Yinan Yuan

Yinan Yuan
"The RNA regulatory system might have been essential prerequisite to both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotyptic complexity into uncontested environment."


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Research Assistant Professor, SFRES

  • PhD, Chinese Academy of Agricultural Sciences
  • MS, Chinese Academy of Agricultural Sciences
  • BS, Henan Agricultural University

Making sense of antisense transcription in tree growth and development

I am interested in deciphering the functional role of noncoding RNA (ncRNA) in gene regulation network governing forest tree growth and development. One significant class of such ncRNA is natural antisense transcripts (NATs) which share complimentary sequence with protein-coding genes. Recent studies in direct transcriptome sequencing (RNA-seq) and whole genome tiling array have revealed that eukaryotic genomes including plant genome encode large amount of NATs transcribed either from opposite strand of genes (cis-NAT) or from different chromosomal locations (trans-NAT). The overwhelming occurrence of NATs represents an important gene phenomenon which has not been characterized in tree genomes.

To reveal these hidden transcripts of tree genomes, we employ a novel experiment method for systematic identification of NATs in Populus and Pine genomes. These identified NATs will be further tested with custom-made oligo DNA chips for its functional relevance in many aspects of tree growth and development under environmental adaptations such as nitrogen deficiency and low light. The biological consequence of characterized NATs will be finally confirmed with RNAi technology. The ultimate goal of my research is to uncover the regulation network mediated by NATs underlying forest tree growth and development. The results generated will advance our current knowledge base of tree biology for efficient grow, manage and genetic manipulation of “super” forest trees.

Areas of Expertise

  • Identification and characterization of natural antisense transcripts in woody plants
  • Alternative splicing and salicylic acid metabolism in populus
  • Sequencing complex plant genome through gene-enriched methods

Recent Publications

  • Yuan Y, Chung J-D, Fu X, Johnson VE, Ranjan P, Booth SL, Harding SA, Tsai C-J (2009) Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis. Proceedings of the National Academy of Sciences USA 106: 22020-22025
  • Tsai C-J, Harding SA, Tschaplinski TJ, Lindroth RL, Yuan Y (2006) Genome-wide analysis of the structuralgenes regulating defense phenylpropanoid metabolism in Populus. New Phytologist 172: 47-62.
  • Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PD (2006) The TIGR Maize Database. Nucleic Acids Research. 34 (Database issue): D771-6.
  • Emberton J, Ma J, Yuan Y, SanMiguel P, Bennetzen JL (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Research. 15(10): 1441-6.
  • Lin, J-Y., B. Hass-Jacobus, P. SanMiguel, J.G. Walling, Y. Yuan, J. Doyle, R.C.Shoemaker, N.D. Young and S.A. Jackson. (2005) Molecular and cytogeneticcharacterization of gene-poor, heterochromatic regions of Glycine max L. Merr. Genetics 170: 1221-1230.
  • Whitelaw,C.A.; Barbazuk,W.B.; Pertea,G.; Chan,A.P.; Cheung,F.; Lee,Y.; Zheng,L.; van Heeringen,S.; Karamycheva,S.; Bennetzen, J.L.; SanMiguel,P.; Lakey,N.; Bedell,J.; Yuan,Y.; Budiman,M.A.; Resnick,A.; Van Aken,S.; Utterback,T.; Riedmuller,S.; Williams,M.; Feldblyum,T.; Schubert,K.; Beachy,R.; Fraser,C.M.; Quackenbush,J. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120.
  • Yuan, Y., SanMiguel, P. and Bennetzen, J. (2003) High Cot sequence analysis of the maize genome. Plant Journal. 34 (2): 249-255.