Skip to main content
SpringerLink
Log in

A Pilot Study of Transcription Unit Analysis in Rice Using Oligonucleotide Tiling-path Microarray

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcription units that will facilitate rice genome annotation.

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

  • A. Baba S. Hasezawa K. Syono (1986) ArticleTitleCultivation of rice protoplasts and their transformation mediated by Agrobacterium spheroplasts Plant Cell Physiol. 27 463–471

    Google Scholar 

  • J.A. Bedell M.A. Budiman A. Nunberg R.W. Citek D. Robbins J. Jones E. Flick T. Rohlfing J. Fries K. Bradford (2005) ArticleTitleSorghum genome sequencing by methylation filtration PLOS. Biol. 3 e13 Occurrence Handle10.1371/journal.pbio.0030013 Occurrence Handle15660154

    Article  PubMed  Google Scholar 

  • J.L. Bennetzen J. Ma (2003) ArticleTitleThe genetic colinearity of rice and other cereals on the basis of genomic sequence analysis Curr. Opin. Plant Biol. 6 128–133

    Google Scholar 

  • P. Bertone V. Stolc T.E. Royce J.S. Rozowsky A.E. Urban X. Zhu W. Tongprasit M. Samanta S. Weissman M. Gerstein (2004) ArticleTitleGlobal identification of human transcribed sequences with genome tiling arrays Science 306 2242–2246 Occurrence Handle10.1126/science.1103388 Occurrence Handle15539566

    Article  PubMed  Google Scholar 

  • J.E. Bowers C. Abbey S. Anderson C. Chang X. Draye A.H. Hoppe R. Jessup C. Lemke J. Lennington Z.K. Li (2003) ArticleTitleA high-density genetic recombination map of sequence-tagged sites for Sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses Genetics 165 367–386 Occurrence Handle14504243

    PubMed  Google Scholar 

  • H.J. Bussemaker H. Li E.D. Siggia (2001) ArticleTitleRegulatory element detection using correlation with expression Nature Genetics 27 167–174 Occurrence Handle10.1038/84792 Occurrence Handle11175784

    Article  PubMed  Google Scholar 

  • M.B. Eisen P.T. Spellman P.O. Brown D. Botstein (1998) ArticleTitleCluster analysis and display of genome-wide expression pattern Proc. Natl. Acad. Sci. USA 95 14863–14868 Occurrence Handle10.1073/pnas.95.25.14863 Occurrence Handle9843981

    Article  PubMed  Google Scholar 

  • Q. Feng Y.J. Zhang P. Hao S.Y. Wang G. Fu Y.C. Huang Y. Li J.J. Zhu Y.L. Liu X. Hu (2002) ArticleTitleSequence and analysis of rice chromosome 4 Nature 420 316–320

    Google Scholar 

  • K.A. Frazer J.B. Sheehan R.P. Stokowski X. Chen R. Hosseini J-F. Cheng S.P.A. Fodor D.R. Cox N. Patil (2001) ArticleTitleEvolutionarily conserved sequences on human Chromosome 21 Genome Res. 11 1651–1659 Occurrence Handle10.1101/gr.198201 Occurrence Handle11591642

    Article  PubMed  Google Scholar 

  • M.D. Gale K.M. Devos (1998a) ArticleTitleComparative genetics in the grasses Proc. Natl. Acad. Sci. USA 95 1971–1974 Occurrence Handle10.1073/pnas.95.5.1971

    Article  Google Scholar 

  • M.D. Gale K.M. Devos (1998b) ArticleTitlePlant comparative genetics after 10 years Science 282 656–659 Occurrence Handle10.1126/science.282.5389.656

    Article  Google Scholar 

  • S.A. Goff (1999) ArticleTitleRice as a model for cereal genomics Curr. Opin. Plant Biol. 2 86–89 Occurrence Handle10.1016/S1369-5266(99)80018-1 Occurrence Handle10322198

    Article  PubMed  Google Scholar 

  • S.A. Goff D. Ricke T.H. Lan G. Presting R.L. Wang M. Dunn J. Glazebrook A. Sessions P. Oeller H. Varma (2002) ArticleTitleA draft sequence of the rice genome (Oryza sativa L. ssp japonica) Science 296 92–100 Occurrence Handle10.1126/science.1068275 Occurrence Handle11935018

