Title: "Statistical modeling in non-coding RNA mediated regulatory network"
Speaker: Yunlong Liu, Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN
Place: HORT 117; March 1, 2011, Tuesday, 4:30pm


Constructing and modeling the gene regulatory network is one of the central themes of systems biology. With the growing understanding of the mechanism of microRNA biogenesis and its biological function, establishing a microRNA-mediated gene regulatory network is not only desirable but also achievable. We propose a bioinformatics strategy to construct the microRNA-mediated regulatory network using genome-wide binding patterns of transcription factor(s) and RNA polymerase II (RPol II) derived using chromatin immunoprecipitation following next generation sequencing (ChIP-seq) technology. Our strategy includes three key steps, identification of transcription start sites and promoter regions of primary microRNA transcripts using RPol II binding patterns, selection of cooperating transcription factors that collaboratively function with the transcription factors targeted by ChIP-seq assay, and construction of the network that contains regulatory cascades of both transcription factors and microRNAs. I will also report on some new findings on long noncoding RNA in determining alcohol dependence in rat brains, using RNA-seq derived transcriptome mapping data.

Associated Reading:
1. Wang G, Wang Y, Shen C, Huang YW, Huang K, Huang TH, Nephew KP, Li L, Liu Y. 2010. RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS One. Nov 2;5(11):e13798.

2. Wang G, Wang Y, Teng M, Zhang D, Li L, Liu Y. 2010. Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon gamma-stimulated HeLa cells. PLoS One. Jul 26;5(7):e11794.

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