Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

An expression atlas of rice mRNAs and small RNAs

Nature Biotechnology volume 25, pages 473–477 (2007)Cite this article

This article has been updated

Abstract

Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technology called 'massively parallel signature sequencing' to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). We sequenced 46,971,553 mRNA transcripts from 22 libraries, and 2,953,855 small RNAs from 3 libraries. The data demonstrate widespread transcription throughout the genome, including sense expression of at least 25,500 annotated genes and antisense expression of nearly 9,000 annotated genes. An additional set of ∼15,000 mRNA signatures mapped to unannotated genomic regions. The majority of the small RNA data represented lower abundance short interfering RNAs that match repetitive sequences, intergenic regions and genes. Among these, numerous clusters of highly regulated small RNAs were readily observed. We developed a genome browser (http://mpss.udel.edu/rice) for public access to the transcriptional profiling data for this important crop.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Genome-wide transcriptional analysis by mRNA MPSS.
Figure 2: Deep sequencing of rice small RNAs by MPSS.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

Change history

  • 23 March 2007

    In the version of this article initially published, the fourth author’s name was misspelled. The correct spelling is André Beló. The error has been corrected for all versions of the article.

References

  1. International Rice Genome Sequencing Project. The map-based sequence of the rice genome Nature 436, 793–800 (2005).

  2. Yuan, Q. et al. The Institute for Genomic Research Osa1 rice genome annotation database. Plant Physiol. 138, 18–26 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kikuchi, S. et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301, 376–379 (2003).

    Article  PubMed  Google Scholar 

  4. Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004).

    Article  CAS  PubMed  Google Scholar 

  5. Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Meyers, B.C. et al. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat. Biotechnol. 22, 1006–1011 (2004).

    Article  CAS  PubMed  Google Scholar 

  7. Lu, C. et al. Elucidation of the small RNA component of the transcriptome. Science 309, 1567–1569 (2005).

    Article  CAS  PubMed  Google Scholar 

  8. Cheng, Z. et al. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14, 1691–1704 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Yan, H. et al. Genomic and genetic characterization of rice cen3 reveals extensive transcription and evolutionary implications of complex centromere. Plant Cell 18, 3227–3238 (2006).

    Article  CAS  Google Scholar 

  10. Yan, H. et al. Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell 17, 3227–3238 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Jen, C.H., Michalopoulos, I., Westhead, D. & Meyer, P. Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol. 6, R51 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Borsani, O., Zhu, J., Verslues, P.E., Sunkar, R. & Zhu, J.K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123, 1279–1291 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Griffiths-Jones, S. The microRNA Registry. Nucleic Acids Res. 32, D109–D111 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lippman, Z. et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471–476 (2004).

    Article  CAS  PubMed  Google Scholar 

  15. Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201 (2006).

    Article  CAS  PubMed  Google Scholar 

  16. Yoo, B.-C. et al. A systemic small RNA signaling system in plants. Plant Cell 16, 1979–2000 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Jiang, N., Bao, Z., Zhang, X., Eddy, S.R. & Wessler, S.R. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431, 569–573 (2004).

    Article  CAS  PubMed  Google Scholar 

  18. Juretic, N., Hoen, D.R., Huynh, M.L., Harrison, P.M. & Bureau, T.E. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 15, 1292–1297 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Morgante, M. et al. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 37, 997–1002 (2005).

    Article  CAS  PubMed  Google Scholar 

  20. Britten, R. Transposable elements have contributed to thousands of human proteins. Proc. Natl. Acad. Sci. USA 103, 1798–1803 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Lipatov, M., Lenkov, K., Petrov, D. & Bergman, C. Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biol. 3, 24 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154 (2005).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We are grateful to C. Haudenschild, TIGR's rice annotation project, S. Singh Tej, M. Nakano, R. German, A. Hetawal, R. Gupta and S. Kaushik. This work was supported by US National Science Foundation awards 0321437 (B.C.M. and G.-l.W.) and 0439186 (P.J.G. and B.C.M.), and US Department of Agriculture 2005-35064-15326 (B.C.M. and P.J.G.).

