Global gene expression analysis of normal and ripening inhibitor (rin) mutant tomatoes during ripening
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ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE28564 | GEO | 2012/04/02
SECONDARY ACCESSION(S): PRJNA139035
REPOSITORIES: GEO
Similar Datasets
Project description:Ripening is an important stage of fruit development to determine its quality as a diet. A tomato (Solanum lycopersicum) MADS-box transcription factor, RIPENING INHIBITOR (RIN), has been believed to serve as a regulator of ripening lying upstream of ethylene-dependent and ethylene-independent pathways. Here, we have conducted global gene expression analysis to comprehensively identify tomato genes whose expressions are affected by the rin mutation using microarray with RNA samples from the normal and rin mutant tomato fruits at the pre-ripening (mature green) and ripening (pink coloring) stages. By analysing this microarray data, we identified 342 of positively regulated and 473 negatively regulated genes by RIN, which showed >5 and <0.2 of the fold change ratio (FC) of normal fruits at the ripening stage relative to those at the pre-ripening stage, respectively, in a RIN-dependent manner. A chromatin immunoprecipitation (ChIP) analysis of the normal ripening tomatoes with the anti-RIN antibody revealed that the positively regulated gene set contained at least 13 direct RIN targets. We monitored global gene expression in normal (PK331 cultivar) and rin mutant (PK353 cultivar) tomatoes at the pre-ripening (mature green, G) and ripening (pink coloring, P) stages using microarray with three biological replicates for each sample.
2012-04-01 | E-GEOD-28564 | biostudies-arrayexpress
Project description:The tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN) acts as a master regulator of tomato fruit ripening. We previously identified a direct RIN target gene Solyc07g052960, which encodes a putative GRAS family protein belonging to the SHORT-ROOT (SHR) branch, but its role was unknown. RNA interference (RNAi)-mediated gene silencing reduced Solyc07g052960 expression in transgenic fruits, but the fruits appeared to ripen normally. However, the transgenic fruits at the ripening stage showed a marked decrease of the expression levels of several ripening-induced genes, especially involved in cell wall modification and secondary metabolism. This suggests that Solyc07g052960 participates in the regulation of these processes as one component of the RIN-activated transcriptional cascade regulating fruit ripening in tomato.
2014-03-01 | GSE45658 | GEO
Project description:[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes. Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant
2012-02-29 | E-GEOD-20720 | biostudies-arrayexpress
Project description:[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes.
2012-02-29 | GSE20720 | GEO
Project description:The tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN) acts as a master regulator of tomato fruit ripening. We previously identified a direct RIN target gene Solyc07g052960, which encodes a putative GRAS family protein belonging to the SHORT-ROOT (SHR) branch, but its role was unknown. RNA interference (RNAi)-mediated gene silencing reduced Solyc07g052960 expression in transgenic fruits, but the fruits appeared to ripen normally. However, the transgenic fruits at the ripening stage showed a marked decrease of the expression levels of several ripening-induced genes, especially involved in cell wall modification and secondary metabolism. This suggests that Solyc07g052960 participates in the regulation of these processes as one component of the RIN-activated transcriptional cascade regulating fruit ripening in tomato. For a preliminary screening, we monitored global gene expression in tomato fruits from untransformed control (Ailsa Craig [AC] cultivar) and three transgenic lines with Solyc07g052960 knockdown by RNAi (lines T-7, T-22 and T-23) at the ripening (pink coloring) stage using microarray without biological replication.
2014-03-01 | E-GEOD-45658 | biostudies-arrayexpress
Project description:The tomato (Solanum lycopersicum) MADS-box transcription factor RIN, one of the earliest-acting fruit-ripening regulators, is required for both ethylene-dependent and -independent regulatory pathways for fruit ripeing. Here, we performed chromatin immunoprecipitation coupled with a DNA microarray (ChIP-chip) for the putative promoters of whole tomato predicted genes (ITAG2) for the genome-wide identification of the direct RIN targets. The ChIP-chip with anti-RIN antibody resulted in detection of 1,046 RIN-binding sites, each of which was assigned a significantly high peak score (FDRM-bM-^IM-$0.05) in at least two of the three biologically independent analyses. Using the information about genomic position of the RIN-binding sites, we found 1,200 genes as potential direct RIN targets that carried one or more RIN-binding sites in the transcription regulatory region (2-kb upstream putative promoter) or in other gene regions, such as exons, introns or a downstream region from the translation termination site (1-kb), where the promoter region of a neighbor gene are overlapped. Three biologically independent samples (chromatin-immunoprecipitated DNA and input DNA) recovered from the ripening tomato fruits.
2013-03-28 | E-GEOD-40257 | biostudies-arrayexpress
Project description:The tomato MADS-box FRUITFULL (FUL) homologs, FUL1 and FUL2, interact with the main ripening regulator RIPENING INHIBITOR (RIN). To clarify their role in fruit ripening, we generated FUL1/FUL2-suppressed transgenic lines by RNAi. We found that five transgenic lines bearing fruits that did not ripen normally: lycopene accumulation and increase of ethylene production were severely inhibited. We then performed next generation RNA sequencing (RNA-Seq) analysis of the fruits of a FUL1/FUL2-suppressed line (TF18) with those of the wild type (Ailsa Craig cultivar; AC) and rin mutant. The comparison of RNA-Seq data among them indicated that FUL1/FUL2-suppression significantly affected the expression of a larger portion of ripening-induced and -repressed genes than the rin mutation did. Moreover, the effect of FUL1/FUL2-suppression was observed not only in the fruits harvested at the wild type ripening age [45 days after pollination (DAP)] but also in those at the pre-ripening age (35 DAP). This suggests that the FUL homologs play an essential role in the regulation of fruit development and ripening, the role which covers a wider range of biological processes than RIN does. Differentially expressed genes (DEGs) between the wild type and TF18 fruits included known ripening-related genes such as ACS2 and ACS4 involved in ethylene production and PSY1 in carotenoid biosynthesis, consistent with the phenotype of TF18 fruits described above. The DEGs also included many direct RIN target genes, which supports the hypothesis that the FUL homologs regulate fruit ripening in a form of MADS-box complex with RIN. mRNA profiles of wild type (Ailsa Craig cultivar), rin mutant and FUL1/FUL2-suppressed tomato fruits harvested at 35DAP and 45 DAP were generated by next generation sequencing, in triplicate, using Illumina Hiseq2000.
