【学术报告】Transcriptome analysis for identifying stress-inducible microRNAs

发稿时间:2010-05-10浏览次数:3786

题目:Transcriptome analysis for identifying stress-inducible microRNAs

报告人:Weixiong Zhang
        Department of Computer Science and Engineering
        Department of Genetics
        Washington University in St. Louis
        http://www.cse.wustl.edu/~zhang


时间:5月10日15:30-16:30
地点:蒙民伟楼404室

摘要:
MicroRNAs (miRNAs) are ~21nt non-coding RNAs that regulate gene expression at
the post-transcriptional level. Plant miRNAs regulate many genes that are
involved in development and stress response. Although a large number of miRNAs
 have been identified and studied, most of them remain to be functionally
annotated. Experimental functional analysis is laborious and costly. It is,
therefore, desirable to develop computational approaches to support and
complement experimental approaches for miRNA functional analysis. In this talk
 I will describe a novel, machine learning/datamining approach for identifying
 microRNA genes in plants that are responsive to environmental stresses. Our
overall approach consists of a new computational method for identifying cis-
regulatory DNA sequences (motifs) from the promoters of mRNA genes, a method
for predicting core promoters of miRNA genes, a new transcriptome-based gene
expression modeling method, and experimental verification of mature miRNAs and
 miRNA precursors. We applied our approach to study cold-responsive microRNA
genes in Arabidospsis thaliana. We predicted nineteen individual microRNAs in
twelve miRNA families to be up-regulated in Arabidopsis seedlings under cold
stress. Our experimental validation showed that among the twelve microRNA
families, eight were differentially induced by cold and three were constantly
expressed under cold stimulus. A promoter analysis also showed that these cold
-inducible microRNA genes contain many known stress-related cis-regulatory
elements in their promoters. I will also discuss putative transcriptional down
-regulation pathways triggered by the induction of these microRNA genes.
Particularly, our result indicated that auxin signaling pathways in
Arabidopsis seedlings may be mediated by many microRNAs.


简介:
Weixiong Zhang is a professor of Computer Science and of Genetics at
Washington University in St. Louis, Missouri, USA. He received his B.S. and M.
S. in computer engineering from Tsinghua University, Beijing, China, and his M
.S. and Ph.D. in computer science from University of California at Los Angeles
 (UCLA). Professor Zhang's research interests include computational systems
biology and genomics, artificial intelligence, data mining, and combinatorial
optimization. He has published more than 100 papers in these areas and is the
author of a research monograph, State-Space Search: Algorithms, Complexity,
Extensions and Applications, published by Springer in 1999. He is currently
associate editors of PLoS Computational Biology, J. Alzheimer's Disease,
Artificial Intelligence, and AI Communications - The European Journal on
Artificial Intelligence.