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Contact Information
Research Interests:
Using rice genomic tiling arrays, we performed experiments that provide expression support to over 35,000 annotated genes, including many that otherwise lack experimental evidence. We identified approximately 25,000 transcriptionally active regions (TARs) in addition to the annotated exons. Over 80% non-exonic TARs was verified and assigned to various putative functional or structural elements of the genome, ranging from splice variants, antisense transcripts, duplicated gene fragments, to non-coding RNAs. Furthermore, mapping of transcribed regions in rice revealed an association between global transcription and cytological chromosome features and an overall similarity of transcriptional activity between duplicated segments of the genome. We are now expanding these efforts to examine the transcriptional programs associated with endosperm development and the phenomenon of hybrid vigor in rice. In eukaryotes, DNA and the core histone proteins are organized into nucleosomes that form the higher-ordered structure of chromatin. The combinatorial covalent modifications to the histone tails have been widely assumed to generate a "histone code" that fundamentally affects chromatin structure and hence transcriptional regulation. Extensive effort has been devoted to mapping the sequences associated with these modifications in model species. We are using the ChIP-on-chip approach (chromatin immunoprecipitation coupled with genomic tiling array analysis) to investigate the transit changes of global histone modification patterns in several signal transduction pathways. Results from these experimental approaches provide measurements of the molecular parameters that define particular biological processes. These measurements represent a hierarchy of information that is likely processed in living cells through complex regulatory networks. We are teaming up with several other researchers on grounds to integrate these data with computational modeling to identify the underlying transcriptional regulatory networks. Representative Publications: Li L, Deng XW (2007) Microarray-based approaches to rice transcriptome analysis. In “ Rice Biology in the Genomics Era. ” H Hirai, T Sasaki, Y Sano, H Hirano, Eds. Springer. In Press. Kikuchi S, Wang G-L, Li L (2007) Genome-wide RNA expression profiling. In “ Rice Functional Genomics: Challenges, Progress and Prospects ”. N. Upadhyaya , Eds. Springer. pp.36-63. Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW (2007) Global identification and characterization of transcriptionally active regions in the rice genome. PLoS ONE 2, e294. Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38, 124-129. Li L, Deng XW (2005) It runs in the family: regulation of brassinosteroid signaling by the BZR1-BES1 class of transcription factors. Trends Plant Sci 10, 266-268. Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Li S, Wang J, Wang X, Deng XW (2005) Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 6, R52. Li L, Wang X, Li X, Su N, Stolc V, Han B, Li J, Xue Y, Wang J, Deng XW (2005) Toward genome-wide transcriptional analysis in rice using MAS oligonucelotide tiling-path microarrays. In “Rice Is Life: Scientific Perspectives For The 21st Century.” K Toriyama, KL Heong, B Hardy, Eds. pp.80-83. Li L, Zhao Y, McCaig BC , Wingerd BA, Wang J, Whalon ME, Pichersky E, Howe GA (2004) The tomato homolog of CORONATINE-INSENSITIVE1 is required for the maternal control of seed maturation, jasmonate-signaled defense responses, and glandular trichome development. Plant Cell 16, 126-143. Li L, Deng XW (2003) The COP9 Signalosome: an alternative lid for the 26S proteasome? Trend Cell Biol 13, 507-509. Li L, Li C, Lee GI, Howe GA (2002) Distinct roles for jasmonate synthesis and action in the systemic wound response of tomato. Proc Natl Acad Sci USA 99, 6416-6421. Li L, Li C, Howe GA (2001) Genetic analysis of wound signaling in tomato: Evidence for a dual role of jasmonic acid in defense and female fertility. Plant Physiol 127, 1414-1417. Li L, Howe GA (2001) Alternative splicing of prosystemin pre-mRNA produces two isoforms that are active as signals in the wound response pathway. Plant Mol Biol 46, 409-419.
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Our current experimental approach centers on high-resolution genomic tiling microarrays, which involve the generation of a ‘tile path' made up of progressive oligonucleotide tiles that represent a target genome. These probes may overlap, lay end to end, or be spaced at regular intervals. The average nucleotide distance between the centers of neighboring probes is called the ‘step', which defines the resolution of a tiling array. Recent technology advances in high-density microarrays that contain short oligonucleotide probes synthesized in situ by photolithography, allow several hundred thousand to several million discrete features per array. This makes it feasible to tile complex genomes with a manageable number of arrays. The tiling probes are immobilized on glass slides and are used to hybridize with various fluorescence-labeled target nucleic acids. Hybridization intensity of each probe can be retrieved and integrated, which leads to a wealth of information on the transcriptional landscape as well as genome architecture. 
