Wang Laboratory ​​​​
   - An RNA Laboratory

PI: Ying Wang  Ph.D.
Assistant Professor
Department of Biological Sciences
Mississippi State University
Email: [email protected]

Laboratory Members:
Jian Jiang (Research Associate)
Heather Smith (Research Associate)
Shachinthaka Dissanayaka Mudiyanselage (PhD Student)
Junfei Ma (Master Student)
Sara Tyrrell (Undergraduate Researcher)

Opportunity to apply
  We encourage enthusiastic candidates with a strong background in molecular biology, biochemistry, and/or bioinformatics to apply for our PhD program or a postdoctoral researcher position.

Research Topics  
     Our research interests are classified into two broad categories:  
1) Using potato spindle tuber viroid (PSTVd) as a model to understand the structure and function of noncoding RNAs (ncRNAs).
2) Deciphering the RNA-based epigenetic control underlying tomato development.
  Viroid research:  
       Understanding structure and function of ncRNAs is of fundamental importance in both basic science and application. PSTVd is a sub-viral agent made up of ncRNAs. Intriguingly, without encoding any protein, PSTVd replicates and spreads in plants, consequently causing disease. This unique feature prompts many interesting biological questions: How do plants perceive the presence of this pathogenic non-coding RNA? How do plants defend against exogenous RNAs? How does foreign RNA survive in plants? Efforts in elucidating these biological processes will advance general principles of pathology and RNA biology.
      Besides, 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 controls the infection of human hepatitis delta virus (HDV). Thus, understanding the RdRP activity of Pol II has significant implications in basic sciences, agriculture and biomedical research. We are dedicated to explore and characterize novel auxiliary factors and their functional mechanisms in the RdRP activity of Pol II.  
  Epigenetic control in tomato development:
        Epigenetic control has been demonstrated to play essential roles in plant growths. Small RNAs (sRNAs) and long noncoding RNAs (lncRNAs) can be key epigenetic regulators of gene expression. My laboratory aims to elucidate the dynamics of RNA regulatory networks underlying tomato development during domestication. 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. We employ comprehensive comparative genomic approaches to identify and characterize such ncRNAs in tomato plants. This endeavor will shed light on novel RNA-based regulatory networks emphasizing functional implications in agriculture.   

- NSF Plant Genome Research Project: Exploitation of Genetics and Epigenetic Variation in the Regulation of Tomato Fruit Quality Traits. (coPI) 01/2017-04/2020.
- College of Arts and Sciences Strategic Research Initiatives, Mississippi State University. (lead PI) 01/2018-12/2018.

Selected Publications
- Dissanayaka Mudiyanselage SD, Qu J, Tian N, Jiang J, Wang Y. 2018. Potato spindle tuber viroid RNA-templated transcription: factors and regulation. Viruses 10:E503. (: Correspondence author)
- Jiang J, Smith HN, Ren D, Dissanayaka Mudiyanselage SD, Dawe AL, Wang L, Wang Y. 2018. Potato spindle tuber viroid modulates its replication through a direct interaction with a splicing regulator. J. Virol. 92:e01004-18. (: Correspondence author; Featured in Journal's " spotlight ")
- Takeda R, Zirbel CL, Leontis NB , Wang Y, Ding B. 2018. Allelic RNA motifs in regulating systemic trafficking of potato spindle tuber viroid. Viruses 10:E160. (: Co-correspondence author)
- Wang Y, Zirbel CL, Leontis NB , Ding B. 2018. RNA three-dimensional structural motifs as a critical constraint of viroid RNA evolution. PLOS Pathog. 14:e1006801. (: Co-correspondence author)  
- Zheng Y§, Ding B, Fei Z, Wang Y§,†. 2017. Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors. Sci. Rep. 7:9771 (§: Equal contribution; : Co-correspondence author)
- 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 phased secondary small interfering RNAs and immune responses. J. Virol. 91:e00247-17. (§: 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.