The Making of Leaves: How Small RNA Networks Modulate Leaf Development

Yang, Tianxiao; Wang, Yongyan; Teotia, Sachin; Zhang, Zhan‐Hui; Tang, Guiliang

doi:10.3389/fpls.2018.00824

Cited by 37 publications

(35 citation statements)

References 81 publications

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“…To test the effectiveness of the hundreds of STTMs that were generated, we subjected A. thaliana to large-scale transformation with STTMs, and scored the impact of STTMs on leaf development, root development, stature, and flowering. By observing different STTM transgenic lines in which different miRNAs were targeted, we found that miR156/157, miR160, miR165/166, miR167, miR171, miR319, miR159, and miR319/159 were involved in the development of leaf shape, as previously reported for some miRNAs (Allen et al, 2007;Todesco et al, 2010;Liu et al, 2011;Schommer et al, 2012;Yan et al, 2012;Yang et al, 2018) ( Figure 2A-2F and Supplemental Figure 1). STTM159 transgenic plants were smaller than wild-type (WT) plants and had upward curled leaves ( Figure 2B and .…”

Section: Multiple Developmental Phenotypes Observed In Arabidopsis Stsupporting

confidence: 82%

A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants

Peng

Qiao

et al. 2018

Molecular Plant

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microRNAs (miRNAs) are endogenous small non-coding RNAs that bind to mRNAs and target them for cleavage and/or translational repression, leading to gene silencing. We previously developed short tandem target mimic (STTM) technology to deactivate endogenous miRNAs in Arabidopsis. Here, we created hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis, tomato, rice, and maize, providing a resource for the functional interrogation of miRNAs. We not only revealed the functions of several miRNAs in plant development, but also demonstrated that tissue-specific inactivation of a few miRNAs in rice leads to an increase in grain size without adversely affecting overall plant growth and development. RNA-seq and small RNA-seq analyses of STTM156/157 and STTM165/166 transgenic plants revealed the roles of these miRNAs in plant hormone biosynthesis and activation, secondary metabolism, and ion-channel activity-associated electrophysiology, demonstrating that STTM technology is an effective approach for studying miRNA functions. To facilitate the study and application of STTM transgenic plants and to provide a useful platform for storing and sharing of information about miRNA-regulated gene networks, we have established an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) to display the transcriptomic and miRNAomic changes in STTM-induced miRNA knockdown plants.

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Section: Multiple Developmental Phenotypes Observed In Arabidopsis Stsupporting

confidence: 82%

A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants

Peng

Qiao

et al. 2018

Molecular Plant

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“…Leaf shape, size and anatomy are tightly controlled, both temporally and spatially, through complex gene regulatory networks. Many of them include the establishment of negative feedback loops between microRNAs and their targets allowing the formation of spatial domains locally controlling growth pattern along leaf morphogenesis ( Yang et al, 2018 ). While such systems confer sharp and robust boundaries to developmental processes, the multiplicity of the regulatory nodes involved offers many opportunities to fine-tune leaf morphology.…”

Section: Discussionmentioning

confidence: 99%

Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology

2018

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The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth. Their final geometry will result from a balance between the need to maximize energy uptake while minimizing the damage caused by environmental stresses. This intimate relationship between leaf and its surroundings has led to an enormous diversification in leaf forms. Leaf shape varies between species, populations, individuals or even within identical genotypes when those are subjected to different environmental conditions. For instance, the extent of leaf margin dissection has, for long, been found to inversely correlate with the mean annual temperature, such that Paleobotanists have used models based on leaf shape to predict the paleoclimate from fossil flora. Leaf growth is not only dependent on temperature but is also regulated by many other environmental factors such as light quality and intensity or ambient humidity. This raises the question of how the different signals can be integrated at the molecular level and converted into clear developmental decisions. Several recent studies have started to shed the light on the molecular mechanisms that connect the environmental sensing with organ-growth and patterning. In this review, we discuss the current knowledge on the influence of different environmental signals on leaf size and shape, their integration as well as their importance for plant adaptation.

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“…We identified 10,714 potential targets for 176 miRNAs, with an average of 60.9 targets per miRNA (Table S14, Supplementary File S2). Family miR-396 had a larger number of targets (>9 targets for each family member), a fact also observed in Manihot esculenta [46] and Jatropha curcas [47].…”

Section: Microrna Targets Predictionmentioning

confidence: 52%

“…Although many studies have pointed out plant ncRNAs playing key roles in developmental [47,78] and regulatory processes [79,80], it is still uncommon to find studies identifying more than one or two ncRNA classes. Nevertheless, our analysis showed that, with several curation steps, it is possible to better assign most of the expected "housekeeping ncRNAs" and predict regulatory ncRNAs with high-confidence.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

Lemos

Foncatti

Guyot

et al. 2020

ncRNA

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Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.

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The Making of Leaves: How Small RNA Networks Modulate Leaf Development

Cited by 37 publications

References 81 publications

A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants

A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants

Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology

Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

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