Identification And Analyses Of Functional Elements In Plant Genomics

Identification and characterization of functional elements is the most fundamental step to understand the roles various functional elements play in plant genomics. It help us to know much more about the plant genomics in the molecular and cellular levels, then hence may improve us to make better use of the plant biomass in other applications, such as agriculture, biofuel, etc.In this dissertation, we presented the studies for three different functional elements (i.e., Z-DNA, housekeeping genes and cell-wall synthesis related (CWSR) proteins) in plants, especially model dicot plant A. thaliana, and model monocot plant O. sativa (rice), in three chapters following the first chapter for the introduction.Chapter two discussed the comparative analyses of distributions and functions of Z-DNA in Arabidopsis and rice. Left-handed Z-DNA is an energetically unfavorable DNA structure that could form mostly under certain physiological conditions and was known to be involved in a number of cellular activities such as transcription regulation. We have compared the distributions and functions of Z-DNA in the genomes of Arabidopsis and rice, and observed that Z-DNA occurs in rice at least 9 times more often than in Arabidopsis; similar observations hold for other monocots and dicots. In addition, Z-DNA is significantly enriched in the coding regions of Arabidopsis, and in the high-GC-content regions of rice. Based on our analyses, we speculate that Z-DNA may play a role in regulating the expression of transcription factors, inhibitors, translation repressors, succinate dehydrogenases and glutathione-disulfide reductases in Arabidopsis, and it may affect the expression of vesicle and nucleosome genes and genes involved in alcohol transporter activity, stem cell maintenance, meristem development and reproductive structure development in rice.Chapter three talked about the identification and characterization of housekeeping genes in rice and Arabidopsis in the genomic level. Housekeeping genes are constitutively expressed genes across different tissue types to maintain the essential cellular functions. We have identified 1,928 and 1,411 housekeeping genes in rice and in Arabidopsis, respectively, based on microarray data. The five most dominating functional classes of our predicted housekeeping genes are binding factor, enzymes, transporters, transcription regulators and structural molecules in rice and enzymes, binding factors, structural molecules, transporters and transcription regulators in Arabidopsis, respectively. We have made several interesting observations of these identified housekeeping genes, including that:(a)their average coding sequence lengths and average gene lengths are significantly shorter than these of all the other genes;(b) housekeeping genes have shorter average exon lengths in rice, whereas they significantly have less exons than the other genes in Arabidopsis; (c)but their introns are significantly longer than introns of all the other genes in both plants. The shorter coding sequences may be a result of natural selection for improved translational efficiency. We have also found housekeeping genes have more Expressed Sequence Tag evidences and broad expression profiles across different tissues.Chapter four focused on identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data. Plant cell wall is mainly composed of lignins and polysaccharides, representing the richest source of biomass for future biofuel production. We report a computational framework for prediction of CWSR proteins, based on known protein-protein interaction data and known CWSR proteins. We predicted 100 new candidate CWSR proteins in Arabidopsis seven of which were public database confirmed to be involved in cell-wall synthesis, 46 have independent supporting evidences and hence are considered as reliable predictions. For 33 of the predicted CWSR proteins, we have predicted their specific functional roles in cell-wall synthesis, based on analyses of their domain architectures, phylogenetic analyses and known functional annotation in conjunction with literature search. Interestingly, although the 571 seed CWSR proteins cover only three components among the six main components of the cell-wall biosynthesis process, our predicted CWSR proteins cover two additional components, highlighting the power of our protein-protein interaction based CWSR protein prediction method.