A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.
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.
Stolc
Viktor
V
Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
Li
Lei
L
Wang
Xiangfeng
X
Li
Xueyong
X
Su
Ning
N
Tongprasit
Waraporn
W
Han
Bin
B
Xue
Yongbiao
Y
Li
Jiayang
J
Snyder
Michael
M
Gerstein
Mark
M
Wang
Jun
J
Deng
Xing Wang
XW
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*
D002232:Carbocyanines; D018076:DNA, Complementary; D018749:RNA, Plant; C089187:cyanine dye 3