An expression atlas of rice mRNAs and small RNAs.
Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technology called 'massively parallel signature sequencing' to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). We sequenced 46,971,553 mRNA transcripts from 22 libraries, and 2,953,855 small RNAs from 3 libraries. The data demonstrate widespread transcription throughout the genome, including sense expression of at least 25,500 annotated genes and antisense expression of nearly 9,000 annotated genes. An additional set of approximately 15,000 mRNA signatures mapped to unannotated genomic regions. The majority of the small RNA data represented lower abundance short interfering RNAs that match repetitive sequences, intergenic regions and genes. Among these, numerous clusters of highly regulated small RNAs were readily observed. We developed a genome browser (http://mpss.udel.edu/rice) for public access to the transcriptional profiling data for this important crop.
Nobuta
Kan
K
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
Venu
R C
RC
Lu
Cheng
C
Beló
André
A
Vemaraju
Kalyan
K
Kulkarni
Karthik
K
Wang
Wenzhong
W
Pillay
Manoj
M
Green
Pamela J
PJ
Wang
Guo-liang
GL
Meyers
Blake C
BC
D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D012342:RNA, Small Nuclear / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
D012333:RNA, Messenger; D018749:RNA, Plant; D012342:RNA, Small Nuclear