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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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qPCR of sense and antisense transcripts regulated by drought stress. The y axis is the normalized relative expression ratio between stressed versus irrigated samples. qPCR reactions were done only for experimental points differentially expressed in microarray experiments. Reactions were done in triplicates; on a third biological replicate and using strand specific cDNA as template. Error bars were calculated as in Rocha et al. (2007). *p = 1.00 for control versus drought sample
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Fig5: qPCR of sense and antisense transcripts regulated by drought stress. The y axis is the normalized relative expression ratio between stressed versus irrigated samples. qPCR reactions were done only for experimental points differentially expressed in microarray experiments. Reactions were done in triplicates; on a third biological replicate and using strand specific cDNA as template. Error bars were calculated as in Rocha et al. (2007). *p = 1.00 for control versus drought sample

Mentions: The expression of genes involved in Photosynthesis was also altered in our experiments. Photosystem I reaction center subunit V was repressed in both sense and antisense transcripts and Photosystem II polypeptide was induced (Fig. 5).Fig. 5


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)

qPCR of sense and antisense transcripts regulated by drought stress. The y axis is the normalized relative expression ratio between stressed versus irrigated samples. qPCR reactions were done only for experimental points differentially expressed in microarray experiments. Reactions were done in triplicates; on a third biological replicate and using strand specific cDNA as template. Error bars were calculated as in Rocha et al. (2007). *p = 1.00 for control versus drought sample
© Copyright Policy
Related In: Results  -  Collection

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

Fig5: qPCR of sense and antisense transcripts regulated by drought stress. The y axis is the normalized relative expression ratio between stressed versus irrigated samples. qPCR reactions were done only for experimental points differentially expressed in microarray experiments. Reactions were done in triplicates; on a third biological replicate and using strand specific cDNA as template. Error bars were calculated as in Rocha et al. (2007). *p = 1.00 for control versus drought sample
Mentions: The expression of genes involved in Photosynthesis was also altered in our experiments. Photosystem I reaction center subunit V was repressed in both sense and antisense transcripts and Photosystem II polypeptide was induced (Fig. 5).Fig. 5

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
Related in: MedlinePlus