Author information

Authors and Affiliations

  1. Delaware Biotechnology Institute, University of Delaware, Newark, 19711, Delaware

    Kan Nobuta, Cheng Lu, Kalyan Vemaraju, Karthik Kulkarni, Wenzhong Wang, Manoj Pillay, Pamela J Green & Blake C Meyers

  2. Department of Plant and Soil Sciences, University of Delaware, Newark, 19711, Delaware

    Kan Nobuta, Cheng Lu, André Beló, Pamela J Green & Blake C Meyers

  3. College of Marine and Earth Studies, University of Delaware, Newark, 19711, Delaware

    Pamela J Green

  4. Department of Plant Pathology, The Ohio State University, Columbus, 43210, OH

    R C Venu & Guo-liang Wang

Authors
  1. Kan Nobuta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R C Venu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cheng Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. André Beló
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kalyan Vemaraju
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Karthik Kulkarni
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wenzhong Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Manoj Pillay
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Pamela J Green
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Guo-liang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Blake C Meyers
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

K.N. performed research, analyzed data and wrote the manuscript, R.C.V. and C.L. performed laboratory research and provided useful discussions, A.B., K.V., K.K., W.W. and M.P. performed computational research; P.J.G. and G.-l.W. designed research and wrote manuscript; B.C.M. designed research, analyzed data, and coordinated and wrote the manuscript.

Corresponding author

Correspondence to Blake C Meyers.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Filter results for 22 mRNA MPSS libraries (PDF 21 kb)

Supplementary Fig. 2

Similarity of the pattern among the diverse tissues (PDF 17 kb)

Supplementary Fig. 3

Representation of library-specific genes in each tissue (PDF 123 kb)

Supplementary Fig. 4

Actively expressed genes and intergenic transcripts (PDF 440 kb)

Supplementary Fig. 5

Correlation of sense and antisense expression (PDF 643 kb)

Supplementary Fig. 6

Rice small RNAs are dispersed throughout the genome (PDF 2410 kb)

Supplementary Fig. 7

Small RNA sequences in the completely sequenced centromere of rice (PDF 35 kb)

Supplementary Fig. 8

Classes of genomic features matched by rice small RNAs (PDF 37 kb)

Supplementary Fig. 9

Distribution of small RNAs across rice chromosomes (PDF 358 kb)

Supplementary Fig. 10

Small RNA sequences in a genic region of the rice genome (PDF 3074 kb)

Supplementary Fig. 11

Patterns of retrotransposon silencing and expression in the rice genome (PDF 37 kb)

Supplementary Fig. 12

Tandem and inverted repeats are substantial sources of small RNAs in rice (PDF 39 kb)

Supplementary Fig. 13

Expression and conservation of rice small RNAs (PDF 94 kb)

Supplementary Fig. 14

Number of genes that are supported by MPSS signatures, based on signatures matching multiple locations in the genome (PDF 31 kb)

Supplementary Fig. 15

Co-expression analysis of adjacent genes (PDF 53 kb)

Supplementary Table 1

Libraries and signature counts – summary statistics (PDF 54 kb)

Supplementary Table 2

Genomic signatures and number of corresponding genes (PDF 71 kb)

Supplementary Table 3

Known microRNAs genes and ncRNAs associated with mRNA signatures (PDF 58 kb)

Supplementary Table 4

Summary statistics for small RNA libraries (PDF 53 kb)

Supplementary Table 5

Genomics localization of small RNA signatures (PDF 54 kb)

Supplementary Table 6

Clusters of small RNAs in the rice genome (PDF 51 kb)

Supplementary Table 7

Differential or constant cluster or genes in the rice small RNA libraries (PDF 97 kb)

Supplementary Data (PDF 81 kb)

Supplementary Methods (PDF 736 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Nobuta, K., Venu, R., Lu, C. et al. An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25, 473–477 (2007). https://doi.org/10.1038/nbt1291

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt1291

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing