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Global identification and characterization of transcriptionally active regions in the rice genome.

Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW - PLoS ONE (2007)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America.

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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Analysis of 5′ proximal antisense TARs. (A) Annotation of TAR Chr4rev_22552532 that locates in a divergent antisense orientation to the gene model Os04g38590. (B) Predicted secondary structure of the RNA transcript derived from the TAR Chr4rev_22552532. RNA secondary structure was predicted using RNAfold, which is available as part of the Vienna RNA Package.
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pone-0000294-g007: Analysis of 5′ proximal antisense TARs. (A) Annotation of TAR Chr4rev_22552532 that locates in a divergent antisense orientation to the gene model Os04g38590. (B) Predicted secondary structure of the RNA transcript derived from the TAR Chr4rev_22552532. RNA secondary structure was predicted using RNAfold, which is available as part of the Vienna RNA Package.

Mentions: Some TARs with corresponding small RNA derivatives were predicted to fold into stable secondary structures in which the nc-RNAs were located near stem-loop motifs (Figure 6C). It is a possibility that the small nc-RNAs are processed from these corresponding TARs. We were also able to predict stable secondary structures for the many intergenic TARs not represented by the 1Mb tiling array, particularly those located in close proximity to gene models in a divergent antisense orientation (Figure 7). We identified 234 intergenic TARs that have homology to sequences in different plant species. These clusters of sequence homologs were used to search for structural conservation using the RNAz algorithm [44], which uses comparative sequence analysis and RNA secondary structure prediction to detect evolutionarily conserved and exceptionally stable secondary structures. By this method, 32 of these 234 non-coding TAR clusters (14%) were predicted form stable secondary structures. This fraction is significantly higher (binomial p<e−15) than that for randomly shuffled TAR alignment blocks, for which only ∼6% are predicted to form structural nc-RNA.


Global identification and characterization of transcriptionally active regions in the rice genome.

Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW - PLoS ONE (2007)

Analysis of 5′ proximal antisense TARs. (A) Annotation of TAR Chr4rev_22552532 that locates in a divergent antisense orientation to the gene model Os04g38590. (B) Predicted secondary structure of the RNA transcript derived from the TAR Chr4rev_22552532. RNA secondary structure was predicted using RNAfold, which is available as part of the Vienna RNA Package.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1808428&req=5

pone-0000294-g007: Analysis of 5′ proximal antisense TARs. (A) Annotation of TAR Chr4rev_22552532 that locates in a divergent antisense orientation to the gene model Os04g38590. (B) Predicted secondary structure of the RNA transcript derived from the TAR Chr4rev_22552532. RNA secondary structure was predicted using RNAfold, which is available as part of the Vienna RNA Package.
Mentions: Some TARs with corresponding small RNA derivatives were predicted to fold into stable secondary structures in which the nc-RNAs were located near stem-loop motifs (Figure 6C). It is a possibility that the small nc-RNAs are processed from these corresponding TARs. We were also able to predict stable secondary structures for the many intergenic TARs not represented by the 1Mb tiling array, particularly those located in close proximity to gene models in a divergent antisense orientation (Figure 7). We identified 234 intergenic TARs that have homology to sequences in different plant species. These clusters of sequence homologs were used to search for structural conservation using the RNAz algorithm [44], which uses comparative sequence analysis and RNA secondary structure prediction to detect evolutionarily conserved and exceptionally stable secondary structures. By this method, 32 of these 234 non-coding TAR clusters (14%) were predicted form stable secondary structures. This fraction is significantly higher (binomial p<e−15) than that for randomly shuffled TAR alignment blocks, for which only ∼6% are predicted to form structural nc-RNA.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America.

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.

Show MeSH
Related in: MedlinePlus