title: A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.
abstract: As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcription units that will facilitate rice genome annotation.
authors.affiliation: Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
authors.forename: Viktor
authors.initials: V
authors.lastname: Stolc
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.forename: Xiangfeng
authors.initials: X
authors.lastname: Wang
authors.forename: Xueyong
authors.initials: X
authors.lastname: Li
authors.forename: Ning
authors.initials: N
authors.lastname: Su
authors.forename: Waraporn
authors.initials: W
authors.lastname: Tongprasit
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.forename: Yongbiao
authors.initials: Y
authors.lastname: Xue
authors.forename: Jiayang
authors.initials: J
authors.lastname: Li
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D002232:Carbocyanines / Q000737:chemistry; D032461:Chromosomes, Plant / Q000235:genetics; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012275:Oryza / Q000235:genetics*; D010865:Pilot Projects; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D002232:Carbocyanines; D018076:DNA, Complementary; D018749:RNA, Plant; C089187:cyanine dye 3