title: Global identification and characterization of transcriptionally active regions in the rice genome.
abstract: Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs) not encoded by annotated exons in the rice (Oryza. sativa) subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83%) japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.
authors: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America.
authors: Lei
authors: L
authors: Li
authors: Xiangfeng
authors: X
authors: Wang
authors: Rajkumar
authors: R
authors: Sasidharan
authors: Viktor
authors: V
authors: Stolc
authors: Wei
authors: W
authors: Deng
authors: Hang
authors: H
authors: He
authors: Jan
authors: J
authors: Korbel
authors: Xuewei
authors: X
authors: Chen
authors: Waraporn
authors: W
authors: Tongprasit
authors: Pamela
authors: P
authors: Ronald
authors: Runsheng
authors: R
authors: Chen
authors: Mark
authors: M
authors: Gerstein
authors: Xing Wang
authors: XW
authors: Deng
mesh_terms: D017124:Conserved Sequence; D016373:DNA, Antisense / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D017343:Genes, Plant; D018745:Genome, Plant; D009690:Nucleic Acid Conformation; D012275:Oryza / Q000235:genetics*; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics; D014158:Transcription, Genetic; D015533:Transcriptional Activation / Q000235:genetics*
chemical_list: D016373:DNA, Antisense; D018076:DNA, Complementary; D018744:DNA, Plant; D018749:RNA, Plant