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PMID: 17764504 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).

The Plant journal : for cell and molecular biology ·Vol. 52 ·No. 3 ·2007-11-00 ·Pages 391-404

Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MC, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon MJ, Schnable PS

Abstract

All above-ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14-day-old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM-collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P < 0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up- and down-regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT-PCR and/or in situ hybridization. The up-regulated ESTs included many regulatory genes including transcription factors, chromatin remodeling factors and components of the gene-silencing machinery, as well as about 900 genes with unknown functions. Surprisingly, transcripts that hybridized to 62 retrotransposon-related cDNAs were also substantially up-regulated in the SAM. Complementary DNAs derived from the LCM-collected SAMs were sequenced to identify additional genes that are expressed in the SAM. This generated around 550 000 ESTs (454-SAM ESTs) from two genotypes. Consistent with the microarray results, approximately 14% of the 454-SAM ESTs from B73 were retrotransposon-related. Possible roles of genes that are preferentially expressed in the SAM are discussed.

MeSH Terms
Gene Expression Profiling Gene Expression Regulation, Plant Genes, Plant In Situ Hybridization Meristem/cytology,genetics Oligonucleotide Array Sequence Analysis RNA, Plant/genetics Retroelements Reverse Transcriptase Polymerase Chain Reaction Zea mays/cytology,genetics
Chemicals
RNA, Plant Retroelements
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Ohtsu Kazuhiro
Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
Smith Marianne B
Emrich Scott J
Borsuk Lisa A
Zhou Ruilian
Chen Tianle
Zhang Xiaolan
Timmermans Marja C P
Beck Jon
Buckner Brent
Janick-Buckner Diane
Nettleton Dan
Scanlon Michael J
Schnable Patrick S
References (70)
70 references, click to expand
  1. All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents.
    Proc Natl Acad Sci U S A. 2006 May 2;103(18):6805-10 PMID: 16641103
  2. Morphogenesis of the endoplasmic reticulum: beyond active membrane expansion.
    Traffic. 2006 Jun;7(6):639-46 PMID: 16683914
  3. Metabolic aspects of organogenesis in the shoot apical meristem.
    J Exp Bot. 2006;57(9):1863-70 PMID: 16690623
  4. An RNA-dependent RNA polymerase is required for paramutation in maize.
    Nature. 2006 Jul 20;442(7100):295-8 PMID: 16855589
  5. Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes.
    Bioinformatics. 2006 Aug 1;22(15):1863-70 PMID: 16731695
  6. The application of laser microdissection to in planta gene expression profiling of the maize anthracnose stalk rot fungus Colletotrichum graminicola.
    Mol Plant Microbe Interact. 2006 Nov;19(11):1240-50 PMID: 17073306
  7. Laser capture microdissection of plant cells from tape-transferred paraffin sections promotes recovery of structurally intact RNA for global gene profiling.
    Plant J. 2006 Nov;48(4):628-37 PMID: 17026538
  8. Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors.
    PLoS Biol. 2006 Oct;4(10):e339 PMID: 16968137
  9. Gene discovery and annotation using LCM-454 transcriptome sequencing.
    Genome Res. 2007 Jan;17(1):69-73 PMID: 17095711
  10. Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies.
    Plant Cell Physiol. 2007 Jan;48(1):3-7 PMID: 17148694
  11. Involving undergraduates in the annotation and analysis of global gene expression studies: creation of a maize shoot apical meristem expression database.
    Genetics. 2007 Jun;176(2):741-7 PMID: 17409087
  12. SNP discovery via 454 transcriptome sequencing.
    Plant J. 2007 Sep;51(5):910-8 PMID: 17662031
  13. Silencing of retrotransposons in arabidopsis and reactivation by the ddm1 mutation.
