An expression atlas of rice mRNAs and small RNAs

Abstract

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.

The Cornucopia of Small RNAs in Plant Genomes

“…Both experimental validation and computational predictions indicate that many of these siRNA targets are transposable elements, consistent with the well-described role of plant endogenous siRNAs in genome defense against transposons and viruses [64]. In other studies, high-throughput sequencing has discovered that siRNAs are widely distributed across the rice chromosomes, inconsistent with Arabidopsis in which small RNAs are concentrated in the pericentromeric regions [36]. The difference in small RNA distributions is primarily due to the wider distribution of transposons and related repeats in rice, a phenomenon likely to be reflected in more complex plant genomes as well.…”

“…This type of experiment has yet to be done in rice due to the lack of well-characterized small RNA biogenesis mutants. However, deep sequencing in rice has already revealed numerous abundant and consistently expressed non-conserved small RNAs [36]. This method of exploring small RNA profiles in rice has also lead to the identification of natural antisense miRNAs in rice [47].…”

“…ration of rice small RNA populations, and many new miRNAs have been discovered recently in rice [34,36,47,67]. This includes a special class of natural antisense transcript miRNAs (nat-miRNAs), which are derived from natural cis-antisense transcripts with exons primarily located antisense to the introns of their target genes; these nat-miRNAs are DCL1-dependent [47].…”

“…MicroRNAs are typically identified using experimental approaches, like cloning and sequencing of small RNA libraries, or through computational predictions that are subsequently experimentally validated or even by forward genetics approaches [30][31][32][33]. High-throughput sequencing such as massively parallel signature sequencing (MPSS), 454 pyrosequencing, and sequencing-by-synthesis (SBS) of small RNA libraries has substantially increased the rate of identification of miRNAs [34][35][36]. Deep sequencing across plant lineages has identified evolutionarily conserved miRNA families in gymnosperms, mosses, monocots, and dicots [37,38].…”

Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data

“…Alternatively, spliced transcripts have been experimentally identified in large numbers through de novo sequencing methods such as conventional expressed sequence tag (EST) sequencing and massively parallel signature sequencing [17,20,21,25]. Oligonucleotide microarray analysis of expression patterns associated with alternatively spliced transcripts has often been used in studies of human disease but has not been widely applied in plants [10,19,31].…”