Frontiers in Biology

, 6:384 | Cite as

Advances in plant cell type-specific genome-wide studies of gene expression

  • Ying Wang
  • Yuling JiaoEmail author


Cell is the functional unit of life. To study the complex interactions of systems of biological molecules, it is crucial to dissect these molecules at the cell level. In recent years, major progresses have been made by plant biologists to profile gene expression in specific cell types at the genome-wide level. Approaches based on the isolation of cells, polysomes or nuclei have been developed and successfully used for studying the cell types from distinct organs of several plant species. These cell-level data sets revealed previously unrecognized cellular properties, such as cell-specific gene expression modules and hormone response centers, and should serve as essential resources for functional genomic analyses. Newly developed technologies are more affordable to many laboratories and should help to provide new insights at the cellular resolution in the near future.


transcriptome cell type plant 


  1. Birnbaum K, Shasha D E, Wang J Y, Jung J W, Lambert G M, Galbraith D W, Benfey P N (2003). A gene expression map of the Arabidopsis root. Science, 302(5652): 1956–1960PubMedCrossRefGoogle Scholar
  2. Brady S M, Orlando D A, Lee J Y, Wang J Y, Koch J, Dinneny J R, Mace D, Ohler U, Benfey P N (2007). A high-resolution root spatiotemporal map reveals dominant expression patterns. Science, 318(5851): 801–806PubMedCrossRefGoogle Scholar
  3. Brooks L 3rd, Strable J, Zhang X, Ohtsu K, Zhou R, Sarkar A, Hargreaves S, Elshire R J, Eudy D, Pawlowska T, Ware D, Janick-Buckner D, Buckner B, Timmermans M C, Schnable P S, Nettleton D, Scanlon M J (2009). Microdissection of shoot meristem functional domains. PLoS Genet, 5(5): e1000476PubMedCrossRefGoogle Scholar
  4. Cai S, Lashbrook C C (2008). Stamen abscission zone transcriptome profiling reveals new candidates for abscission control: enhanced retention of floral organs in transgenic plants overexpressing Arabidopsis ZINC FINGER PROTEIN2. Plant Physiol, 146(3): 1305–1321PubMedCrossRefGoogle Scholar
  5. Casson S, Spencer M, Walker K, Lindsey K (2005). Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis. Plant J, 42(1): 111–123PubMedCrossRefGoogle Scholar
  6. Cho Y, Fernandes J, Kim S H, Walbot V (2002). Gene-expression profile comparisons distinguish seven organs of maize. Genome Biol, 3: research0045.1-0045.16Google Scholar
  7. Deal R B, Henikoff S (2010). A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell, 18(6): 1030–1040PubMedCrossRefGoogle Scholar
  8. Dembinsky D, Woll K, Saleem M, Liu Y, Fu Y, Borsuk L A, Lamkemeyer T, Fladerer C, Madlung J, Barbazuk B, Nordheim A, Nettleton D, Schnable P S, Hochholdinger F (2007). Transcriptomic and proteomic analyses of pericycle cells of the maize primary root. Plant Physiol, 145(3): 575–588PubMedCrossRefGoogle Scholar
  9. Demura T, Tashiro G, Horiguchi G, Kishimoto N, Kubo M, Matsuoka N, Minami A, Nagata-Hiwatashi M, Nakamura K, Okamura Y, Sassa N, Suzuki S, Yazaki J, Kikuchi S, Fukuda H (2002). Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc Natl Acad Sci USA, 99(24): 15794–15799PubMedCrossRefGoogle Scholar
  10. Dinneny J R, Long T A, Wang J Y, Jung J W, Mace D, Pointer S, Barron C, Brady S M, Schiefelbein J, Benfey P N (2008). Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science, 320(5878): 942–945PubMedCrossRefGoogle Scholar
  11. Edwards D, Murray J A, Smith A G (1998). Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. Plant Physiol, 117(3): 1015–1022PubMedCrossRefGoogle Scholar
  12. Emrich S J, Barbazuk W B, Li L, Schnable P S (2007). Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res, 17(1): 69–73PubMedCrossRefGoogle Scholar
  13. Engel M L, Chaboud A, Dumas C, McCormick S (2003). Sperm cells of Zea mays have a complex complement of mRNAs. Plant J, 34(5): 697–707PubMedCrossRefGoogle Scholar
  14. Galbraith D W, Birnbaum K (2006). Global studies of cell type-specific gene expression in plants. Annu Rev Plant Biol, 57(1): 451–475PubMedCrossRefGoogle Scholar
  15. Honys D, Twell D (2004). Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol, 5(11): R85PubMedCrossRefGoogle Scholar
  16. Ideker T, Galitski T, Hood L (2001). A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet, 2(1): 343–372PubMedCrossRefGoogle Scholar
  17. Jiao Y, Lau O S, Deng X W (2007). Light-regulated transcriptional networks in higher plants. Nat Rev Genet, 8(3): 217–230PubMedCrossRefGoogle Scholar
  18. Jiao Y, Meyerowitz E M (2010). Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol Syst Biol, 6: 419PubMedCrossRefGoogle Scholar
  19. Jiao Y, Tausta S L, Gandotra N, Sun N, Liu T, Clay N K, 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(2): 258–263PubMedCrossRefGoogle Scholar
  20. Lee J Y, Colinas J, Wang J Y, Mace D, Ohler U, Benfey P N (2006). Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc Natl Acad Sci USA, 103(15): 6055–6060PubMedCrossRefGoogle Scholar
  21. Lee J Y, Levesque M, Benfey P N (2005). High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems. Plant Physiol, 138(2): 585–590Google Scholar
  22. Leonhardt N, Kwak J M, Robert N, Waner D, Leonhardt G, Schroeder J I (2004). Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant. Plant Cell, 16(3): 596–615PubMedCrossRefGoogle Scholar
  23. Levesque M P, Vernoux T, Busch W, Cui H, Wang J Y, Blilou I, Hassan H, Nakajima K, Matsumoto N, Lohmann J U, Scheres B, Benfey P N (2006). Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol, 4(5): e143PubMedCrossRefGoogle Scholar
  24. Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta S L, Kebrom T H, Provart N, Patel R, Myers C R, Reidel E J, Turgeon R, Liu P, Sun Q, Nelson T, Brutnell T P (2010). The developmental dynamics of the maize leaf transcriptome. Nat Genet, 42(12): 1060–1067PubMedCrossRefGoogle Scholar
  25. Long T A, Brady S M, Benfey P N (2008). Systems approaches to identifying gene regulatory networks in plants. Annu Rev Cell Dev Biol, 24(1): 81–103PubMedCrossRefGoogle Scholar
  26. Ma L, Sun N, Liu X, Jiao Y, Zhao H, Deng X W (2005). Organ-specific expression of Arabidopsis genome during development. Plant Physiol, 138(1): 80–91PubMedCrossRefGoogle Scholar
  27. Motose H, Sugiyama M, Fukuda H (2004). A proteoglycan mediates inductive interaction during plant vascular development. Nature, 429(6994): 873–878PubMedCrossRefGoogle Scholar
  28. Mustroph A, Zanetti M E, Jang C J, Holtan H E, Repetti P P, Galbraith D W, Girke T, Bailey-Serres J (2009). Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci USA, 106(44): 18843–18848PubMedCrossRefGoogle Scholar
  29. Nakazono M, Qiu F, Borsuk L A, Schnable P S (2003). Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell, 15(3): 583–596PubMedCrossRefGoogle Scholar
  30. Nawy T, Lee J Y, Colinas J, Wang J Y, Thongrod S C, Malamy J E, Birnbaum K, Benfey P N (2005). Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell, 17(7): 1908–1925PubMedCrossRefGoogle Scholar
  31. Nelson T, Gandotra N, Tausta S L (2008). Plant cell types: reporting and sampling with new technologies. Curr Opin Plant Biol, 11(5): 567–573PubMedCrossRefGoogle Scholar
  32. Nelson T, Tausta S L, Gandotra N, Liu T (2006). Laser microdissection of plant tissue: what you see is what you get. Annu Rev Plant Biol, 57(1): 181–201PubMedCrossRefGoogle Scholar
  33. Pina C, Pinto F, Feijó J A, Becker J D (2005). Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol, 138(2): 744–756PubMedCrossRefGoogle Scholar
  34. Schmid M, Davison T S, Henz S R, Pape U J, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann J U (2005). A gene expression map of Arabidopsis thaliana development. Nat Genet, 37(5): 501–506PubMedCrossRefGoogle Scholar
  35. Spencer M W, Casson S A, Lindsey K (2007). Transcriptional profiling of the Arabidopsis embryo. Plant Physiol, 143(2): 924–940PubMedCrossRefGoogle Scholar
  36. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch B B, Siddiqui A, Lao K, Surani M A (2009). mRNASeq whole-transcriptome analysis of a single cell. Nat Methods, 6(5): 377–382PubMedCrossRefGoogle Scholar
  37. Van Gelder R N, von Zastrow M E, Yool A, Dement W C, Barchas J D, Eberwine J H (1990). Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA, 87(5): 1663–1667PubMedCrossRefGoogle Scholar
  38. Wienkoop S, Zoeller D, Ebert B, Simon-Rosin U, Fisahn J, Glinski M, Weckwerth W (2004). Cell-specific protein profiling in Arabidopsis thaliana trichomes: identification of trichome-located proteins involved in sulfur metabolism and detoxification. Phytochemistry, 65(11): 1641–1649PubMedCrossRefGoogle Scholar
  39. Wuest S E, Vijverberg K, Schmidt A, Weiss M, Gheyselinck J, Lohr M, Wellmer F, Rahnenführer J, von Mering C, Grossniklaus U (2010). Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes. Curr Biol, 20(6): 506–512PubMedCrossRefGoogle Scholar
  40. Yadav R K, Girke T, Pasala S, Xie M, Reddy G V (2009). Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proc Natl Acad Sci USA, 106(12): 4941–4946PubMedCrossRefGoogle Scholar
  41. Zanetti M E, Chang I F, Gong F, Galbraith D W, Bailey-Serres J (2005). Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol, 138(2): 624–635PubMedCrossRefGoogle Scholar
  42. Zhang C, Barthelson R A, Lambert G M, Galbraith D W (2008). Global characterization of cell-specific gene expression through fluorescenceactivated sorting of nuclei. Plant Physiol, 147(1): 30–40PubMedCrossRefGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  1. 1.Division of BiologyCalifornia Institute of TechnologyPasadenaUSA
  2. 2.State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina

Personalised recommendations