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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 with signal above background. a Expression pattern of sense and antisense probes pairs separated by time of water withholding. The Y axis indicates the number of probes. The X axis indicates the expression pattern of antisense probes. The colors on the legend indicate the expression pattern of the sense probe from the probe pair. b Expression pattern of sense and antisense probes pairs with opposite expression pattern in each experimental time course
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Fig8: Expression pattern of sense and antisense probe pairs with signal above background. a Expression pattern of sense and antisense probes pairs separated by time of water withholding. The Y axis indicates the number of probes. The X axis indicates the expression pattern of antisense probes. The colors on the legend indicate the expression pattern of the sense probe from the probe pair. b Expression pattern of sense and antisense probes pairs with opposite expression pattern in each experimental time course

Mentions: To compare expression profile between sense and antisense transcripts, we selected only oligonucleotides that are represented by both sense and antisense probe pairs in the array. Using the signal intensity log ratio between experimental and control sample, we classified the probe as up-regulated if logratio > 0,down-regulated if logratio < 0 and as inside if the signal intensity is not significantly above the background, based on the filtering background methodology. At first, we could observe that the expression pattern of sense and antisense pairs is quite similar in the three different experimental time points. As cited earlier, there are more sense transcripts above background than antisense transcripts. This can be observed in Fig. 8 where the majority of sense up and sense down transcripts has its antisense pair classified as inside (black and gray bars on the third (antisense inside) group of each experiment time group). The following observations are relative only to pairs which sense and antisense probes were classified as up or down-regulated. When the sense probe is up-regulated (black bars) its respective antisense probe is in most cases also up (first black bar of each time group) (Fig. 8a) and when sense probe is down (gray bars), its respective antisense is in most cases also down (gray bar on the second group of each time group) (Fig. 8a). There are also some examples which sense and antisense have different expression patterns (Fig. 8b) and it is interesting that the increase of drought stress period is accompanied with a decrease in the proportion of pairs of sense and antisense with different expression patterns (Fig. 8b).Fig. 8


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 with signal above background. a Expression pattern of sense and antisense probes pairs separated by time of water withholding. The Y axis indicates the number of probes. The X axis indicates the expression pattern of antisense probes. The colors on the legend indicate the expression pattern of the sense probe from the probe pair. b Expression pattern of sense and antisense probes pairs with opposite expression pattern in each experimental time course
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Related In: Results  -  Collection

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

Fig8: Expression pattern of sense and antisense probe pairs with signal above background. a Expression pattern of sense and antisense probes pairs separated by time of water withholding. The Y axis indicates the number of probes. The X axis indicates the expression pattern of antisense probes. The colors on the legend indicate the expression pattern of the sense probe from the probe pair. b Expression pattern of sense and antisense probes pairs with opposite expression pattern in each experimental time course
Mentions: To compare expression profile between sense and antisense transcripts, we selected only oligonucleotides that are represented by both sense and antisense probe pairs in the array. Using the signal intensity log ratio between experimental and control sample, we classified the probe as up-regulated if logratio > 0,down-regulated if logratio < 0 and as inside if the signal intensity is not significantly above the background, based on the filtering background methodology. At first, we could observe that the expression pattern of sense and antisense pairs is quite similar in the three different experimental time points. As cited earlier, there are more sense transcripts above background than antisense transcripts. This can be observed in Fig. 8 where the majority of sense up and sense down transcripts has its antisense pair classified as inside (black and gray bars on the third (antisense inside) group of each experiment time group). The following observations are relative only to pairs which sense and antisense probes were classified as up or down-regulated. When the sense probe is up-regulated (black bars) its respective antisense probe is in most cases also up (first black bar of each time group) (Fig. 8a) and when sense probe is down (gray bars), its respective antisense is in most cases also down (gray bar on the second group of each time group) (Fig. 8a). There are also some examples which sense and antisense have different expression patterns (Fig. 8b) and it is interesting that the increase of drought stress period is accompanied with a decrease in the proportion of pairs of sense and antisense with different expression patterns (Fig. 8b).Fig. 8

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