TY - JOUR
AU - Deng, Xing
AB - Background: Transposable element (TE)-related genes comprise a significant portion of the gene catalog of grasses, although their functions are insufficiently characterized. The recent availability of TE-related gene annotation from the complete genome sequence of rice (Oryza sativa) has created an opportunity to conduct a comprehensive evaluation of the transcriptional activities of these potentially mobile elements and their related genes. Results: We conducted a genome-wide survey of the transcriptional activity of TE-related genes associated with 15 developmental stages and stress conditions. This dataset was obtained using a microarray encompassing 2,191 unique TE-related rice genes, which were represented by oligonucleotide probes that were free from cross-hybridization. We found that TE-related genes exhibit much lower transcriptional activities than do non-TE-related genes, although representative transcripts were detected from all superfamilies of both type I and II TE-related genes. The strongest transcriptional activities were detected in TE-related genes from among the MULE and CACTA superfamilies. Phylogenetic analyses suggest that domesticated TE-related genes tend to form clades with active transcription. In addition, chromatin-level regulations through histone and DNA modifications, as well as enrichment of certain cis elements in the promoters, appear to contribute to the transcriptional activation of representative TE-related genes. Conclusion: Our findings reveal 
TI - A genome-wide transcriptional activity survey of rice transposable element-related genes
JF - Genome Biology
DO - 10.1186/gb-2007-8-2-r28
DA - 2007-02-27
UR - https://www.deepdyve.com/lp/springer-journals/a-genome-wide-transcriptional-activity-survey-of-rice-transposable-AOSXtZDb8m
SP - 1
EP - 19
VL - 8
IS - 2
DP - DeepDyve
ER -