title: MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation.
abstract: The development and ripening of tomato fruit are complex processes involving many gene regulatory pathways at the transcriptional and post-transcriptional level. Ripening inhibitor (RIN) is a vital transcription factor, which targets numerous ripening-related genes at the transcriptional level during tomato fruit ripening. MicroRNAs (miRNAs) are a class of short noncoding RNAs that play important roles in post-transcriptional gene regulation. To elucidate the potential regulatory relationship between rin and miRNAs during fruit development and ripening, we identified known miRNAs and profiled their expression in wild-type tomato and rin mutant using a deep sequencing approach combined with quantitative RT-PCR. A total of 33 known miRNA families were identified, of which 14 miRNA families were differently accumulated. Subsequent promoter analysis showed that possible RIN-binding motifs (CArG-box) tended to occur frequently in the promoter regions of partial differently expressed miRNAs. In addition, ethylene may participate in the regulation of miRNAs accumulation during tomato fruit ripening. Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assay confirmed the direct binding of RIN to the promoter of MIR172a. Collectively, these results showed a close correlation between miRNA expression and RIN as well as ethylene, which further elucidated the regulatory roles of miRNAs during fruit development and ripening and enriched the regulatory network of RIN in tomato fruit.
authors.affiliation: Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Gao
authors.forename: Zheng
authors.initials: Z
authors.lastname: Ju
authors.forename: Dongyan
authors.initials: D
authors.lastname: Cao
authors.forename: Baiqiang
authors.initials: B
authors.lastname: Zhai
authors.forename: Guozheng
authors.initials: G
authors.lastname: Qin
authors.forename: Hongliang
authors.initials: H
authors.lastname: Zhu
authors.forename: Daqi
authors.initials: D
authors.lastname: Fu
authors.forename: Yunbo
authors.initials: Y
authors.lastname: Luo
authors.forename: Benzhong
authors.initials: B
authors.lastname: Zhu
mesh_terms: D047369:Chromatin Immunoprecipitation; D024202:Electrophoretic Mobility Shift Assay; D005030:Ethylenes / Q000378:metabolism*; D005638:Fruit / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010937:Plant Growth Regulators / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D005030:Ethylenes; D035683:MicroRNAs; D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors; C036216:ethylene
keywords: RIN; ethylene; fruit ripening; high-throughput sequencing; microRNA; tomato