Research Accomplishment Reports 2010

Roles of MicroRNA Structures in Plant RNA Silencing

G. Tang
Department of Plant and Soil Sciences

 

Non-Technical Summary

MicroRNAs (miRNAs) are recently discovered endogenous small RNAs of ~22 nucleotides in plants and animals. They regulate gene expression after the gene transcription by cleaving the mRNA and prevent mRNA from translation into proteins. Various miRNAs from both plants and animals were cloned and their precursors and genes were identified. Stem-loop RNA structure is the hallmark of miRNA precursors and helps produce highly efficient RNA silencing triggers, the miRNAs. Here we propose to dissect the miRNA precursor structures using informatics approach and find rules of their structures in RNA silencing. This will involve the establishment of a miRNA structure database and its analysis in detail. The rules found from the database analysis will be applied to design highly efficient small RNAs or small RNA vectors for silencing any genes of interest. The proposed activities also include a training of three graduate students and several undergraduate students.

2010 Project Description

We created an online database to demonstrate the microRNA structures and compositions. This database can be reached online to users. The database was also used for teaching and mentoring graduate students. We attended various symposia and workshops to demonstrate the basic research results and applications We provided consulting, counseling, and tutoring to collaborators and colleagues inside and outside this university.

We created the mirnainfo database (http://mirnainfo.com/miRNAResearchHome.aspx) We provided service to researchers inside and outside this university regarding how to design effective artificial miRNAs based on the outcomes of this project.

We also created a teaching website (http://www.uky.edu/%7Egtang2/Teaching.html) for the education of graduate and undergraduate students. This educational website can be reached to users from inside and outside this university.

2010 Impact

RNAi and microRNA added cutting-edge knowledge to the education of the public and the academic. The outcome of this project led to several research and education publications. We generated improved artificial miRNA vector that can express single or multiple endogenous miRNA or artificial miRNAs to target any gene for silencing. This vector was used to over express the endogenous miR165/166 to study the role of miR165/166 in flower development in collaboration with Dr. Xuemei Chen at UC Riverside.

2010 Publications

Xiaoyun Jia, Venugopal Mendu, and Guiliang Tang (2010) An array platform for identification of stress-responsive miRNAs in plants. Methods Mol Biol. 639: 253-69.

Guiliang Tang (2010) Plant microRNAs: An insight into their gene structures and evolution. Seminars in Cell and Developmental Biology 21:782-789.(PDF)

Dianwei Han, Jun Zhang, and Guiliang Tang (2011) MicroRNAfold: pre-microRNA secondary structure prediction based on Modified NCM model with thermodynamics-based scoring strategy. International Journal of Data Mining and Bioinformatics (In press)

Xiaoyun Jia, Jun Yan, and Guiliang Tang (2011) MicroRNA-mediated DNA methylation in plants. Frontiers in Biology (In press)

Lijuan Ji, Xigang Liu, Jun Yan, Wenming Wang, Rae Eden Yumul, Yu Ju Kim, Thanh Theresa Dinh, Jun Liu, Xia Cui, Binglian Zheng, Manu Agarwal, Chunyan Liu, Xiaofeng Cao, Guiliang Tang, and Xuemei Chen* (2011) ARGONAUTE10 and ARGONAUTE1 Regulate the Termination of Floral Stem Cells through Two microRNAs in Arabidopsis. PLOS Genetics (In press)