Regulation of early endosperm development in maize
Chromatin and epigenomic landscape of the developing maize endosperm
Another research interest in our Lab is to understand the epigenomic regulatory mechanisms that function during early maize endosperm development. In collaboration with Dr. Ramin Yadegari’s Lab, We are currently producing selected histone marks and DNA methylation using Illumina sequencing in a famous maize hybrid B73 cross Mo17. Another potential direction we are interested in is to study if the genomic imprinting influence the heterosis phenomena.
What is heterosis
Heterosis, or hybrid vigor, is the increased function of any biological quality in a hybrid offspring. It is the occurrence of a genetically superior offspring from mixing the genes of its parents. Nearly all field corn (maize) grown in most developed nations exhibits heterosis. Modern corn hybrids substantially outyield conventional cultivars and respond better to fertilizer.
Above figure was modified from two papers by (Springer and Stupar 2007 and He et al, 2010)
Improve maize gene prediction using active histone marks
We are sequencing two activating histone marks H3K9ac and H3K36me3, which are usually associated with transcription initiation and elongation, respectively. The former peaks at TSSs of actively transcribed genes, while the latter spreads along the entire gene body regions (A). Therefore, the two modifications have been considered hallmarks for active promoters or actively transcribed genes (B). The current version maize genome annotation contains certain computationally predicted genes with wrongly defined gene borders (multiple genes were predicted as one gene). Because H3K9ac marks the gene start and H3K36me3 marks the gene body region, we can use these information to correct the wrongly annotated genes. In our Lab, we are developing supervised Hidden Markov Model (HMM) to integrate the epigenetic information with RNA-Seq signal information to finally improve the gene models in maize.
Genome-wide search for epigenetically imprinted genes in maize endosperm
Genomic imprinting refers to the preferential expression of maternal or paternal alleles of genes in progeny. The imprinted genes are usually marked by silencing epigenetic modifications. In flowering plants, the endosperm is the primary tissue where gene imprinting is associated with a developmental control mechanism. However, only a handful of imprinted genes have been discovered.
Assembly and annotation of Thellungiella halophila genome
We are also collaborating with Dr. Karen Schumaker Lab on genome sequencing project of Thellungiella halophila, which is a halophytic relative of both the genetic model Arabidopsis thaliana (Arabidopsis). The genome sequence of T. halophila will be a critical resource for the fields of stress biology, evolutionary biology, and comparative genomics. We are currently working on using Arabidopsis as reference genome to assemble the hellungiella halophila. We are also analyzing the mRNA transcriptome sequenced by 454 under several stress libraries such cold, salinity and drought to identify the genes involved in stress resistance.