Li, Lei
Primary Appointment
Biology
Contact Information
PO Box 400328
Telephone: 2-5481
Email: ll4jn@virginia.edu
Research Interests
Genome organization, evolution, and transcriptional regulation in model plant systems.
Research Description
The long-term research interest of my laboratory is to understand in model plant systems how gene expression is regulated in response to internal signals and external stimuli. We use combined experimental and informatic approaches to address this question at the genome scale. The rapidly accumulating genome sequences in recent years are having two marked, complementary effects on the relatively new discipline of plant genomics. First, the sequences enable genetic, epigenetic and comparative analysis of plant genomes on an unprecedented scale. Second, the complexity and impending completeness of the genomic and transcriptomic data are simultaneously demanding and creating opportunities for new avenues to discovery.
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.
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.