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Title: Identification of direct target genes of the tomato FRUITFULL homologs during ripening by promoter ChIP-chip      
dateReleased:
06-23-2014
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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-49125
refinement:
raw
alternateIdentifiers:
49125
keywords:
functional genomics
dateModified:
06-28-2014
availability:
available
types:
gene expression
name:
Solanum lycopersicum
ID:
A-GEOD-15968
name:
NimbleGen Tomato ITAG2 gene promoters 720K array
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-49125/E-GEOD-49125.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-49125/E-GEOD-49125.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49125
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress