The use of fluorescence-activated cell sorting in studying plant development and environmental responses

International Journal of Developmental Biology

Volumn 57, Issue 6-8, 2013, Pages 545-552

  Carter, Anthony D ^a,b   Bonyadi, Roxanna ^a   Gifford, Miriam L ^a,b  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Arabidopsis; Cell sorting; Cell specificity; Fluorescent reporter; Plant root

Indexed keywords

FLUORESCENT DYE; GREEN FLUORESCENT PROTEIN;

ABIOTIC STRESS; ACCURACY; APICAL MERISTEM; ARABIDOPSIS THALIANA; CELL ISOLATION; CELL SPECIFICITY; ENVIRONMENTAL FACTOR; FLOW CYTOMETRY; FLUORESCENCE ACTIVATED CELL SORTING; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GROWTH REGULATION; MICROARRAY ANALYSIS; NONHUMAN; PLANT DEVELOPMENT; PLANT GROWTH; PLANT NUTRITION; PLANT ROOT; PRIORITY JOURNAL; REVIEW; SINGLE CELL ANALYSIS; TRANSCRIPTOMICS; TRANSGENIC PLANT;

ARABIDOPSIS; CELL SEPARATION; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, REPORTER; LUMINESCENT PROTEINS; MERISTEM; PLANT DEVELOPMENT; PLANT ROOTS; PLANTS; PLANTS, GENETICALLY MODIFIED; SYSTEMS BIOLOGY; TRANSCRIPTOME; TRANSGENES;

EID: 84886877193     PISSN: 02146282     EISSN: None     Source Type: Journal    
DOI: 10.1387/ijdb.130195mg     Document Type: Review

References (54)

1. BARGMANN BOR, BIRNBAUM KD. (2009). Positive fluorescent selection permits precise, rapid, and indepth overexpression analysis in plant protoplasts. Plant Physiol 149: 1231-1239.
2. BECKER JD, BOAVIDA LC, CARNEIRO J, HAURY M, FEIJÓ JA. (2003). Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome. Plant Physiol 133: 713-725.
3. BIRNBAUM K, JUNG JW, WANG JY, LAMBERT GM, HIRST JA, GALBRAITH DW, BENFEY PN. (2005). Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat Methods 2: 615-619.
4. BIRNBAUM K, SHASHA DE, WANG JY, JUNG JW, LAMBERT GM, GALBRAITH DW, BENFEY PN. (2003). A gene expression map of the Arabidopsis root. Science 302: 1956-1960.
5. BONNER WA, HULETT HR, SWEET RG, HERZENBERG LA. (1972). Fluorescence activated cell sorting. Rev Sci Instrum 43: 404-409.
6. BRADY SM, ORLANDO DA, LEE J-Y, WANG JY, KOCH J, DINNENY JR, MACE D, OHLER U, BENFEY PN. (2007). A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318: 801-806.
7. DAVIES WJ, WILKINSON S, LOVEYS B. (2002). Stomatal control by chemical signalling and the exploitation of this mechanism to increase water use efficiency in agriculture. New Phytol 153: 449-460.
8. DE SMET I, TETSUMURA T, DE RYBEL B, FREY DIT FREI N, LAPLAZE L, CASIMIRO I, SWARUP R, NAUDTS M, VANNESTE S, AUDENAERT D, INZÉ D, BENNETT MJ, BEECKMAN T. (2007). Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis. Development 134: 681-690.
9. DE SMET I, VASSILEVA V, DE RYBEL B, LEVESQUE MP, GRUNEWALD W, VAN DAMME D, VAN NOORDEN G, NAUDTS M, VAN ISTERDAEL G, DE CLERCQ R, WANG JY, MEULI N, VANNESTE S, FRIML J, HILSON P, JÜRGENS G, INGRAM GC, INZÉ D, BENFEY PN, BEECKMAN T. (2008). Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root. Science 322: 594-597.
10. DEAL RB, HENIKOFF S. (2010). A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell 18: 1030-1040.
11. DINNENY JR, LONG TA, WANG JY, JUNG JW, MACE D, POINTER S, BARRON C, BRADY SM, SCHIEFELBEIN J, BENFEY PN. (2008). Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320: 942-945.
12. EVRARD A, BARGMANN BOR, BIRNBAUM KD, TESTER M, BAUMANN U, JOHNSON AAT. (2012). Fluorescence-activated cell sorting for analysis of cell typespecific responses to salinity stress in Arabidopsis and rice. Methods Mol Biol 913: 265-276.
13. FERRÁNDIZ C, GU Q, MARTIENSSEN R, YANOFSKY MF. (2000). Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1 and CAULIFLOWER. Development 127: 725-734.
14. GALBRAITH D. (2012). Flow cytometry and cell sorting: the next generation. Methods 57: 249-250.
15. GEURTS R, FEDOROVA E, BISSELING T. (2005). Nod factor signaling genes and their function in the early stages of Rhizobium infection. Curr Opin Plant Biol 8: 346-352.
16. GIFFORD ML, DEAN S, INGRAM GC. (2003). The Arabidopsis ACR4 gene plays a role in cell layer organisation during ovule integument and sepal margin development. Development 130: 4249-4258.
17. GIFFORD ML, DEAN A, GUTIERREZ RA, CORUZZI GM, BIRNBAUM KD. (2008). Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci USA 105: 803-808.
18. GRØNLUND JT, EYRES A, KUMAR S, BUCHANANWOLLASTON V, GIFFORD ML. (2012). Cell specific analysis of Arabidopsis leaves using fluorescence activated cell sorting. J Vis Exp 68: e4214.
19. HARTMANN CH, KLEIN CA. (2006). Gene expression profiling of single cells on large-scale oligonucleotide arrays. Nucleic Acids Res 34: e143.
20. HASELOFF J. (1998). GFP variants for multispectral imaging of living cells. Methods Cell Biol 58: 139-151.
21. HEBENSTREIT D. (2012). Methods, challenges and potentials of single cell RNAseq. Biology 1: 658-667.
22. HIRSCH AM, KAPULNIK Y. (1998). Signal transduction pathways in mycorrhizal associations: comparisons with the Rhizobium-legume symbiosis. Fungal Genet Biol 23: 205-212.
23. JIAO Y, TAUSTA SL, GANDOTRA N, SUN N, LIU T, CLAY NK, CESERANI T, CHEN M, MA L, HOLFORD M, ZHANG H-Y, ZHAO H, DENG X-W, NELSON T. (2009). A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet 41: 258-263.
24. JULIUS MH, MASUDA T, HERZENBERG LA. (1972). Demonstration that antigenbinding cells are precursors of antibody-producing cells after purification with a fluorescence-activated cell sorter. Proc Natl Acad Sci USA 69: 1934-1938.
25. KANTLEHNER M, KIRCHNER R, HARTMANN P, ELLWART JW, ALUNNIFABBRONI M, SCHUMACHER A. (2011). A high-throughput DNA methylation analysis of a single cell. Nucleic Acids Res 39: e44.
26. KIDNER C, SUNDARESAN V, ROBERTS K, DOLAN L. (2000). Clonal analysis of the Arabidopsis root confirms that position, not lineage, determines cell fate. Planta 211: 191-199.
