Publications by authors named "Xin-Ying Ren"
Chromosomal coexpression domains are found in a number of different genomes under various developmental conditions. The size of these domains and the number of genes they contain vary. Here, we define local coexpression domains as adjacent genes where all possible pair-wise correlations of expression data are higher than 0.
View Article and Find Full Text PDFIn both the monocot rice and the dicot Arabidopsis, highly expressed genes have more and longer introns and a larger primary transcript than genes expressed at a low level: higher expressed genes tend to be less compact than lower expressed genes. In animal genomes, it is the other way round. Although the length differences in plant genes are much smaller than in animals, these findings indicate that plant genes are in this respect different from animal genes.
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- White Spot Syndrome Virus (WSSV) is a large DNA virus that infects shrimp and crustaceans, and its gene expression is thought to follow a coordinated pattern.
- Researchers used two methods to analyze promoter motifs in WSSV gene sequences, revealing similarities to known RNA polymerase II promoters in early genes and identifying a potential motif for late transcription.
- Findings suggest there are two types of late WSSV genes, one that uses the host's transcription machinery and another that may rely on a viral mechanism for mRNA synthesis.
Article Synopsis
- Researchers defined local coexpression domains as groups of physically adjacent genes that are closely coexpressed in the Arabidopsis genome.
- By analyzing various gene expression data, they identified 689 and 1,481 local coexpression domains composed of 2-4 genes, which exceeded the expected numbers by 1- to 5-fold.
- These domains, important for understanding gene function, showed that a small portion (5%-10%) of genes are organized this way, but their coexpression does not seem to be influenced by common factors like gene distance or shared promoter sequences.