TITLE

Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation

AUTHOR(S)
Fujisawa, Masaki; Nakano, Toshitsugu; Ito, Yasuhiro
PUB. DATE
January 2011
SOURCE
BMC Plant Biology;2011, Vol. 11 Issue 1, p26
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: During ripening, climacteric fruits increase their ethylene level and subsequently undergo various physiological changes, such as softening, pigmentation and development of aroma and flavor. These changes occur simultaneously and are caused by the highly synchronized expression of numerous genes at the onset of ripening. In tomatoes, the MADS-box transcription factor RIN has been regarded as a key regulator responsible for the onset of ripening by acting upstream of both ethylene- and non-ethylene-mediated controls. However, except for LeACS2, direct targets of RIN have not been clarified, and little is known about the transcriptional cascade for ripening. Results: Using immunoprecipitated (IPed) DNA fragments recovered by chromatin immunoprecipitation (ChIP) with anti-RIN antibody from ripening tomato fruit, we analyzed potential binding sites for RIN (CArG-box sites) in the promoters of representative ripening-induced genes by quantitative PCR. Results revealed nearly a 5- to 20-fold enrichment of CArG boxes in the promoters of LeACS2, LeACS4, PG, TBG4, LeEXP1, and LeMAN4 and of RIN itself, indicating direct interaction of RIN with their promoters in vivo. Moreover, sequence analysis and genome mapping of 51 cloned IPed DNAs revealed potential RIN binding sites. Quantitative PCR revealed that four of the potential binding sites were enriched 4- to 17-fold in the IPed DNA pools compared with the controls, indicating direct interaction of RIN with these sites in vivo. Near one of the four CArG boxes we found a gene encoding a protein similar to thioredoxin y1. An increase in the transcript level of this gene was observed with ripening in normal fruit but not in the rin mutant, suggesting that RIN possibly induces its expression. Conclusions: The presented results suggest that RIN controls fruit softening and ethylene production by the direct transcriptional regulation of cell-wall-modifying genes and ethylene biosynthesis genes during ripening. Moreover, the binding of RIN to its own promoter suggests the presence of autoregulation for RIN expression. ChIP-based analyses identified a novel RIN-binding CArG-box site that harbors a gene associated with RIN expression in its flanking region. These findings clarify the crucial role of RIN in the transcriptional regulation of ripening initiation and progression.
ACCESSION #
59156740

 

Related Articles

  • TUMOUR SUPPRESSORS: Unfold with BRCA1. Greenwood, Emma // Nature Reviews Cancer;Jan2002, Vol. 2 Issue 1, p8 

    Provides evidence on the regulation of transcription and DNA repair by chromatin unfolding. Alteration of many cancer-predisposing mutations; Visualization of the heterochromatic region as a compact nuclear dot.

  • Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder. Vaillant, C.; Audit, B.; Thermes, C.; Arnéodo, A. // European Physical Journal E -- Soft Matter;Mar2006, Vol. 19 Issue 3, p263 

    The understanding of the long-range correlations (LRC) observed in DNA sequences is still an open and very challenging problem. In this paper, we start reviewing recent results obtained when exploring the scaling properties of eucaryotic, eubacterial and archaeal genomic sequences using the...

  • An activation-independent role of transcription factors in insulator function. Fourel, Geneviève; Boscheron, Cécile; Revardel, Émanuelle; Lebrun, Éléonore; Yan-Fen Hu; Simmen, Katia Carmine; Müller, Karin; Li, Rong; Mermod, Nicolas; Gilson, Éric // EMBO Reports;Feb2001, Vol. 2 Issue 2, p124 

    Chromatin insulators are defined as transcriptionally neutral elements that prevent negative or positive influence from extending across chromatin to a promoter. Here we show that yeast subtelomeric anti-silencing regions behave as boundaries to telomere-driven silencing and also allow...

  • Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo. Guertin, Michael J.; Martins, André L.; Siepel, Adam; Lis, John T. // PLoS Genetics;Mar2012, Vol. 8 Issue 3, Special section p1 

    DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding followed by high-throughput sequencing (PB-seq), that allows the binding...

  • Integrated Assessment and Prediction of Transcription Factor Binding. Beyer, Andreas; Workman, Christopher; Hollunder, Jens; Radke, Dörte; Möller, Ulrich; Wilhelm, Thomas; Ideker, Trey // PLoS Computational Biology;Jun2006, Vol. 2 Issue 6, pe70 

    Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of chromatin binding does not necessarily imply regulation, and binding may be difficult to detect if it...

  • Mapping higher order structure of chromatin domains. Espinoza, Celso A.; Ren, Bing // Nature Genetics;Jul2011, Vol. 43 Issue 7, p615 

    Large-scale mapping of chromatin state and transcription factor binding have uncovered many broad chromatin domains along linear genomic DNA, but it is unclear how these functional domains are organized in three-dimensional nuclear space. A new study now shows that many domains exist as loops...

  • Prolonged glucocorticoid exposure dephosphorylates histone H1 and inactivates the MMTV promoter. Huay-Leng Lee; Archer, Trevor K. // EMBO Journal;3/1/98, Vol. 17 Issue 5, p1454 

    Glucocorticoids rapidly induce transcription from the mouse mammary tumour virus (MMTV) promoter via a glucocorticoid receptor (GR)-mediated chromatin disruption event. This remodelling of chromatin is transient such that upon prolonged exposure to hormone the promoter becomes refractory to...

  • Transcription factor TEAD4 regulates expression of Myogenin and the unfolded protein response genes during C2C12 cell differentiation. Benhaddou, A; Keime, C; Ye, T; Morlon, A; Michel, I; Jost, B; Mengus, G; Davidson, I // Cell Death & Differentiation;Feb2012, Vol. 19 Issue 2, p220 

    The TEAD (1-4) transcription factors comprise the conserved TEA/ATTS DNA-binding domain recognising the MCAT element in the promoters of muscle-specific genes. Despite extensive genetic analysis, the function of TEAD factors in muscle differentiation has proved elusive due to redundancy among...

  • Genome-wide predictors of NF-κB recruitment and transcriptional activity. Cieślik, Marcin; Bekiranov, Stefan // BioData Mining;11/26/2015, Vol. 8, p1 

    Background: Inducible transcription factors (TFs) mediate transcriptional responses to environmental cues. In response to multiple inflammatory signals active NF-κB dimers enter the nucleus and trigger cell-type-, and stimulus-specific transcriptional programs. Although much is known about...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics