J.F.2    Abedi, M.3    Hsieh, C.C.4    Carlson, J.E.5    Stewart, F.M.6    Quesenberry, P.J.7
  • 50
    • 84889281816 scopus 로고
    • Elements of information theory
    • New York: Wiley-Interscience
    • Cover TM, Thomas JA. Elements of information theory. New York: Wiley-Interscience; 1991.
    • (1991)
    • Cover, T.M.1    Thomas, J.A.2
  • 51
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008; 18(11):1851-8. doi: 10.1101/gr.078212.108.
    • (2008) Genome Res , vol.18 , Issue.11 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 53
    • 84887892419 scopus 로고    scopus 로고
    • Arrayed lentiviral barcoding for quantification analysis of hematopoietic dynamics
    • Grosselin J, Sii-Felice K, Payen E, Chretien S, Roux DT, Leboulch P. Arrayed lentiviral barcoding for quantification analysis of hematopoietic dynamics. Stem Cells. 2013; 31(10):2162-71. doi: 10.1002/stem.1383.
    • (2013) Stem Cells , vol.31 , Issue.10 , pp. 2162-2171
    • Grosselin, J.1    Sii-Felice, K.2    Payen, E.3    Chretien, S.4    Roux, D.T.5    Leboulch, P.6
  • 54
    • 84861083487 scopus 로고    scopus 로고
    • The analysis of singletons in generalized birthday problems
    • Koot MR, Mandjes M. The analysis of singletons in generalized birthday problems. Probab Eng Inform Sc. 2012; 26(2):245-62. doi: 10.1017/s0269964811000350.
    • (2012) Probab Eng Inform Sc , vol.26 , Issue.2 , pp. 245-262
    • Koot, M.R.1    Mandjes, M.2
  • 55
    • 0010974144 scopus 로고    scopus 로고
    • Introduction to Probability, 2 revised edn
    • Providence, Rhode Island, U.S.A: American Mathematical Society
    • Grinstead CM, Snell JL. Introduction to Probability, 2 revised edn. Providence, Rhode Island, U.S.A: American Mathematical Society; 1997.
    • (1997)
    • Grinstead, C.M.1    Snell, J.L.2
  • 56
    • 84856090845 scopus 로고    scopus 로고
    • Lineage Tracing
    • Kretzschmar K, Watt FM. Lineage Tracing. Cell. 2012; 148(1-2):33-45. doi: 10.1016/j.cell.2012.01.002.
    • (2012) Cell , vol.148 , Issue.1-2 , pp. 33-45
    • Kretzschmar, K.1    Watt, F.M.2
  • 58
    • 29144433945 scopus 로고    scopus 로고
    • Inferring the in vivo looping properties of DNA. Proc Natl Acad Sci U S A. 2005; 102(49):17642-5. doi: 10.1073/pnas.0505693102.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.49 , pp. 17642-17645


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