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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.

Show MeSH
Functional categories of genes differentially expressed in sugarcane plants submitted to drought stress for 24, 72 and 120 h. Numbers indicate the total of genes identified in each category
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Fig3: Functional categories of genes differentially expressed in sugarcane plants submitted to drought stress for 24, 72 and 120 h. Numbers indicate the total of genes identified in each category

Mentions: A total of 987 probes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h (Electronic Supplementary Table 3). Among them, 928 were sense transcripts and 59 were antisense. Only 24 differentially expressed genes had both sense and antisense transcripts regulated by drought and 22 of them had the same expression pattern between antisense and sense, meaning, when sense transcript was up-regulated, the antisense transcript was also up-regulated and vice versa. As seen before (Rocha et al. 2007), the number of differentially expressed genes increased significantly after 72 and 120 h of water stress compared to 24 h of stress. From the thirty functional categories created, only two categories were not represented (Fig. 3). Using the GeneMerge Tool, we could identify functional categories enriched in each experimental time point (Table 2).Fig. 3


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)

Functional categories of genes differentially expressed in sugarcane plants submitted to drought stress for 24, 72 and 120 h. Numbers indicate the total of genes identified in each category
© Copyright Policy
Related In: Results  -  Collection

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

Fig3: Functional categories of genes differentially expressed in sugarcane plants submitted to drought stress for 24, 72 and 120 h. Numbers indicate the total of genes identified in each category
Mentions: A total of 987 probes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h (Electronic Supplementary Table 3). Among them, 928 were sense transcripts and 59 were antisense. Only 24 differentially expressed genes had both sense and antisense transcripts regulated by drought and 22 of them had the same expression pattern between antisense and sense, meaning, when sense transcript was up-regulated, the antisense transcript was also up-regulated and vice versa. As seen before (Rocha et al. 2007), the number of differentially expressed genes increased significantly after 72 and 120 h of water stress compared to 24 h of stress. From the thirty functional categories created, only two categories were not represented (Fig. 3). Using the GeneMerge Tool, we could identify functional categories enriched in each experimental time point (Table 2).Fig. 3

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