Identification of miRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

Laboratory of Molecular Biology, Wageningen University, 6700 ET Wageningen, The Netherlands.
Journal of Experimental Botany (Impact Factor: 5.53). 03/2013; 64(7). DOI: 10.1093/jxb/ert049
Source: PubMed


MicroRNAs (miRNAs) play important roles in plant development through regulation of gene expression by mRNA degradation or
translational inhibition. Despite the fact that tomato (Solanum lycopersicum) is the model system for studying fleshy fruit development and ripening, only a few experimentally proven miRNA targets are
known, and the role of miRNA action in these processes remains largely unknown. Here, by using parallel analysis of RNA ends
(PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development, a total
of 119 target genes of miRNAs were identified. Of these, 106 appeared to be new targets. A large part of the identified targets
(56) coded for transcription factors. Auxin response factors, as well as two known ripening regulators, COLORLESS NON-RIPENING (CNR) and APETALA2a (SlAP2a), with developmentally regulated degradation patterns were identified. The levels of the intact messenger of both CNR and AP2a are actively modulated during ripening, by miR156/157 and miR172, respectively. Additionally, two TAS3-mRNA loci were identified
as targets of miR390. Other targets such as ARGONAUTE 1 (AGO1), shown to be involved in miRNA biogenesis in other plant species, were identified, which suggests a feedback loop regulation
of this process. In this study, it is shown that miRNA-guided cleavage of mRNAs is likely to play an important role in tomato
fruit development and ripening.

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Available from: Rumyana Karlova, Jun 25, 2015
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    • "For example, the target of miR156/157 is Colorless Non-Ripening (CNR) (Karlova et al., 2013), an epigenetic mutation of which could inhibit tomato fruit ripening (Manning et al., 2006). The target of miR172 is APETALA2 (AP2) (Karlova et al., 2013), which is a negative regulator of tomato fruit ripening (Chung et al., 2010; Karlova et al., 2011). In contrast, ripening-related lncRNAs have not been as comprehensively identified and functionally examined in tomato. "
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    ABSTRACT: Recently, long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in model plants, such as Arabidopsis, rice, and maize. However, the presence of lncRNAs and how they function in fleshy fruit ripening are still largely unknown because fleshy fruit ripening is not present in the above model plants. Tomato is the model system for fruit ripening studies due to its dramatic ripening process. To investigate further the role of lncRNAs in fruit ripening, it is necessary and urgent to discover and identify novel lncRNAs and understand the function of lncRNAs in tomato fruit ripening. Here it is reported that 3679 lncRNAs were discovered from wild-type tomato and ripening mutant fruit. The lncRNAs are transcribed from all tomato chromosomes, 85.1% of which came from intergenic regions. Tomato lncRNAs are shorter and have fewer exons than protein-coding genes, a situation reminiscent of lncRNAs from other model plants. It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening. In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit. Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.
    Journal of Experimental Botany 05/2015; 66(15). DOI:10.1093/jxb/erv203 · 5.53 Impact Factor
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    • "During prickly pear cactus fruit development, miR164 expression was observed at meristematic zones in floral buds, in open flowers at places of organ fusion (carpel base with stamens and receptacle), and homogenously in the complete ripening fruit. These results suggest that miR164 is highly regulated and furthermore , that it probably performs different functions during fruit development by regulating different NAC transcription factors (Karlova et al. 2013). In addition to boundary morphogenesis and leaf senescence, NAC genes are involved in different developmental processes such as biotic and abiotic stress responses and ripening (Delessert et al. 2005; He et al. 2005; Liu et al. 2009; Greco et al. 2012). "
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    ABSTRACT: miRNAs are a class of small non-coding RNAs that regulate gene expression. They are involved in the control of many developmental processes, including fruit development. The increasing amount of information on miRNAs, on their expression, abundance, and conservation between various species, provides a new opportunity to study the role of miRNAs in non-model plant species. In this work, we used a combination of Northern blot and tissue print hybridization analysis to identify conserved miRNAs expressed during prickly pear cactus (Opuntia ficus indica) fruit development. Comparative profiling detected the expression of 34 miRNAs, which were clustered in three different groups that were associated with the different phases of fruit development. Variation in the level of miRNA expression was observed. Gradual expression increase of several miRNAs was observed during fruit development, including miR164. miR164 was selected for stem-loop RT-PCR and for a detailed spatial–temporal expression analysis. At early floral stages, miR164 was mainly localized in meristematic tissues, boundaries and fusion zones, while it was more homogenously expressed in fruit tissues. Our results provide the first evidence of miRNA expression in the prickly pear cactus and provide the basis for future research on miRNAs in Opuntia. Moreover, our analyses suggest that miR164 plays different roles during prickly pear cactus fruit development.
    Planta 02/2015; 241:435-448. DOI:10.1007/s00425-014-2193-0 · 3.26 Impact Factor
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    • "Please cite this article as: C. Xin, et al., Genomics (2015), homeostasis [9], stress responses [10], and diverse developmental processes, including seed development, meristem and lateral organ development, root initiation, flowering and sex determination, fruit development, timing and phase transitions [11] [12]. Since the first discovery of miRNAs from Arabidopsis in 2002 [13], plant miRNAs from various species have been intensely studied through both experimental and computational approaches. "
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    ABSTRACT: MicroRNAs (miRNAs) play crucial roles in multiple stages of plant development and regulate gene expression at posttranscriptional and translational levels. In this study, we first identified 238 conserved miRNAs in date palm (Phoenix dactylifera) based on a high-quality genome assembly and defined 78 fruit-development-associated (FDA) miRNAs, whose expression profiles are variable at different fruit development stages. Using experimental data, we subsequently detected 276 novel P. dactylifera-specific FDA miRNAs and predicted their targets. We also revealed that FDA miRNAs function mainly in regulating genes involved in starch/sucrose metabolisms and other carbon metabolic pathways; among them, 221 FDA miRNAs exhibit negative correlation with their corresponding targets, which suggests their direct regulatory roles on mRNA targets. Our data define a comprehensive set of conserved and novel FDA miRNAs along with their expression profiles, which provide a basis for further experimentation in assigning discrete functions of these miRNAs in P. dactylifera fruit development.
    Genomics 01/2015; 105(4). DOI:10.1016/j.ygeno.2015.01.004 · 2.28 Impact Factor
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