title: A genome-wide transcriptional activity survey of rice transposable element-related genes.
abstract: 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.
  
  
  CONCLUSIONS
  Our findings reveal clear, albeit low, general transcription of TE-related genes. In combination with phylogenetic analysis, transcriptional analysis has the potential to lead to the identification of domesticated TEs with adapted host functions.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA. yuling.jiao@yale.edu
authors.forename: Yuling
authors.initials: Y
authors.lastname: Jiao
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D016000:Cluster Analysis; D004251:DNA Transposable Elements / Q000235:genetics*; D030541:Databases, Genetic; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements