Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.
Ripening of tomato fruits is triggered by the plant hormone ethylene, but its effect is restricted by an unknown developmental cue to mature fruits containing viable seeds. To determine whether this cue involves epigenetic remodeling, we expose tomatoes to the methyltransferase inhibitor 5-azacytidine and find that they ripen prematurely. We performed whole-genome bisulfite sequencing on fruit in four stages of development, from immature to ripe. We identified 52,095 differentially methylated regions (representing 1% of the genome) in the 90% of the genome covered by our analysis. Furthermore, binding sites for RIN, one of the main ripening transcription factors, are frequently localized in the demethylated regions of the promoters of numerous ripening genes, and binding occurs in concert with demethylation. Our data show that the epigenome is not static during development and may have been selected to ensure the fidelity of developmental processes such as ripening. Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenome.
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA.
Silin
S
Zhong
Zhangjun
Z
Fei
Yun-Ru
YR
Chen
Yi
Y
Zheng
Mingyun
M
Huang
Julia
J
Vrebalov
Ryan
R
McQuinn
Nigel
N
Gapper
Bao
B
Liu
Jenny
J
Xiang
Ying
Y
Shao
James J
JJ
Giovannoni
D001374:Azacitidine / Q000494:pharmacology; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping; D019175:DNA Methylation / Q000235:genetics* / Q000502:physiology; D044127:Epigenesis, Genetic; D005030:Ethylenes / Q000378:metabolism; D005638:Fruit / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D008780:Methyltransferases / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism
D005030:Ethylenes; C036216:ethylene; D008780:Methyltransferases; D001374:Azacitidine