Skip to main content
SpringerLink
Log in

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

  • Review
  • Published:
Frontiers in Biology

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • 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): 1956–1960

    Article  PubMed  CAS  Google Scholar 

  • 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): 801–806

    Article  PubMed  CAS  Google Scholar 

  • 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): e1000476

    Article  PubMed  Google Scholar 

  • 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): 1305–1321

    Article  PubMed  CAS  Google Scholar 

  • 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): 111–123

    Article  PubMed  CAS  Google Scholar 

  • Cho Y, Fernandes J, Kim S H, Walbot V (2002). Gene-expression profile comparisons distinguish seven organs of maize. Genome Biol, 3: research0045.1-0045.16

  • 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): 1030–1040

    Article  PubMed  CAS  Google Scholar 

  • 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): 575–588

    Article  PubMed  CAS  Google Scholar 

  • 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): 15794–15799

    Article  PubMed  Google Scholar 

  • 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): 942–945

    Article  PubMed  CAS  Google Scholar 

  • 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): 1015–1022

    Article  PubMed  CAS  Google Scholar 

  • 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): 69–73

    Article  PubMed  CAS  Google Scholar 

  • 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): 697–707

    Article  PubMed  CAS  Google Scholar 

  • Galbraith D W, Birnbaum K (2006). Global studies of cell type-specific gene expression in plants. Annu Rev Plant Biol, 57(1): 451–475

    Article  PubMed  CAS  Google Scholar 

  • Honys D, Twell D (2004). Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol, 5(11): R85

    Article  PubMed  Google Scholar 

  • Ideker T, Galitski T, Hood L (2001). A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet, 2(1): 343–372

    Article  PubMed  CAS  Google Scholar 

  • Jiao Y, Lau O S, Deng X W (2007). Light-regulated transcriptional networks in higher plants. Nat Rev Genet, 8(3): 217–230

    Article  PubMed  CAS  Google Scholar 

  • 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: 419

    Article  PubMed  Google Scholar 

  • 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): 258–263

    Article  PubMed  CAS  Google Scholar 

  • 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): 6055–6060

    Article  PubMed  CAS  Google Scholar 

  • 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): 585–590

    CAS  Google Scholar 

  • 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): 596–615

    Article  PubMed  CAS  Google Scholar 

  • 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): e143

    Article  PubMed  Google Scholar 

  • 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): 1060–1067

    Article  PubMed  CAS  Google Scholar 

  • 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): 81–103

    Article  PubMed  CAS  Google Scholar 

  • 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): 80–91

    Article  PubMed  CAS  Google Scholar 

  • Motose H, Sugiyama M, Fukuda H (2004). A proteoglycan mediates inductive interaction during plant vascular development. Nature, 429(6994): 873–878

    Article  PubMed  CAS  Google Scholar 

  • 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): 18843–18848

    Article  PubMed  CAS  Google Scholar 

  • 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): 583–596

    Article  PubMed  CAS  Google Scholar 

  • 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): 1908–1925

    Article  PubMed  CAS  Google Scholar 

  • Nelson T, Gandotra N, Tausta S L (2008). Plant cell types: reporting and sampling with new technologies. Curr Opin Plant Biol, 11(5): 567–573

    Article  PubMed  CAS  Google Scholar 

  • 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): 181–201

    Article  PubMed  CAS  Google Scholar 

  • 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): 744–756

    Article  PubMed  CAS  Google Scholar 

  • 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): 501–506

    Article  PubMed  CAS  Google Scholar 

  • Spencer M W, Casson S A, Lindsey K (2007). Transcriptional profiling of the Arabidopsis embryo. Plant Physiol, 143(2): 924–940

    Article  PubMed  CAS  Google Scholar 

  • 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): 377–382

    Article  PubMed  CAS  Google Scholar 

  • 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): 1663–1667

    Article  PubMed  Google Scholar 

  • 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): 1641–1649

    Article  PubMed  CAS  Google Scholar 

  • 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): 506–512

    Article  PubMed  CAS  Google Scholar 

  • 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): 4941–4946

    Article  PubMed  CAS  Google Scholar 

  • 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): 624–635

    Article  PubMed  CAS  Google Scholar 

  • 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): 30–40

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA

    Ying Wang

  2. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Yuling Jiao

Authors
  1. Ying Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuling Jiao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuling Jiao.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, Y., Jiao, Y. Advances in plant cell type-specific genome-wide studies of gene expression. Front. Biol. 6, 384–389 (2011). https://doi.org/10.1007/s11515-011-1141-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11515-011-1141-7

Keywords

Search

Navigation