PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs)

Karakülah, Gökhan; Kurtoğlu, Kuaybe Yücebilgili; Ünver, Turgay

doi:10.1371/journal.pone.0167698

Cited by 53 publications

(31 citation statements)

References 32 publications

(33 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…LncRNAs, miRNAs and TFs have an important and broadspectrum impact on the lignin biosynthesis pathway, which affects the genetic architecture of tree growth and wood formation. Also, the endogenous target mimicry also provides a crucial regulatory mechanism of miRNA-lncRNA-mRNA in plants, which should be considered in the future (Franco-Zorrilla et al, 2007;Karak€ ulah et al, 2016). Importantly, more major regulators (lncRNAs, miRNAs and TFs) will be found if we used the integrated mapping strategy (genomewide association studies and eQTN mapping), which have the substantial potential to accelerate the genetic improvement in perennial trees.…”

Section: Functional Interpretation Of Causal Genes Associated With Grmentioning

confidence: 99%

Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus

Quan

Liang

et al. 2018

Plant Biotechnology Journal

View full text Add to dashboard Cite

Lignin provides structural support in perennial woody plants and is a complex phenolic polymer derived from phenylpropanoid pathway. Lignin biosynthesis is regulated by coordinated networks involving transcription factors (TFs), microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). However, the genetic networks underlying the lignin biosynthesis pathway for tree growth and wood properties remain unknown. Here, we used association genetics (additive, dominant and epistasis) and expression quantitative trait nucleotide (eQTN) mapping to decipher the genetic networks for tree growth and wood properties in 435 unrelated individuals of Populus tomentosa. We detected 124 significant associations (P ≤ 6.89E-05) for 10 growth and wood property traits using 30 265 single nucleotide polymorphisms from 203 lignin biosynthetic genes, 81 TF genes, 36 miRNA genes and 71 lncRNA loci, implying their common roles in wood formation. Epistasis analysis uncovered 745 significant pairwise interactions, which helped to construct proposed genetic networks of lignin biosynthesis pathway and found that these regulators might affect phenotypes by linking two lignin biosynthetic genes. eQTNs were used to interpret how causal genes contributed to phenotypes. Lastly, we investigated the possible functions of the genes encoding 4-coumarate: CoA ligase and cinnamate-4-hydroxylase in wood traits using epistasis, eQTN mapping and enzymatic activity assays. Our study provides new insights into the lignin biosynthesis pathway in poplar and enables the novel genetic factors as biomarkers for facilitating genetic improvement of trees.

show abstract

Section: Functional Interpretation Of Causal Genes Associated With Grmentioning

confidence: 99%

Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus

Quan

Liang

et al. 2018

Plant Biotechnology Journal

View full text Add to dashboard Cite

show abstract

“…Then, co-localized mRNA-lncRNA pairs on the reference genome were identified with Bedtools v2.25.0 (Quinlan, 2014). We considered the mRNA-lncRNA pair as co-expressed if the Spearmen’s rho is equal or greater than 0.90 (p-val<0.01) between the expression values of coding and lncRNA transcripts, and as co-localized when the distance between two transcripts were less than 10 kb..To dissect putative eTM sequences among the transcripts annotated as lncRNA, we employed our analysis pipeline previously introduced by our group (Karakulah et al, 2016). In the eTM sequences analysis pipeline, we utilized mature miRNA sequences of barley collected from miRBase (release 21) (Griffiths-Jones, 2006).…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, it was suggested that some plant lncRNAs might have peptide coding potential (Liu et al 2015). In addition, miRNA activity can be regulated by endogeneous target mimicry (eTM) molecules, being a type of lncRNAs (Karakulah et al, 2016). Such an example, an endogenous lncRNA called Induced by Phosphate Starvation 1 (IPS1) of Arabidopsis thaliana binds to miR399 to inhibit the cleavage of the miR399 target transcript (Franco-Zorrilla et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Barley Long Non-Coding RNAs and Their Tissue-Specific Co-expression Pattern with Coding-Transcripts

