B.S. Biological Sciences, Wuhan University, China
Ph.D. Plant Cellular & Molecular Biology, Ohio State University, USA
Postdoctoral Researcher, Department of Molecular Genetics, Ohio State University, USA
Research Scientist, Department of Molecular Genetics, Ohio State University, USA
Statement of Research Interests
My research interests are classified into two broad categories:
1) Using Potato spindle tuber viroid as a model to understand plant-microbe interactions.
2) Deciphering the RNA-based epigenetic control underlying tomato development.
Understanding plant-microbe interactions is of fundamental importance in both basic science and agriculture. Viroids are sub-viral agents made up of noncoding RNAs. Potato spindle tuber viroid (PSTVd) is the type species of the Pospiviroidae family. In general, viroids do not encode proteins but replicate and spread in plants, consequently causing diseases. This unique feature prompts many interesting biological questions regarding the biogenesis and pathogenesis of viroids. For example, how do plants perceive the presence of viroids? How do plants defend against viroid invasion? How do viroids make plant sick? There is little information regarding these questions; however, viroids can be a promising model to dissect the biology of pathogenic noncoding RNAs. In addition, viroids are sensitive probes to discover cellular machinery underlying various RNA biology.
Transcription from PSTVd RNA genome to antisense RNA intermediates utilizes RNA-dependent RNA Polymerase (RdRP) activity of DNA-dependent RNA Polymerase II (Pol II). Pol II typically uses DNA templates for generating mRNAs, and its shift to using RNA templates confers novel regulation of gene expression. Such RdRP activity of Pol II regulates the stability of a mammalian B2 RNA and the infection of human Hepatitis delta virus (HDV). Thus, understanding RdRP activity of Pol II has enormous implications in basic sciences, agriculture and biomedical research. My laboratory will continue to explore novel transcription factors, such as Transcription Factor IIIA variants (TFIIIA-7ZF and TFIIIA-9ZF), and their mechanisms underpinning the RdRP activity of Pol II.
Epigenetic control of tomato development:
Epigenetic control has been demonstrated to play essential roles in plant growths. My laboratory aims to elucidate the dynamics of RNA regulatory networks underlying tomato development during domestication. Small RNAs (sRNAs) and long noncoding RNAs (lncRNAs) are key regulators of gene expression. Recent research showed that sRNAs and lncRNAs exhibit dynamic expression patterns even among closely related species. Furthermore, a few less-conserved sRNAs and lncRNAs regulate critical crop traits. My laboratory employs comprehensive comparative genomic approaches to identify and characterize such RNAs in tomato plants. This endeavor will shed light on novel RNA regulatory networks as well as facilitate agricultural applications.
- Zheng Y§, Wang Y§,†, Ding B, Fei Z†. 2017. Comprehensive transcriptome analyses reveal that potato spindle tuber viroid triggers genome-wide changes in alternative splicing, inducible trans-acting activity of phasiRNAs and immune responses. J. Virol. In press. (§: Equal contribution; †: Co-correspondence author)
- Wang Y§,†, Qu J§, Ji S, Wallace AJ, Wu J, Li Y, Gopalan V, Ding B. 2016. A Land Plant-specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-dependent RNA Polymerase II. Plant Cell 28:1094-1107. (§: Equal contribution; †: Correspondence author;
Journal Featured Article
- Zheng Y§, Wang Y§, Wu J, Ding B, Fei Z. 2015. A dynamic evolutionary and functional landscape of plant phased small interfering RNAs. BMC Biol. 13:32. (§: Equal contribution)
- Wang Y, Itaya A, Zhong X, Wu Y, Zhang J, van der Knaap E, Olmstead R, Qi Y, Ding B. 2011. Function and evolution of a microRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. Plant Cell 23:3185-3203. (Journal Featured Article)
- Wang Y, Ding B. 2010. Viroids: small probes for exploring the vast universe of RNA trafficking in plants. J. Integr. Plant Biol. 52:28-39.
- Ding B, Wang Y. 2009. Viroids, uniquely simple and tractable models to elucidate regulation of cell-to-cell trafficking of RNA. DNA Cell Biol. 28:51-56.
- Itaya A, Zhong X, Bundschuh R, Qi Y, Wang Y, Takeda R, Harris AR, Molina C, Nelson RS, Ding B. 2007. A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. J. Virol. 81:2980-2994. (
Highlighted by Faculty1000 Biology as “Must Read” in 2007)
- Wang Y, Zhong X, Itaya A, Ding B. 2007. Evidence for the existence of the loop E motif of Potato spindle tuber viroid in vivo. J. Virol. 81:2074-2077.