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Identification of sense and antisense transcripts regulated by drought in sugarcane.

Lembke CG, Nishiyama MY, Sato PM, de Andrade RF, Souza GM - Plant Mol. Biol. (2012)

Bottom Line: We validated the results obtained using quantitative real-time PCR (qPCR).Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs).The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Transdução de Sinal, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil.

ABSTRACT
Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90%. From the probes presented on the array, 75% of the sense probes and 11.9% of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

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Log ratio of sense and antisense features vs. the log of their red and green processed signals. The gray color represents the sense features and the black color represents the antisense features, showing the low log ratio signal for antisense probes
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Fig7: Log ratio of sense and antisense features vs. the log of their red and green processed signals. The gray color represents the sense features and the black color represents the antisense features, showing the low log ratio signal for antisense probes

Mentions: The intensity-based analysis has identified a large number of significantly expressed transcript probes, especially for antisense probes. The low number of differentially expressed antisense probes may be due to their low signal intensity (Figs. 6, 7), as it is known that antisense expression in generally represented in low levels (Verjovski-Almeida et al. 2007; Chan et al. 2006). This fact led us to analyze the signal intensities in the two channels normalized and used separately. This approach has increased the reproducibility and sensitivity for the identification of expressed genes in two independent datasets (Hoen et al. 2004; Bossers et al. 2010).Fig. 6


Identification of sense and antisense transcripts regulated by drought in sugarcane.

Lembke CG, Nishiyama MY, Sato PM, de Andrade RF, Souza GM - Plant Mol. Biol. (2012)

Log ratio of sense and antisense features vs. the log of their red and green processed signals. The gray color represents the sense features and the black color represents the antisense features, showing the low log ratio signal for antisense probes
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369129&req=5

Fig7: Log ratio of sense and antisense features vs. the log of their red and green processed signals. The gray color represents the sense features and the black color represents the antisense features, showing the low log ratio signal for antisense probes
Mentions: The intensity-based analysis has identified a large number of significantly expressed transcript probes, especially for antisense probes. The low number of differentially expressed antisense probes may be due to their low signal intensity (Figs. 6, 7), as it is known that antisense expression in generally represented in low levels (Verjovski-Almeida et al. 2007; Chan et al. 2006). This fact led us to analyze the signal intensities in the two channels normalized and used separately. This approach has increased the reproducibility and sensitivity for the identification of expressed genes in two independent datasets (Hoen et al. 2004; Bossers et al. 2010).Fig. 6

Bottom Line: We validated the results obtained using quantitative real-time PCR (qPCR).Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs).The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Transdução de Sinal, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil.

ABSTRACT
Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90%. From the probes presented on the array, 75% of the sense probes and 11.9% of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

Show MeSH