Karakülah

Ünver

2017

Preprint

Self Cite

View full text Add to dashboard Cite

Long non-coding RNAs (lncRNA) with non-protein or small peptide-coding potential transcripts are emerging regulatory molecules. With the advent of next-generation sequencing technologies and novel bioinformatics tools, a tremendous number of lncRNAs has been identified in several plant species. Recent reports demonstrated roles of plant lncRNAs such as development and environmental response. Here, we reported a genome-wide discovery of ~8,000 barley lncRNAs and measured their expression pattern upon excessive boron (B) treatment. According to the tissue-based comparison, leaves have a greater number of B-responsive differentially expressed lncRNAs than the root. Functional annotation of the coding transcripts, which were co-expressed with lncRNAs, revealed that molecular function of the ion transport, establishment of localization, and response to stimulus significantly enriched only in the leaf. On the other hand, 32 barley endogenous target mimics (eTM) as lncRNAs, which potentially decoy the transcriptional suppression activity of 18 miRNAs, were obtained. Presented data including identification, expression measurement, and functional characterization of barley lncRNAs suggest that B-stress response might also be regulated by lncRNA expression via cooperative interaction of miRNA-eTM-coding target transcript modules.

show abstract

“…Similar to the overexpression of MIR genes, the negative regulation of the accumulation of some specific miRNAs allows the achievement of desirable agronomic characteristics. Endogenous target mimicry (eTMs) is another natural mechanism involved in modulating miRNA accumulation, controlling several biological processes in plants (Karak€ ulah et al, 2016;Lin et al, 2015). These eTMs are innumerous long noncoding RNA (lncRNA) or circular noncoding RNAs (circRNAs) transcribed from genome and differential expressed usually in response to stresses or other adverse conditions (Karak€ ulah et al, 2016;Liu et al, 2017).…”

Section: Endogenous and Artificial Target Mimicrymentioning

confidence: 99%

MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants

Basso

Ferreira

Kobayashi

et al. 2019

Plant Biotechnology Journal

108

View full text Add to dashboard Cite

Summary Micro RNA s (mi RNA s) modulate the abundance and spatial–temporal accumulation of target mRNA s and indirectly regulate several plant processes. Transcriptional regulation of the genes encoding mi RNA s ( MIR genes) can be activated by numerous transcription factors, which themselves are regulated by other mi RNA s. Fine‐tuning of MIR genes or mi RNA s is a powerful biotechnological strategy to improve tolerance to abiotic or biotic stresses in crops of economic importance. Current approaches for mi RNA fine‐tuning are based on the down‐ or up‐regulation of MIR gene transcription and the use of genetic engineering tools to manipulate the final concentration of these mi RNA s in the cytoplasm. Transgenesis, cisgenesis, intragenesis, artificial MIR genes, endogenous and artificial target mimicry, MIR genes editing using Meganucleases, ZNF proteins, TALEN s and CRISPR /Cas9 or CRISPR /Cpf1, CRISPR / dC as9 or dC pf1, CRISPR 13a, topical delivery of mi RNA s and epigenetic memory have been successfully explored to MIR gene or mi RNA modulation and improve agronomic traits in several model or crop plants. However, advantages and drawbacks of each of these new biotechnological tools ( NBT s) are still not well understood. In this review, we provide a brief overview of the biogenesis and role of mi RNA s in response to abiotic or biotic stresses, we present critically the main NBT s used for the manipulation of MIR genes and mi RNA s, we show current efforts and findings with the MIR genes and mi RNA s modulation in plants, and we summarize the advantages and drawbacks of these NBT s and provide some alternatives to overcome. Finally, challenges and future perspectives to mi RNA modulating in important crops are also discussed.

show abstract

PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs)

Cited by 53 publications

References 32 publications

Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus

Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus

Barley Long Non-Coding RNAs and Their Tissue-Specific Co-expression Pattern with Coding-Transcripts

MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants

Contact Info

Product

Resources

About