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Identification of direct target genes of the tomato FRUITFULL homologs during ripening by promoter ChIP-chip

ABSTRACT: Tomato (Solanum lycopersicum) has two MADS-box FRUITFULL homologs, FUL1 and FUL2, both of which are able to interact with the master ripening regulator RIN. Here, we performed chromatin immunoprecipitation coupled with a DNA microarray (ChIP-chip) for the 2-kb upstream putative promoters of whole tomato predicted genes (ITAG2) for a large-scale identification of the direct target genes of FUL1 and FUL2 during ripening. The ChIP-chip with antibodies of FUL1 and FUL2 identified 1,877 and 1,919 of FUL1- and FUL2-binding sites, respectively, 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 FUL1- and FUL2-binding sites, we found 1,943 and 2,051 potential direct targets of FUL1 and FUL2, respectively, that carried one or more binding sites in the 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. The majority of the direct target genes are common between FUL1, FUL2 and RIN, suggesting that FUL1 and FUL2 act redundantly in the regulation of fruit ripening, and that these factors regulate the expression of their targets in a form of heteromer complex. Interestingly, the analysis also found direct targets unique to each of FUL1, FUL2 and RIN, implying their exclusive roles during ripening.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE49125 | GEO | 2014/06/23

SECONDARY ACCESSION(S): PRJNA213106

REPOSITORIES: GEO

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Identification of direct target genes of the tomato FRUITFULL homologs during ripening by promoter ChIP-chip

Project description:Tomato (Solanum lycopersicum) has two MADS-box FRUITFULL homologs, FUL1 and FUL2, both of which are able to interact with the master ripening regulator RIN. Here, we performed chromatin immunoprecipitation coupled with a DNA microarray (ChIP-chip) for the 2-kb upstream putative promoters of whole tomato predicted genes (ITAG2) for a large-scale identification of the direct target genes of FUL1 and FUL2 during ripening. The ChIP-chip with antibodies of FUL1 and FUL2 identified 1,877 and 1,919 of FUL1- and FUL2-binding sites, respectively, 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 FUL1- and FUL2-binding sites, we found 1,943 and 2,051 potential direct targets of FUL1 and FUL2, respectively, that carried one or more binding sites in the 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. The majority of the direct target genes are common between FUL1, FUL2 and RIN, suggesting that FUL1 and FUL2 act redundantly in the regulation of fruit ripening, and that these factors regulate the expression of their targets in a form of heteromer complex. Interestingly, the analysis also found direct targets unique to each of FUL1, FUL2 and RIN, implying their exclusive roles during ripening. Three biologically independent samples (chromatin-immunoprecipitated DNA and input DNA) recovered from the ripening tomato fruits.

2014-06-23 | E-GEOD-49125 | biostudies-arrayexpress

Identification of direct target genes of the tomato fruit-ripening regulator RIN by promoter ChIP-chip

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

Identification of direct target genes of the tomato fruit-ripening regulator RIN by promoter ChIP-chip

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

Transcriptome profiling of tomato fruits of a FRUITFULL-suppressed line and rin mutant by next generation RNA sequencing

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

Transcriptome profiling of tomato fruits of a FRUITFULL-suppressed line and rin mutant by next generation RNA sequencing

2014-06-23 | GSE49289 | GEO

Global gene expression analysis of normal and ripening inhibitor (rin) mutant tomatoes during ripening

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.

2012-04-02 | GSE28564 | GEO

Global gene expression analysis of normal and ripening inhibitor (rin) mutant tomatoes during ripening

2012-04-01 | E-GEOD-28564 | biostudies-arrayexpress

Targets of FRUITFULL in the pistil/silique [ChIP-Seq]

Project description:To learn more about the role of FRUITFULL (FUL), in pistil/silique development, we performed a ChIP-seq experiment to identify direct targets of FUL in the pistil/silique.

2017-11-03 | GSE79554 | GEO

Microarray analysis of ripening tomato fruits with RNAi knockdown of a direct RIN-target GRAS family gene

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

Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening

Project description:Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. The proteins that changed abundance across ripening stages are involved in various cellular processes. We additionally evaluated the changes in the nuclear proteome in the ripening-deficient mutant ripening inhibitor (rin) carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assay, we provide evidence that RIN directly bound to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affected protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and genome-wide survey of the E2 gene family in tomatoes identified five more E2s as the direct targets of RIN. Two E2s were demonstrated to be involved in the regulation of fruit ripening based on virus-induced gene silencing assays. Our results uncover the novel function of protein ubiquitination, identifying specific E2s as regulator in fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.

2014-11-18 | PXD001414 | Pride

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