    Plant Cell. 2000 Mar;12(3):357-69 PMID: 10715322
  14. Molecular cloning and partial characterization of a plant VAP33 homologue with a major sperm protein domain.
    Biochem Biophys Res Commun. 2000 Apr 2;270(1):286-92 PMID: 10733941
  15. MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes.
    Plant J. 2000 Nov;24(4):457-66 PMID: 11115127
  16. The hAT family: a versatile transposon group common to plants, fungi, animals, and man.
    Chromosoma. 2001 Apr;110(1):1-9 PMID: 11398971
  17. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome.
    Genome Res. 2001 Oct;11(10):1660-76 PMID: 11591643
  18. DNA sequence quality trimming and vector removal.
    Bioinformatics. 2001 Dec;17(12):1093-104 PMID: 11751217
  19. Intercellular trafficking of a KNOTTED1 green fluorescent protein fusion in the leaf and shoot meristem of Arabidopsis.
    Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):4103-8 PMID: 11891300
  20. Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control.
    Science. 2002 Jul 12;297(5579):243-6 PMID: 12114624
  21. Centromeric retroelements and satellites interact with maize kinetochore protein CENH3.
    Plant Cell. 2002 Nov;14(11):2825-36 PMID: 12417704
  22. Mutator transposons.
    Trends Plant Sci. 2002 Nov;7(11):498-504 PMID: 12417150
  23. The Arabidopsis GNOM ARF-GEF mediates endosomal recycling, auxin transport, and auxin-dependent plant growth.
    Cell. 2003 Jan 24;112(2):219-30 PMID: 12553910
  24. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation.
    Science. 2003 Jan 31;299(5607):716-9 PMID: 12522258
  25. 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. 2003 Mar;15(3):583-96 PMID: 12615934
  26. Laser capture microdissection of cells from plant tissues.
    Plant Physiol. 2003 May;132(1):27-35 PMID: 12746508
  27. Sperm cells of Zea mays have a complex complement of mRNAs.
    Plant J. 2003 Jun;34(5):697-707 PMID: 12787250
  28. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world.
    Plant Cell. 2003 Jul;15(7):1538-51 PMID: 12837945
  29. Shoot apical meristem maintenance: the art of a dynamic balance.
    Trends Plant Sci. 2003 Aug;8(8):394-401 PMID: 12927973
  30. Apical meristems: the plant's fountain of youth.
    Bioessays. 2003 Oct;25(10):961-70 PMID: 14505363
  31. Retrotransposons provide an evolutionarily robust non-telomerase mechanism to maintain telomeres.
    Annu Rev Genet. 2003;37:485-511 PMID: 14616071
  32. Regulation of phyllotaxis by polar auxin transport.
    Nature. 2003 Nov 20;426(6964):255-60 PMID: 14628043
  33. Local, efflux-dependent auxin gradients as a common module for plant organ formation.
    Cell. 2003 Nov 26;115(5):591-602 PMID: 14651850
  34. RNA silencing genes control de novo DNA methylation.
    Science. 2004 Feb 27;303(5662):1336 PMID: 14988555
  35. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity.
    Nature. 2004 Mar 4;428(6978):84-8 PMID: 14999285
  36. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification.
    PLoS Biol. 2003 Dec;1(3):E67 PMID: 14691539
  37. Genetic and functional diversification of small RNA pathways in plants.
    PLoS Biol. 2004 May;2(5):E104 PMID: 15024409
  38. The maize duplicate genes narrow sheath1 and narrow sheath2 encode a conserved homeobox gene function in a lateral domain of shoot apical meristems.
    Development. 2004 Jun;131(12):2827-39 PMID: 15169755
  39. Role of transposable elements in heterochromatin and epigenetic control.
    Nature. 2004 Jul 22;430(6998):471-6 PMID: 15269773
  40. Chromatin-based silencing mechanisms.
    Curr Opin Plant Biol. 2004 Oct;7(5):521-6 PMID: 15337094
  41. PINning down the connections: transcription factors and hormones in leaf morphogenesis.
    Curr Opin Plant Biol. 2004 Oct;7(5):575-81 PMID: 15337101
  42. Specification of adaxial cell fate during maize leaf development.
    Development. 2004 Sep;131(18):4533-44 PMID: 15342478