    Article  PubMed  Google Scholar 

  • R. Guigó P.A. Agarwal J.F. Abril M. Burset J.W. Fickett (2000) ArticleTitleAn assessment of gene prediction accuracy in large DNA sequences Genome Res. 10 1631–1642 Occurrence Handle10.1101/gr.122800 Occurrence Handle11042160

    Article  PubMed  Google Scholar 

  • Hass B.J., Volfovsky N., Town C.D., Troukhan M., Alexandrov N., Feldmann K.A., Flavell R.B., White O. and Salzberg S.L. 2002. Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol. 3: research0029.1–0029.12

    Google Scholar 

  • M. Hild B. Beckman S.A. Hass B. Koch V. Solovyev C. Busold K. Fellenberg M. Boutros M. Vingron F. Sauer (2003) ArticleTitleAn integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome Genome Biol. 5 R3 Occurrence Handle10.1186/gb-2003-5-1-r3 Occurrence Handle14709175

    Article  PubMed  Google Scholar 

  • K. Hoshikawa (1993) Science of the Rice Plant, vol 1: Morphology Nobunkyo Tokyo 133–186

    Google Scholar 

  • V.R. Iyer C.E. Horak C.S. Scafe D. Botstein M. Snyder P.O. Brown (2001) ArticleTitleGenomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature 409 533–538 Occurrence Handle10.1038/35054095 Occurrence Handle11206552

    Article  PubMed  Google Scholar 

  • Jiao Y., Jia P., Wang X., Su N., Yu S., Zhang D., Ma L., Feng Q., Jin Z., Li L., et al. 2005. A tiling microarray expression analysis of rice chromosome 4 suggests a chromosomal level regulation of transcription. Plant Cell: In Press

  • P. Kapranov S.E. Cawley J. Drenkow S. Bekiranov R.L. Strausberg S.P.A. Fodor T.R. Gingeras (2002) ArticleTitleLarge-scale transcriptional activity in chromosomes 21 and 22 Science 296 916–919 Occurrence Handle10.1126/science.1068597 Occurrence Handle11988577

    Article  PubMed  Google Scholar 

  • S. Kikuchi K. Satoh T. Nagata N. Kawagashira K. Doi N. Kishimoto J. Yazaki M. Ishikawa H. Yamada H. Ooka (2003) ArticleTitleCollection, mapping, and annotation of over 28,000 cDNA Clones from japonica Rice Science 300 1566–1569 Occurrence Handle10.1126/science.1083523 Occurrence Handle12791992

    Article  PubMed  Google Scholar 

  • P.E. Klein R.R. Klein J. Vrebalov J.E. Mullet (2003) ArticleTitleSequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement Plant J. 34 605–621 Occurrence Handle10.1046/j.1365-313X.2003.01751.x Occurrence Handle12787243

    Article  PubMed  Google Scholar 

  • H. Li W. Wang (2003) ArticleTitleDissecting the transcription networks of a cell using computational genomics Curr. Opin. Gen. Dev. 13 611–616 Occurrence Handle10.1016/j.gde.2003.10.012

    Article  Google Scholar 

  • N.M. Luscombe T.E. Royce P. Bertone N. Echols C.E. Horak J.T. Chang M. Snyder M. Gerstein (2003) ArticleTitleExpressYourself: a modular platform for processing and visualizingmicroarray data Nucl. Acids Res. 31 3477–3482 Occurrence Handle10.1093/nar/gkg628 Occurrence Handle12824348

    Article  PubMed  Google Scholar 

  • L. Ma J. Li L. Qu J. Hager Z. Chen H. Zhao X.W. Deng (2001) ArticleTitleLight control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways Plant Cell 13 2589–2607 Occurrence Handle10.1105/tpc.13.12.2589 Occurrence Handle11752374

    Article  PubMed  Google Scholar 

  • C. Mathé M-F. Sagot T. Schiex P. Rouzé (2002) ArticleTitleCurrent methods of gene prediction, their strengths and weaknesses Nucl. Acids. Res. 30 4103–4117 Occurrence Handle10.1093/nar/gkf543 Occurrence Handle12364589

    Article  PubMed  Google Scholar 

  • G. Moore (2000) ArticleTitleCereal chromosome structure, evolution, and pairing Annu. Rev. Plant Physiol. Mol. Biol. 51 195–222 Occurrence Handle10.1146/annurev.arplant.51.1.195

