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Dongyuan Liu

Publications and source records attributed to Dongyuan Liu.

8 recordsLinked to original sources
PubMed2007

Rapid evolution in a pair of recent duplicate segments of rice.

Gene duplication has been considered the most important way of generating genetic novelties. The subsequent evolution right after gene duplication is critical for new function to occur. Here we analyzed the evolutionary pattern for a recently duplicated segment between rice chromosomes 11 and 12. This duplication event was estimated to occur about 6 million years ago, during the divergence of the B- and C-genome rice species. The duplicate segment in chromosome 12 has significantly higher frequency of sequence rearrangement rate than non-duplicated regions. The rearrangement rate is approximately 6.5 breakages/Mb per million years, about six times higher than the fastest rate ever reported in eukaryotes. The genes within both segments experienced accelerated nucleotide substitution rates revealed by synonymous (Ks) and non-synonymous divergence (Ka) between Oryza sativa indica and O. sativa japonica. Analysis using EST data also implicates rapid divergence in expression between these segmental duplicate genes. These overall rapid changes from different perspective for the first time provide evidence that relaxation of selection also occurs in large-scale duplications.

Base Sequence↗
PubMed2006

Estrogen related receptor-alpha enhances surfactant protein-A gene expression in fetal lung type II cells.

Surfactant protein-A (SP-A) gene expression is developmentally regulated in fetal lung type II cells in concert with surfactant glycerophospholipid synthesis. In studies using transfected type II cells, we characterized a nuclear receptor element (NRE(SP-A), 5'-TGACCTTA-3') at -242 bp in the 5'-flanking sequence of human SP-A2 (hSP-A) gene that is essential for basal and cAMP-induced expression. NRE(SP-A) has high sequence similarity to the consensus binding site for estrogen-related receptor (ERR). In the present study, we observed that ERRalpha and ERRgamma, but not ERRbeta, were expressed in human fetal lung type II cells. In vitro transcribed/translated ERRalpha and ERRgamma bound to the NRE(SP-A); DNase I footprinting using bacterially expressed ERRalpha revealed a single DNase I protected region that included NRE(SP-A). In transient transfection assays of COS-7 and primary cultures of lung type II cells, ERRalpha acting through NRE(SP-A) increased hSP-A promoter activity, whereas ERRgamma had no effect. ERRalpha overexpression in lung type II cells enhanced cAMP induction of endogenous hSP-A expression, whereas cotransfection of protein kinase A catalytic subunit enhanced ERRalpha stimulation of hSP-A promoter activity in lung adenocarcinoma cells. Mice homozygous null for the ERRalpha gene manifested decreased SP-A expression relative to wild-type and heterozygous littermates. The ERRalpha-specific inverse agonist XCT790 inhibited cAMP induced hSP-A expression in human fetal lung type II cells in a concentration-dependent manner, suggesting a role of peroxisome proliferator-activated receptor-gamma coactivator 1alpha. These findings suggest that ERRalpha acting through NRE(SP-A) is an important mediator of hSP-A gene expression and its induction by cAMP.

Cells, Cultured↗
PubMed2006

High rate of chimeric gene origination by retroposition in plant genomes.

Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species.

Evolution, Molecular↗
PubMed2005

The Genomes of Oryza sativa: a history of duplications.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Base Sequence↗
PubMed2004

A draft sequence for the genome of the domesticated silkworm (Bombyx mori).

We report a draft sequence for the genome of the domesticated silkworm (Bombyx mori), covering 90.9% of all known silkworm genes. Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content.

Algorithms↗
PubMed2002

[Serum levels of soluble intercellular molecule 1 (sICAM-1) in endometriosis].

OBJECTIVE: To investigate the serum levels of ICAM-1 and its relationship to the extent of the disease. METHODS: Serum sICAM-1 levels of 21 women with endometriosis were measured with a specific enzyme-linked immunosorbent assay, and 21 women without endometriosis were selected as control. Serum sICAM-1 levels were compared between endometriotic and non-endometriotic women, and among patients at different stages of endometriosis. RESULTS: Significantly higher serum sICAM-1 levels were observed in women with endometriosis [(0.30 +/- 0.07) microgram/ml] than in those without endometriosis [(0.18 +/- 0.05) microgram/ml] (P < 0.01); in women with stage I approximately II of endometriosis, the serum sICAM-1 levels were (0.24 +/- 0.06) microgram/ml, while in those with stage III approximately IV of endometriosis, the serum sICAM-1 level was (0.32 +/- 0.06) microgram/ml, the difference is of statistically significant.No differences of serum sICAM-1 level was found between proliferative and secretary phase in women with and without endometriosis. CONCLUSIONS: Significantly elevated serum sICAM-1 levels in women with endometriosis, especially in those with advanced stages of the disease suggests the molecule might be of value in pathogenesis of endometriosis.

Adult↗
PubMed2002

Effect of trans-acting factor on rat glutathione S-transferase P1 gene transcription regulation in tumor cells.

OBJECTIVE: To investigate the effect of trans-acting factor(s) on rat glutathione S-transferase P1 gene (rGSTP1) transcription regulation in tumor cells. METHODS: The binding of trans-acting factor(s) to two enhancers of the rGSTP1 gene, glutathione S-transferase P enhancer I (GPEI) and glutathione S-transferase P enhancer II-1 (GPE II-1), was identified by an electrophoretic mobility shift assay (EMSA). The molecular weight of trans-acting factor was measured in a UV cross-linking experiment. RESULTS: Trans-acting factor interacting with the core sequence of GPEI (cGPEI) were found in human cervical adenocarcinoma cell line (HeLa) and rat hepatoma cell line (CBRH7919). These proteins were not expressed in normal rat liver. Although specific binding proteins that bound to GPE II-1 were detected in all three cell types, a 64 kDa binding protein that exists in HeLa and CBRH7919 cells was absent in normal rat liver. CONCLUSION: cGPEI, GPEII specific binding proteins expressed in HeLa and CBRH7919 cells may play an important role in the high transcriptional level of the rGSTP1 gene in tumor cells.

Animals↗