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Revision as of 20:11, 12 March 2011
PROJECT 1. Regulation of early endosperm development in maize
Endosperm is biologically and economically important. Endosperm provides nutrients and signals to the embryo during seed development. Endosperm is an important source of food and industrial raw materials. Additionally, cereal endosperm is used as a raw material for numerous industrial products including ethanol. We are currently collaborating with Prof. Brian Larkins and Prof. Ramin Yadegari on a NSF funded project to study the regulation of maize early endosperm development. In this project we are using Illumina high-throughput sequencing to profile the mRNA transcriptome (RNA-Seq) to identify the core transcription factors, and build the regulatory network that controls the maize endosperm development in early stages.
See the UA news for the description of this project at 
A genome browser for maize endosperm transcriptome.
We have constructed a local UCSC genome browser at UA to display the maize endosperm RNA-Seq transcriptome.
Identification of important TFs in maize endosperm development
We first conducted a in silico search of maize annotated genes in its 5.0a version in plant transcription factor database, and identify hundreds potential TF maize genes. Then we utilized publish gene microarray expression data and our self-produced RNA-seq data to further filter the gene sets. Our efforts identified ~200 candidate genes that specifically expressed in early stages of endosperm development (A). We are currently performing experimental validation of selected candidate TFs. In the next step, to construct the regulatory network of those identified TFs, we identified the genes whose expression highly correlated with those TFs and calculated their topological structures (B). The regulatory network is finally illustrated in (C). Additionally, we are developing hidden markov model (HMM) to detect the alternative splicing genes during the development (D).
PROJECT 2. Chromatin and epigenomic landscape of the developing maize endosperm