    Article  Google Scholar 

  • E.F. Nuwaysir W. Huang T.J. Albert J. Singh K. Nuwaysir A. Pitas T. Richmond T. Gorski J.P. Berg J. Ballin (2002) ArticleTitleGene expression analysis using oligonucleotide arrays produced by maskless photolithography Genome Res. 12 1749–1755 Occurrence Handle10.1101/gr.362402 Occurrence Handle12421762

    Article  PubMed  Google Scholar 

  • A.H. Paterson J.E. Bowers D.G. Peterson J.C. Estill B.A. Chapman (2003) ArticleTitleStructure and evolution of cereal genomes Curr. Opin. Genet. Dev.13 644–650 Occurrence Handle10.1016/j.gde.2003.10.002

    Article  Google Scholar 

  • B. Ren F. Robert J.J. Wyrick O. Aparicio E.G. Jennings I. Simon J. Zeitlinger J. Schreiber N. Hannett E. Kanin (2000) ArticleTitleGenome-wide location and function of DNA binding proteins Science 290 2306–2309 Occurrence Handle10.1126/science.290.5500.2306 Occurrence Handle11125145

    Article  PubMed  Google Scholar 

  • J.L. Rinn G. Euskirchen P. Bertone R. Martone N.M. Luscombe S. Hartman P.M. Harrison F.K. Nelson P. Miller M. Gerstein (2003) ArticleTitleThe transcriptional activity of human Chromosome 22 Genes Dev. 17 529–540 Occurrence Handle10.1101/gad.1055203 Occurrence Handle12600945

    Article  PubMed  Google Scholar 

  • T. Sasaki T. Matsumoto K. Yamamoto K. Sakata T. Baba Y. Katayose J.Z. Wu Y. Niimura Z.K. Cheng Y. Nagamura (2002) ArticleTitleThe genome sequence and structure of rice chromosome 1 Nature 420 312–316 Occurrence Handle10.1038/nature01184 Occurrence Handle12447438

    Article  PubMed  Google Scholar 

  • C. Schwechheimer M. Zourelidou M.W. Bevan (1998) ArticleTitlePlant transcription factor studies Annu. Rev. Plant Physiol. Plant Mol. Biol. 49 127–150 Occurrence Handle10.1146/annurev.arplant.49.1.127 Occurrence Handle15012230

    Article  PubMed  Google Scholar 

  • D.D. Shoemaker E.E. Schadt C.D. Armour Y.D. He P. Garrett-Engele P.D. McDonagh P.M. Loerch A. Leonardson P.Y. Lum G. Cavet (2001) ArticleTitleExperimental annotation of the human genome using microarray technology Nature 409 922–927 Occurrence Handle10.1038/35057141 Occurrence Handle11237012

    Article  PubMed  Google Scholar 

  • K. Shimamoto J. Kyozuka (2002) ArticleTitleRice as a model for comparative genomics of plants Annu. Rev. Plant Biol. 53 399–419 Occurrence Handle10.1146/annurev.arplant.53.092401.134447 Occurrence Handle12221982

    Article  PubMed  Google Scholar 

  • S. Singh-Gasson R.D. Green Y.J. Yue C. Nelson F. Blattner M.R. Sussman F. Cerrina (1999) ArticleTitleMaskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array Nat. Biotech. 17 974–978 Occurrence Handle10.1038/13664

    Article  Google Scholar 

  • M. Snyder M. Gerstein (2003) ArticleTitleDefining genes in the genomics era Science 300 258–260 Occurrence Handle10.1126/science.1084354 Occurrence Handle12690176

    Article  PubMed  Google Scholar 

  • V. Stolc Z. Gauhar C. Mason G. Halasz M.F. Batenburg Particlevan S.A. Rifkin S. Hua T. Herreman W. Tongprasit P.E. Barbano (2004) ArticleTitleA gene expression map for the euchromatic genome of Drosophila melanogaster Science 306 655–660 Occurrence Handle10.1126/science.1101312 Occurrence Handle15499012

    Article  PubMed  Google Scholar 

  • InstitutionalAuthorNameThe Rice Chromosome 10 Sequencing Consortium (2003) ArticleTitleIn-depth view of structure, activity, and evolution of rice Chromosome 10 Science 300 1566–1569

    Google Scholar 

  • W. Wang B. Vinocur A. Altman (2003) ArticleTitlePlant response to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance Planta 218 1–14 Occurrence Handle10.1007/s00425-003-1105-5 Occurrence Handle14513379

