Biomedical subjects

Xueyong Li

Publications and source records attributed to Xueyong Li.

5 recordsLinked to original sources

PubMed2006

Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice.

Most plant cells retain the capacity to differentiate into all the other cell and organ types that constitute a plant. However, genome-wide transcriptional activities underlying the process of cell differentiation are poorly understood, especially in monocot plants. Here we used a rice (Oryza sativa) cell culture system to generate somatic embryos, which were further induced into shoots and roots. The global transcriptional reorganization during the development of somatic embryos, shoots, and roots from cultured cells was studied using a rice whole genome microarray and verified by RNA blotting analysis of representative genes. Overall, only 1-3% of expressed genes were differentially regulated during each organogenesis process at the examined time point. Also metabolic pathways were minimally regulated. Thus the genes that dictating organ formation should be relatively small in number. Comparison of these three transcriptomes revealed little overlap during these three organogenesis processes. These results indicate that each organogenesis involves specific reorganization of genome expression.

Cells, Cultured↗

PubMed2006

Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels.

In addition to DNA sequence information, site-specific histone modifications are another important determinant of gene expression in a eukaryotic organism. We selected four modification sites in common histones that are known to significantly impact chromatin function and generated monoclonal or polyclonal antibodies that recognize each of those site-specific modifications. We used these antibodies to demonstrate that the site-specific histone modification levels remain relatively constant in different organs of the same organism. We also compared the levels of selected histone modifications among several representative organisms and found that site-specific modifications are highly variable among different organisms, providing new insight into the evolutionary divergence of specific histone modifications.

Acetylation↗

PubMed2005

Genome-wide transcription analyses in rice using tiling microarrays.

Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species. We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions that share similar compositional properties with the annotated exons and have significant homology to other plant proteins. Elucidating and mapping of all transcribed regions revealed an association between global transcription and cytological chromosome features, and an overall similarity of transcriptional activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome.

Chromosomes↗

PubMed2005

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcription units that will facilitate rice genome annotation.

Carbocyanines↗

PubMed2003

Control of tillering in rice.

Tillering in rice (Oryza sativa L.) is an important agronomic trait for grain production, and also a model system for the study of branching in monocotyledonous plants. Rice tiller is a specialized grain-bearing branch that is formed on the unelongated basal internode and grows independently of the mother stem (culm) by means of its own adventitious roots. Rice tillering occurs in a two-stage process: the formation of an axillary bud at each leaf axil and its subsequent outgrowth. Although the morphology and histology and some mutants of rice tillering have been well described, the molecular mechanism of rice tillering remains to be elucidated. Here we report the isolation and characterization of MONOCULM 1 (MOC1), a gene that is important in the control of rice tillering. The moc1 mutant plants have only a main culm without any tillers owing to a defect in the formation of tiller buds. MOC1 encodes a putative GRAS family nuclear protein that is expressed mainly in the axillary buds and functions to initiate axillary buds and to promote their outgrowth.

Agriculture↗