27. KLEBER R, KEHR J. (2006). Preparation and quality assessment of RNA from cell-specific samples obtained by laser microdissection. Methods Mol Biol 323: 367-377.
28. LAU OS, BERGMANN DC. (2012). Stomatal development: a plant's perspective on cell polarity, cell fate transitions and intercellular communication. Development 139: 3683-3692.
29. LAUX T, WÜRSCHUM T, BREUNINGER H. (2004). Genetic regulation of embryonic pattern formation. Plant Cell 16: S190-S202.
30. LIU J, LUO X, SHAFF J, LIANG C, JIA X, LI Z, MAGALHAES J, KOCHIAN LV. (2012). A promoter-swap strategy between the AtALMT and AtMATE genes increased Arabidopsis aluminum resistance and improved carbonuse efficiency for aluminum resistance. Plant J 71: 327-337.
31. MALAMY JE, BENFEY PN. (1997). Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development 124: 33-44.
32. MAMANOVA L, TURNER DJ. (2011). Lowbias, strandspecific transcriptome Illumina sequencing by on-flowcell reverse transcription (FRTseq). Nat Protoc 6: 1736-1747.
33. MARTIN C, PAZARES J. (1997). MYB transcription factors in plants. Trends Genet 13: 67-73.
34. MATTANOVICH D, BORTH N. (2006). Applications of cell sorting in biotechnology. Microb Cell Fact 5: 12.
35. 2. Plant Cell Environ 8: 467-474.
36. MOUSSAIEFF A, ROGACHEV I, BRODSKY L, MALITSKY S, TOAL TW, BELCHER H, YATIV M, BRADY SM, BENFEY PN, AHARONI A. (2013). High-resolution metabolic mapping of cell types in plant roots. Proc Natl Acad Sci USA 110: E1232-E1241.
37. MUNSKY B, NEUERT G, VAN OUDENAARDEN A. (2012). Using gene expression noise to understand gene regulation. Science 336: 183-187.
38. MUSTROPH A, ZANETTI ME, JANG CJH, HOLTAN HE, REPETTI PP, GALBRAITH DW, GIRKE T, BAILEYSERRES J. (2009). Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci USA 106: 18843-18848.
39. NAKAJIMA K, SENA G, NAWY T, BENFEY PN. (2001). Intercellular movement of the putative transcription factor SHR in root patterning. Nature 413: 307-311.
40. NAWY T, LEE J. Y, COLINAS J, WANG JY, THONGROD SC, MALAMY JE, BIRNBAUM K, BENFEY PN. (2005). Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell 17: 1908-1925.
41. NELSON M. (1999). An overview of the use of flow cytometry in the analysis of mixed red cell populations. Pathology 31: 191-198.
42. OLDROYD GED, DOWNIE JA. (2008). Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu Rev Plant Biol 59: 519-546.
43. PETERSSON SV, JOHANSSON AI, KOWALCZYK M, MAKOVEYCHUK A, WANG JY, MORITZ T, GREBE M, BENFEY PN, SANDBERG G, LJUNG K. (2009). An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. Plant Cell 21: 1659-1668.
44. PETRICKA JJ, SCHAUER MA, MEGRAW M, BREAKFIELD NW, THOMPSON JW, GEORGIEV S, SODERBLOM EJ, OHLER U, MOSELEY MA, GROSSNIKLAUS U, BENFEY PN. (2012). The protein expression landscape of the Arabidopsis root. Proc Natl Acad Sci USA 109: 6811-6818.
45. R DEVELOPMENT CORE TEAM (2012). R: A language and environment for statistical computing. Vienna, Austria, R Foundation for Statistical Computing.
46. ROGERS ED, JACKSON T, MOUSSAIEFF A, AHARONI A, BENFEY PN. (2012). Cell typespecific transcriptional profiling: implications for metabolite profiling. Plant J 70: 5-17.
47. RUBAKHIN SS, LANNI EJ, SWEEDLER JV. (2013). Progress toward single cell metabolomics. Curr Opin Biotechnol 24: 95-104.
48. RUSHTON PJ, SOMSSICH IE, RINGLER P, SHEN QJ. (2010). WRKY transcription factors. Trends Plant Sci 15: 247-258.
49. SALEHIREYHANI A, KAPLINSKY J, BURGIN E, NOVAKOVA M, DEMELLO AJ, TEMPLER RH, PARKER P, NEIL MAA, CES O, FRENCH P, WILLISON KR, KLUG D. (2011). A first step towards practical single cell proteomics: a microfluidic antibody capture chip with TIRF detection. Lab Chip 11: 1256-1261.
50. SCHOLL RL, MAY ST, WARE DH. (2000). Seed and molecular resources for Arabidopsis. Plant Physiol 124: 1477-1480.
51. TAN DWM, JENSEN KB, TROTTER MWB, CONNELLY JT, BROAD S, WATT FM. (2013). Single-cell gene expression profiling reveals functional heterogeneity of undifferentiated human epidermal cells. Development 140: 1433-1444.
52. TANG F, BARBACIORU C, BAO S, LEE C, NORDMAN E, WANG X, LAO K, SURANI MA. (2010). Tracing the derivation of embryonic stem cells from the inner cell mass by singlecell RNASeq analysis. Cell Stem Cell 6: 468-478.
53. TANIGUCHI Y, CHOI PJ, LI G. W, CHEN H, BABU M, HEARN J, EMILI A, XIE XS. (2010). Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
54. YADAV RK, GIRKE T, PASALA S, XIE M, REDDY GV. (2009). Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proc Natl Acad Sci USA 106: 4941-4946.