2014-06-23 | E-GEOD-49289 | biostudies-arrayexpress
Project description:The tomato MADS-box FRUITFULL (FUL) homologs, FUL1 and FUL2, interact with the main ripening regulator RIPENING INHIBITOR (RIN). To clarify their role in fruit ripening, we generated FUL1/FUL2-suppressed transgenic lines by RNAi. We found that five transgenic lines bearing fruits that did not ripen normally: lycopene accumulation and increase of ethylene production were severely inhibited. We then performed next generation RNA sequencing (RNA-Seq) analysis of the fruits of a FUL1/FUL2-suppressed line (TF18) with those of the wild type (Ailsa Craig cultivar; AC) and rin mutant. The comparison of RNA-Seq data among them indicated that FUL1/FUL2-suppression significantly affected the expression of a larger portion of ripening-induced and -repressed genes than the rin mutation did. Moreover, the effect of FUL1/FUL2-suppression was observed not only in the fruits harvested at the wild type ripening age [45 days after pollination (DAP)] but also in those at the pre-ripening age (35 DAP). This suggests that the FUL homologs play an essential role in the regulation of fruit development and ripening, the role which covers a wider range of biological processes than RIN does. Differentially expressed genes (DEGs) between the wild type and TF18 fruits included known ripening-related genes such as ACS2 and ACS4 involved in ethylene production and PSY1 in carotenoid biosynthesis, consistent with the phenotype of TF18 fruits described above. The DEGs also included many direct RIN target genes, which supports the hypothesis that the FUL homologs regulate fruit ripening in a form of MADS-box complex with RIN.
2014-06-23 | GSE49289 | GEO
Project description:Purpose: The goals of this study was to provide genome-wide data to investigate the molecular mechanism of the interaction between ABA and ethylene during tomato fruit ripening Methods: Regarding the fruits sampled at the 9th day as a well-characterized stage, we used RNA-seq to conducted a comparative analysis of exogenous ABA and NDGA effects on all components involved in biosynthesis and signaling of ethylene and ABA.The identified crucial genes in response to ABA were further performed a ripening time-course analysis by RT-PCR. In addition, we also detected how ethylene affected ABA action at the onset of ripening by treating the fruits with 1-MCP immediately after ABA application. Results: Our study not only illustrated how ABA regulated itself at the transcription level, but also elucidated that ABA can facilitate ethylene production and response by regulating some crucial genes such as LeACS4, LeACO1 and LeETR6 etc. In addition, investigation on the fruits treated with 1-MCP immediately after ABA exposure revealed that ethylene might be essential for the induction of ABA biosynthesis and signaling at the onset of fruit ripening. Furthermore, some specific transcription factors (TFs) known as regulators of ethylene synthesis and sensibility (e.g. MADS-RIN, TAGL1, CNR and NOR etc.) were also observed to be ABA responsive, which implied that ABA influenced ethylene action possibly through the regulation of these TFs expression. Conclusions: Our data suggested that ABA may act as an upstream regulator to modulate ethylene synthesis and signal transduction, which consequently influenced the ripening process. This comprehensive survey not only demonstrated how ABA regulated itself at the molecular level, but also indicated that ABA had a positive impact on ethylene production and action by regulating key genes such as LeACS2, LeACS4, LeACO1 and LeETR6. Besides, our results also revealed that ethylene might be of great importance to induce ABA accumulation and response at the onset of ripening. Moreover, many ripening related TFs, such as MADS-RIN, TAGL1, CNR and NOR, were observed to be affected by ABA, implying that a TF-mediated manner may be involved in the interaction between ABA and ethylene. This study extends our understanding of the mechanism that how ABA-triggered tomato fruit ripening, and illustrates the complex mechanism of reciprocity between ABA and ethylene at the transcription level.
2017-02-11 | GSE75276 | GEO
Project description:The tomato (Solanum lycopersicum) MADS-box transcription factor RIN, one of the earliest-acting fruit-ripening regulators, is required for both ethylene-dependent and -independent regulatory pathways for fruit ripeing. Here, we performed chromatin immunoprecipitation coupled with a DNA microarray (ChIP-chip) for the putative promoters of whole tomato predicted genes (ITAG2) for the genome-wide identification of the direct RIN targets. The ChIP-chip with anti-RIN antibody resulted in detection of 1,046 RIN-binding sites, each of which was assigned a significantly high peak score (FDR≤0.05) in at least two of the three biologically independent analyses. Using the information about genomic position of the RIN-binding sites, we found 1,200 genes as potential direct RIN targets that carried one or more RIN-binding sites in the transcription regulatory region (2-kb upstream putative promoter) or in other gene regions, such as exons, introns or a downstream region from the translation termination site (1-kb), where the promoter region of a neighbor gene are overlapped.
2013-03-28 | GSE40257 | GEO