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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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Characterization of japonica TARs. (A) Classification of all identified TARs based on known transcriptional evidence and sequences of known origin. Exon, exons of annotated gene models; Unigene, rice Unigenes in GenBank; Repeat, plant repetitive sequences and organelle insertions. (B) Density of different sets of transcription units along Chromosome 8. The number of transcription units was calculated in 500 Kb-sliding-windows with a 100 Kb step. Position of the centromere is indicated by the triangle. (C) Venn diagram showing the comparison of japonica non-exonic TARs with indica transcription units. Two independent comparisons were made. First, the japonica non-exonic TARs were compared with annotated indica gene models. Second, the japonica non-exonic TARs were compared with indica non-exonic TARs, which were identified outside of gene models from tiling array analysis of the indica genome. Shaded areas indicate japonica TARs that overlap with indica gene models or non-exonic TARs.
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pone-0000294-g001: Characterization of japonica TARs. (A) Classification of all identified TARs based on known transcriptional evidence and sequences of known origin. Exon, exons of annotated gene models; Unigene, rice Unigenes in GenBank; Repeat, plant repetitive sequences and organelle insertions. (B) Density of different sets of transcription units along Chromosome 8. The number of transcription units was calculated in 500 Kb-sliding-windows with a 100 Kb step. Position of the centromere is indicated by the triangle. (C) Venn diagram showing the comparison of japonica non-exonic TARs with indica transcription units. Two independent comparisons were made. First, the japonica non-exonic TARs were compared with annotated indica gene models. Second, the japonica non-exonic TARs were compared with indica non-exonic TARs, which were identified outside of gene models from tiling array analysis of the indica genome. Shaded areas indicate japonica TARs that overlap with indica gene models or non-exonic TARs.

Mentions: We next scored genome-wide transcription blind to the annotated gene models and described a transcriptome consisting of 39,018 unique TARs (see Materials and Methods). Of these, 13,666 (35%) intersected with annotated exons (exonic-TAR; Figure 1A). Comparison of the corresponding sequences of non-exonic TARs to plant repeat databases yielded 748 hits (E≤e−10). Comparing the non-exonic TARs with rice organelle genome sequences, which have inserted into and contribute to ∼0.4% of the nuclear genome [7], revealed 136 and 238 matches (>95% sequence identity) to the mitochondrial and chloroplast genomes, respectively. Thus, only 1122 (4%) non-exonic TARs are encoded by repeats (Figure 1A). Not surprisingly, distribution of the non-exonic TARs along the chromosomes indicates that the TE-abundant centromere regions are depleted of TARs (Figure 1B and S2).


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)

Characterization of japonica TARs. (A) Classification of all identified TARs based on known transcriptional evidence and sequences of known origin. Exon, exons of annotated gene models; Unigene, rice Unigenes in GenBank; Repeat, plant repetitive sequences and organelle insertions. (B) Density of different sets of transcription units along Chromosome 8. The number of transcription units was calculated in 500 Kb-sliding-windows with a 100 Kb step. Position of the centromere is indicated by the triangle. (C) Venn diagram showing the comparison of japonica non-exonic TARs with indica transcription units. Two independent comparisons were made. First, the japonica non-exonic TARs were compared with annotated indica gene models. Second, the japonica non-exonic TARs were compared with indica non-exonic TARs, which were identified outside of gene models from tiling array analysis of the indica genome. Shaded areas indicate japonica TARs that overlap with indica gene models or non-exonic TARs.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0000294-g001: Characterization of japonica TARs. (A) Classification of all identified TARs based on known transcriptional evidence and sequences of known origin. Exon, exons of annotated gene models; Unigene, rice Unigenes in GenBank; Repeat, plant repetitive sequences and organelle insertions. (B) Density of different sets of transcription units along Chromosome 8. The number of transcription units was calculated in 500 Kb-sliding-windows with a 100 Kb step. Position of the centromere is indicated by the triangle. (C) Venn diagram showing the comparison of japonica non-exonic TARs with indica transcription units. Two independent comparisons were made. First, the japonica non-exonic TARs were compared with annotated indica gene models. Second, the japonica non-exonic TARs were compared with indica non-exonic TARs, which were identified outside of gene models from tiling array analysis of the indica genome. Shaded areas indicate japonica TARs that overlap with indica gene models or non-exonic TARs.
Mentions: We next scored genome-wide transcription blind to the annotated gene models and described a transcriptome consisting of 39,018 unique TARs (see Materials and Methods). Of these, 13,666 (35%) intersected with annotated exons (exonic-TAR; Figure 1A). Comparison of the corresponding sequences of non-exonic TARs to plant repeat databases yielded 748 hits (E≤e−10). Comparing the non-exonic TARs with rice organelle genome sequences, which have inserted into and contribute to ∼0.4% of the nuclear genome [7], revealed 136 and 238 matches (>95% sequence identity) to the mitochondrial and chloroplast genomes, respectively. Thus, only 1122 (4%) non-exonic TARs are encoded by repeats (Figure 1A). Not surprisingly, distribution of the non-exonic TARs along the chromosomes indicates that the TE-abundant centromere regions are depleted of TARs (Figure 1B and S2).

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