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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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Expression pattern of sense and antisense probe pairs that were identified as differentially expressed by the modified HTself method. The Y axis indicates the number of probes. The X axis indicates the expression pattern of the antisense probe. The colors on the legend indicate the expression pattern of the sense probe from the probe pair
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Fig9: Expression pattern of sense and antisense probe pairs that were identified as differentially expressed by the modified HTself method. The Y axis indicates the number of probes. The X axis indicates the expression pattern of the antisense probe. The colors on the legend indicate the expression pattern of the sense probe from the probe pair

Mentions: When we analyzed the expression pattern between sense and antisense pairs that were identified as differentially expressed by the modified HTself method, we could not observe the pairs with opposite pattern between sense and antisense transcripts (sense up and antisense down, and/or sense down and antisense up) and at 24 h of water withholding all of the pairs had both probes classified as inside (Fig. 9). This may be due to the high stringency used in the Outlier method.Fig. 9


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)

Expression pattern of sense and antisense probe pairs that were identified as differentially expressed by the modified HTself method. The Y axis indicates the number of probes. The X axis indicates the expression pattern of the antisense probe. The colors on the legend indicate the expression pattern of the sense probe from the probe pair
© Copyright Policy
Related In: Results  -  Collection

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

Fig9: Expression pattern of sense and antisense probe pairs that were identified as differentially expressed by the modified HTself method. The Y axis indicates the number of probes. The X axis indicates the expression pattern of the antisense probe. The colors on the legend indicate the expression pattern of the sense probe from the probe pair
Mentions: When we analyzed the expression pattern between sense and antisense pairs that were identified as differentially expressed by the modified HTself method, we could not observe the pairs with opposite pattern between sense and antisense transcripts (sense up and antisense down, and/or sense down and antisense up) and at 24 h of water withholding all of the pairs had both probes classified as inside (Fig. 9). This may be due to the high stringency used in the Outlier method.Fig. 9

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