PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes

Lorenzetti, Alan Péricles Rodrigues; Antonio, Gabriel Y. A. de; Paschoal, Alexandre Rossi; Domingues, Douglas Silva

doi:10.1007/s10142-016-0480-5

Cited by 32 publications

(19 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We opted for the identification of fewer genuine miRNAs as opposed to a larger number that would likely have contained false positives. Third, the IWGSC draft assembly26 excluded short contigs of <200 bp matching the Triticeae Repeat Database (http://wheat.pw.usda.gov/ITMI/Repeats) and, as a consequence, precluded the identification of likely most of the genuine transposon-derived precursor loci such as MITE-derived precursor loci37.…”

Section: Discussionmentioning

confidence: 99%

Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV

Ragupathy

Ravichandran

Mahdi

et al. 2016

Sci Rep

View full text Add to dashboard Cite

Understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform generating ~524 million reads corresponding to ~129 million distinct tags from which 232 conserved miRNAs were identified. The expression levels of 1, 2 and 79 miRNAs were affected by ultraviolet radiation, continuous light and heat, respectively. Approximately 55% of the differentially expressed miRNAs were downregulated at 0 and 1 DAT including miR398, miR528 and miR156 that control mRNAs involved in activation of signal transduction pathways and flowering. Other putative targets included histone variants and methyltransferases. These results suggest a temporal miRNA-guided post-transcriptional regulation that enables wheat to respond to abiotic stresses, particularly heat. Designing novel wheat breeding strategies such as regulatory genebased marker assisted selection depends on accurate identification of stress induced miRNAs.Plant speciation and long term adaptation to specific ecological niches involve genetic mutations and selection 1 . However, rapid adaptation to sudden exposure to abiotic stresses entails regulation of gene expression. In general, plants adapt to stress conditions by inducing an array of stress-responsive genes that are precisely regulated at the transcriptional, post-transcriptional and post-translational levels. Plant adaptation to environmental stress begins with its perception by sensory kinases followed by activation of signal transduction pathways culminating in expression modulation of regulatory as well as structural genes. Stress perception induces rapid accumulation of reactive oxygen species (ROS) and changes in cytosolic calcium (Ca 2+ ) 2 . ROS and Ca 2+ oscillation operate as secondary messengers to activate signal transduction pathways such as mitogen-activated protein kinases (MAPKs) 3,4 . Upon activation, MAPKs are imported into the nucleus where they phosphorylate stress-specific regulatory components such as transcription factors that modulate gene expression 5,6 . The products of these stress-responsive genes control several physiological processes such as stomatal closure and synthesis of hormones and metabolites (reviewed in ref. 7). In recent years, regulatory small noncoding RNAs (snRNAs) such as short interfering RNAs (siRNAs) and microRNAs (miRNAs) have emerged as key regulators of gene expression at both transcriptional and post-transcriptional levels 8 . Small RNAs (sRNAs), which are approximately 18-24 nt long, are classified based on differences in their biogenesis and function. Small RNAs derived from

show abstract

Section: Discussionmentioning

confidence: 99%

Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV

Ragupathy

Ravichandran

Mahdi

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Another role of TEs is to be an important source of microRNAs in animals (Borchert et al, 2011;Gim et al, 2014) and plants (Li et al, 2011;Lorenzetti et al, 2016), which is a confirmation of the universality and conservation of transposons evolution. At the same time, up to 40 % of all the microRNAs that have a regulatory effect on the nerve-cell function are expressed in the brain.…”

Section: Transposon and Noncoding Rna Activity In Brainmentioning

confidence: 83%

Interrelation of Prions With Non-Coding Rnas

Мустафин¹,

Хуснутдинова²

2018

Vestn. VOGiS

View full text Add to dashboard Cite

Prions are alternative infectious conformations for some cellular proteins. For the protein PrPC (PrP – prion protein, С – common), a prion conformation, called PrPSc (S – scrapie), is pathological. For example, in mammals the PrPSc prion causes transmissible spongiform encephalopathies accumulating in the brain tissues of PrPSc aggregates that have amyloid properties. MicroRNAs and long non-coding RNAs can be translated into functional peptides. These peptides can have a regulatory effect on genes from which their non-coding RNAs are transcribed. It has been assumed that prions, like peptides, due to the presence of specific domains, can also activate certain non-coding RNAs. Some of the activated non-coding RNAs can catalyze the formation of new prions from normal protein, playing their role in the pathogenesis of prion diseases. Confirmation of this assumption is the presence of the association of alleles of microRNA with the development of the disease, which indicates the role of the specific sequences of noncoding RNAs in the catalysis of prion formation. In the brain tissues of patients with prion diseases, as well as in exosomes containing an abnormal PrPSc isoform, changes in the levels of microRNA have been observed. A possible cause is the interaction of the spatial domains of PrPSc with the sequences of the non-coding RNA genes, which causes a change in their expression. MicroRNAs, in turn, affect the synthesis of long non-coding RNAs. We hypothesize that long noncoding RNAs and possibly microRNAs can interact with PrPC catalyzing its transformation into PrPSc. As a result, the number of PrPSc increases exponentially. In the brain of animals and humans, transposon activity has been observed, which has a regulatory effect on the differentiation of neuronal stem cells. Transposons form the basis of domain structures of long non-coding RNAs. In addition, they are important sources of microRNA. Since prion diseases can arise as sporadic and hereditary cases, and hereditary predisposition is important for the development of pathology, we hypothesize the role of individual features of activation of transposons in the pathogenesis of prion diseases. The activation of transposons in the brain at certain stages of development, as well as under the influence of stress, is reflected in the peculiarities of expression of specific non-coding RNAs that are capable of catalyzing the transition of the PrPC protein to PrPSc. Research in this direction can be the basis for targeted anti-microRNA therapy of prion diseases.

show abstract

“…1-MITEs are abundant repeat elements in eukaryote genomes and they play critical roles during genome evolution 45,46 . For example, MITE elements represent the most usual type of TEs in rice genome 47 In silico analyses show that MITE sequences are involved with RNA-mediated gene regulation 53 , it either by hairpin-like miRNA precursors (pre-miRNA) 54 or by siRNA biogenesis 55 . In addition, MITE insertions can also mediate gene silencing by epigenetic mechanisms such as, for example, repressive DNA and histone methylation.…”

Section: Control Of Host Transcription By Induced Te Drivesmentioning

confidence: 99%

“…In silico analyses show that MITE sequences are involved with RNA-mediated gene regulation 53 , it either by hairpin-like miRNA precursors (pre-miRNA) 54 or by siRNA biogenesis 55 . In addition, MITE insertions can also mediate gene silencing by the establishment of epigenetic hallmarks such as, for example, repressive DNA and histone methylation.…”

Section: Control Of Host Transcription By Induced Te Drivesmentioning

confidence: 99%

MITE-based drives to transcriptional control of genome host

Vaschetto

2017

Preprint

View full text Add to dashboard Cite

In a recent past, Transposable Elements (TEs) were referred as selfish genetic components only capable of copying themselves with the aim to increase the odds that will be inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into genome host comprise an important evolutionary mechanism capable to produce diverse chromosome rearrangements and thus increase the adaptive fitness. According to as insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility to setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred as Miniature Inverted-repeat Transposable Elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to outline an effective strategy that allows to deploy the TE potential for control of the host transcriptional activity.

show abstract

PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes

Cited by 32 publications

References 35 publications

Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV

Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV

Interrelation of Prions With Non-Coding Rnas

MITE-based drives to transcriptional control of genome host

Contact Info

Product

Resources

About