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      Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome

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          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.

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          Most cited references46

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          A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

          J. Yu (2002)
          We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.
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            Global identification of human transcribed sequences with genome tiling arrays.

            Elucidating the transcribed regions of the genome constitutes a fundamental aspect of human biology, yet this remains an outstanding problem. To comprehensively identify coding sequences, we constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome. Transcribed sequences were located across the genome via hybridization to complementary DNA samples, reverse-transcribed from polyadenylated RNA obtained from human liver tissue. In addition to identifying many known and predicted genes, we found 10,595 transcribed sequences not detected by other methods. A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins.
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              Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis.

              In higher eukaryotes, miRNAs and siRNAs guide translational inhibition, mRNA cleavage, or chromatin regulation. We found that the antisense overlapping gene pair of Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH), a stress-related gene, and SRO5, a gene of unknown function, generates two types of siRNAs. When both transcripts are present, a 24-nt siRNA is formed by a biogenesis pathway dependent on DCL2, RDR6, SGS3, and NRPD1A. Initial cleavage of the P5CDH transcript guided by the 24-nt siRNA establishes a phase for the subsequent generation of 21-nt siRNAs by DCL1 and further cleavage of P5CDH transcripts. The expression of SRO5 is induced by salt, and this induction is required to initiate siRNA formation. Our data suggest that the P5CDH and SRO5 proteins are also functionally related, and that the P5CDH-SRO5 gene pair defines a mode of siRNA function and biogenesis that may be applied to other natural cis-antisense gene pairs in eukaryotic genomes.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                PLoS ONE
                plos
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2007
                14 March 2007
                : 2
                : 3
                : e294
                Affiliations
                [1 ]Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
                [2 ]National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing, China
                [3 ]Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, China
                [4 ]Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
                [5 ]Genome Research Facility, NASA Ames Research Center, Moffett Field, California, United States of America
                [6 ]Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
                [7 ]Department of Plant Pathology, University of California, Davis, California, United States of America
                [8 ]Eloret Corporation, Sunnyvale, California, United States of America
                University of California, Davis, United States of America
                Author notes
                * To whom correspondence should be addressed. E-mail: xingwang.deng@ 123456yale.edu

                Conceived and designed the experiments: MG XD LL. Performed the experiments: LL. Analyzed the data: VS WT LL XW RS HH JK. Contributed reagents/materials/analysis tools: PR RC VS WD XC. Wrote the paper: XD LL.

                Article
                06-PONE-RA-00494R2
                10.1371/journal.pone.0000294
                1808428
                17372628
                1c419fc0-feb8-41a9-a5d3-e3a5faf3f6d7
                Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 18 December 2006
                : 21 February 2007
                Page count
                Pages: 13
                Categories
                Research Article
                Genetics and Genomics
                Genetics and Genomics/Bioinformatics
                Genetics and Genomics/Functional Genomics
                Genetics and Genomics/Gene Discovery
                Genetics and Genomics/Gene Expression
                Genetics and Genomics/Genomics
                Genetics and Genomics/Plant Genetics and Gene Expression

                Uncategorized
                Uncategorized

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