Continuing analysis of microRNA origins

Roberts, Justin T; Cooper, Elvera A; Favreau, Connor J; Howell, J.; Lane, Lee G; Mills, James E.; Newman, Derrick C; Perry, T.; Russell, Meaghan E; Wallace, Brittany M; Borchert, Glen M.

doi:10.4161/mge.27755

Cited by 35 publications

(15 citation statements)

References 47 publications

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“…Approximately half of the human genome and ~80% of several plant genomes are composed of transposable elements, making the origin of miRNAs from such elements more likely. Although many models for the origin of miRNAs from repetitive elements have been proposed, the one proposed by Smalheiser and Torvik remains the most highlighted one [ 126 ]. Plant miRNAs have been reported to be derived from different families of transposable elements.…”

Section: Resultsmentioning

confidence: 99%

A Deluge of Complex Repeats: The Solanum Genome

2015

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Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50–60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats.

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Section: Resultsmentioning

confidence: 99%

A Deluge of Complex Repeats: The Solanum Genome

2015

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“…tRNA sequences are some of the most ancient and conserved RNA species known; they form secondary structures comprising short hairpins, and their tDNA is repeated multiple times, providing redundancy for the role of a single tDNA locus. It has also recently been suggested that the tRNA structure may be transformed into a foldback structure by very simple changes in the nucleotide sequence (Roberts et al ., ). Hence, we assessed the evidence for the hypothesis that miR1511 originated from a tRNA iMet locus.…”

Section: Discussionmentioning

confidence: 97%

“…The question of molecular ancestry for sequences that probably originated before the split between Rosaceae and Fabaceae more than a hundred million years ago (Crepet et al ., ) is a difficult one to answer beyond doubt; however, the data available at present provide a number of clues in support of the hypothesis that the miR1511 hairpin derived from a tRNA iMet locus. Several studies in animals have already suggested a link between small non‐coding RNAs and microRNA silencing mechanisms (Haussecker et al ., ; Maute et al ., ; Roberts et al ., ), and it has been shown that tRNA molecules are readily cleaved by the Dicer machinery in human cells (Cole et al ., ), implying that the transition between the functions of tRNA and an miRNA need not have been a long one.…”

Section: Discussionmentioning

confidence: 99%

A highly specific microRNA‐mediated mechanism silences LTR retrotransposons of strawberry

et al. 2015

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SUMMARYSmall RNAs are involved in a plethora of functions in plant genomes. In general, transcriptional gene silencing is mediated by 24-nucleotide siRNAs and is required for maintaining transposable elements in a silenced state. However, microRNAs are not commonly associated with transposon silencing. In this study, we performed small RNA transcriptome and degradome analyses of the Rosaceae model plant Fragaria vesca (the woodland strawberry) at the genome-wide level, and identified miRNA families and their targets. We report a highly specific mechanism of LTR retrotransposon silencing mediated by an abundant, ubiquitously expressed miRNA (fve-miR1511) generated from a single locus. This miRNA specifically targets LTR retroelements, silencing them post-transcriptionally by perfectly pairing to the highly conserved primer binding site for methionyl initiator tRNA that is essential for reverse transcription. We investigated the possible origins of this miRNA, and present evidence that the pre-miR1511 hairpin structure probably derived from a locus coding for tRNA iMet through a single microinversion event. Our study shows that this miRNA targets retrotransposons specifically and constitutively, and contributes to features such as genome stability, size and architecture in a far more direct way than previously thought.

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“…Hairpin structures are supposed to arise either by inverted duplication of the target gene locus (Allen et al 2004) or juxtaposed TEs (Roberts et al 2013). Piriyapongsa and Jordan (2008) also describe a model in which folded expressed miniature inverted-repeat transposable elements (MITEs) may be processed by the miRNA biogenesis pathway.…”

Section: Introductionmentioning

confidence: 99%

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

Lorenzetti

Antonio

Paschoal

et al. 2016

Funct Integr Genomics

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Transposable elements (TEs) comprise a major fraction of many plant genomes and are known to drive their organization and evolution. Several studies show that these repetitive elements have a prominent role in shaping noncoding regions of the genome such as microRNA (miRNA) loci, which are components of post-transcriptional regulation mechanisms. Although some studies have reported initial formation of miRNA loci from TE sequences, especially in model plants, the approaches that were used did not employ systems that would allow results to be delivered by a user-friendly database. In this study, we identified 152 precursor miRNAs overlapping TEs in 10 plant species. PlanTE-MIR DB was designed to assemble this data and deliver it to the scientific community interested in miRNA origin, evolution, and regulation pathways. Users can browse the database through a web interface and search for entries using various parameters. This resource is cross-referenced with repetitive element (Repbase Update) and miRNA (miRBase) repositories, where sequences can be checked for further analysis. All data in PlanTE-MIR DB are publicly available for download in several file formats to facilitate their understanding and use. The database is hosted at http://bioinfo-tool.cp.utfpr.edu.br/plantemirdb/ .

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Continuing analysis of microRNA origins

Cited by 35 publications

References 47 publications

A Deluge of Complex Repeats: The Solanum Genome

A Deluge of Complex Repeats: The Solanum Genome

A highly specific microRNA‐mediated mechanism silences LTR retrotransposons of strawberry

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

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