    Article  PubMed  Google Scholar 

  • G.K. Wong J. Wang L. Tao J. Tan J. Zhang A. Douglas J. Yu (2002) ArticleTitleCompositional gradients in Gramineae genes Genome Res. 12 851–856 Occurrence Handle10.1101/gr.189102 Occurrence Handle12045139

    Article  PubMed  Google Scholar 

  • K. Yamada J. Lim J.M. Dale H. Chen P. Shinn C.J. Palm A.M. Southwick H.C. Wu C. Kim M. Nguyen (2003) ArticleTitleEmpirical analysis of transcriptional activity in the Arabidopsis genome Science 302 842–846 Occurrence Handle10.1126/science.1088305 Occurrence Handle14593172

    Article  PubMed  Google Scholar 

  • J. Yu S. Hu J. Wang W.G Shu S. Li B. Liu Y. Deng L. Dai Y. Zhou X. Zhang (2002) ArticleTitleA Draft Sequence of the rice genome (Oryza sativa L. ssp. indica) Science 296 79–92 Occurrence Handle10.1126/science.1068037 Occurrence Handle11935017

    Article  PubMed  Google Scholar 

  • J. Yu J. Wang W. Lin S. Li H. Li J. Zhou P. Ni W. Dong S. Hu C. Zeng (2005) ArticleTitleThe genomes of Oryza sativa: A history of duplications PLOS Biol. 3 e38 Occurrence Handle10.1371/journal.pbio.0030038 Occurrence Handle15685292

    Article  PubMed  Google Scholar 

  • Q.P. Yuan J. Quackenbush R. Sultana M. Pertea S.L. Salzberg. C.R. Buell (2001) ArticleTitleRice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species Plant Physiol. 125 1166–1174 Occurrence Handle10.1104/pp.125.3.1166 Occurrence Handle11244096

    Article  PubMed  Google Scholar 

  • M.Q. Zhang (2002) ArticleTitleComputational prediction of eukaryotic protein-coding genes Nature Rev. Gent. 3 698–710 Occurrence Handle10.1038/nrg890

    Article  Google Scholar 

  • W.M. Zhao J. Wang X. He X. Huang Y. Jiao M. Dai S. Wei J. Fu Y. Chen X. Ren (2004) ArticleTitleBGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics Nucl. Acids Res. 32 D377–D382 Occurrence Handle10.1093/nar/gkh085 Occurrence Handle14681438

    Article  PubMed  Google Scholar 

Download references

Author information

Author notes

  1. Viktor Stolc, Lei Li & Xiangfeng Wang

    Present address: Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA

Authors and Affiliations

  1. Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA

    Xueyong Li, Ning Su, Michael Snyder & Xing Wang Deng

  2. Genome Research Facility, NASA Ames Research Center, MS 239–11, Moffett Field, CA, 94035, USA

    Viktor Stolc

  3. National Institute of Biological Sciences, Zhongguancun Life Science Park, 102206, Beijing, China

    Xiangfeng Wang

  4. Beijing Institute of Genomics, Chinese Academy of Sciences, 101300, Beijing, China

    Xiangfeng Wang & Jun Wang

  5. Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, 100871, Beijing, China

    Xiangfeng Wang

  6. National Center of Crop Design, China Bioway Biotech Group Co., LTD, 100085 , Beijing, China

    Xueyong Li

  7. National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, 200233, Shanghai, China

    Waraporn Tongprasit & Bin Han

  8. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, 100101, Beijing, China

    Yongbiao Xue & Jiayang Li

  9. Department of Molecular Biophysics and Biochemistry, Yale University, 06511, New Haven, CT, USA

    Mark Gerstein

Authors
  1. Viktor Stolc
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lei Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiangfeng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xueyong Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ning Su
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Waraporn Tongprasit
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Bin Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yongbiao Xue
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jiayang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Michael Snyder
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Mark Gerstein
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Jun Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Xing Wang Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xing Wang Deng.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Stolc, V., Li, L., Wang, X. et al. A Pilot Study of Transcription Unit Analysis in Rice Using Oligonucleotide Tiling-path Microarray. Plant Mol Biol 59, 137–149 (2005). https://doi.org/10.1007/s11103-005-6164-5

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11103-005-6164-5

Keywords

Search

Navigation