  43. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos.
    Dev Cell. 2004 Oct;7(4):597-606 PMID: 15469847
  44. Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize.
    Genes Dev. 1990 Mar;4(3):331-43 PMID: 2159936
  45. The developmental gene Knotted-1 is a member of a maize homeobox gene family.
    Nature. 1991 Mar 21;350(6315):241-3 PMID: 1672445
  46. Arabidopsis thaliana DNA methylation mutants.
    Science. 1993 Jun 25;260(5116):1926-8 PMID: 8316832
  47. A VAMP-binding protein from Aplysia required for neurotransmitter release.
    Science. 1995 Sep 15;269(5230):1580-3 PMID: 7667638
  48. Retrotransposons of rice involved in mutations induced by tissue culture.
    Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7783-8 PMID: 8755553
  49. Laser capture microdissection.
    Science. 1996 Nov 8;274(5289):998-1001 PMID: 8875945
  50. Regulation of leaf initiation by the terminal ear 1 gene of maize.
    Nature. 1998 May 14;393(6681):166-8 PMID: 9603518
  51. Laser-capture microdissection: opening the microscopic frontier to molecular analysis.
    Trends Genet. 1998 Jul;14(7):272-6 PMID: 9676529
  52. Gene expression profiles of laser-captured adjacent neuronal subtypes.
    Nat Med. 1999 Jan;5(1):117-22 PMID: 9883850
  53. ROUGH SHEATH2: a Myb protein that represses knox homeobox genes in maize lateral organ primordia.
    Science. 1999 Apr 2;284(5411):151-3 PMID: 10102816
  54. The maize rough sheath2 gene and leaf development programs in monocot and dicot plants.
    Science. 1999 Apr 2;284(5411):154-6 PMID: 10102817
  55. Maintenance of genomic methylation requires a SWI2/SNF2-like protein.
    Nat Genet. 1999 May;22(1):94-7 PMID: 10319870
  56. Chromosome organization and genic expression.
    Cold Spring Harb Symp Quant Biol. 1951;16:13-47 PMID: 14942727
  57. Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis.
    Plant J. 2005 Apr;42(1):111-23 PMID: 15773857
  58. RNA polymerase IV directs silencing of endogenous DNA.
    Science. 2005 Apr 1;308(5718):118-20 PMID: 15692015
  59. WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis.
    Genes Dev. 2005 Apr 15;19(8):992-1003 PMID: 15833920
  60. Gardening the genome: DNA methylation in Arabidopsis thaliana.
    Nat Rev Genet. 2005 May;6(5):351-60 PMID: 15861207
  61. Atypical RNA polymerase subunits required for RNA-directed DNA methylation.
    Nat Genet. 2005 Jul;37(7):761-5 PMID: 15924141
  62. Regulation of meristem activity by chromatin remodelling.
    Trends Plant Sci. 2005 Jul;10(7):332-8 PMID: 15953752
  63. The role of the RNAi machinery in heterochromatin formation.
    Cell. 2005 Jul 15;122(1):13-6 PMID: 16009128
  64. Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.
    Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12282-7 PMID: 16103354
  65. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.
    Genes Dev. 2005 Sep 1;19(17):2030-40 PMID: 16140984
  66. Genome sequencing in microfabricated high-density picolitre reactors.
    Nature. 2005 Sep 15;437(7057):376-80 PMID: 16056220
  67. Maize rough sheath2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis.
    Plant Cell. 2005 Nov;17(11):2886-98 PMID: 16243907
  68. Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1.
    Plant Physiol. 2005 Nov;139(3):1255-67 PMID: 16215225
  69. Structure and architecture of the maize genome.
    Plant Physiol. 2005 Dec;139(4):1612-24 PMID: 16339807
  70. A transcriptome-based characterization of habituation in plant tissue culture.
    Plant Physiol. 2006 Apr;140(4):1255-78 PMID: 16489130
Article Info
Journal
The Plant journal : for cell and molecular biology
Abbr.
Plant J
ISSN
0960-7412
DOI
10.1111/j.1365-313X.2007.03244.x
Published
2007-11-00
Epub
2007-00-23
Pages
391-404
Language
English
Region
England
NLM ID
9207397
PMCID
PMC2156186
Subset
IM
External Links
PubMed source DOI: 10.1111/j.1365-313X.2007.03244.x PMC Full Text View journal details
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