Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus

Chen, Chongjian; Liu, Qing; Zhang, Yuchan; Qu, Liang‐Hu; Chen, Yue‐Qin; Gautheret, Daniel

doi:10.4161/rna.8.3.15199

Cited by 114 publications

(81 citation statements)

References 70 publications

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“…tRF-5D from tRNA Asp (GTC) or tRNA Gly (TCC)) upon phosphate starvation in Arabidopsis roots (26). Genome-wide analysis of sncRNAs from rice callus allowed the identification of several tRF-5D and tRF-3T (27). In chinese cabbage, tRFs originating from plastid tRNAs and in wheat, tRFs originating from nuclear tRNAs were shown to be created under heat stress (8,28).…”

Section: Introductionmentioning

confidence: 99%

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

Cognat

Morelle

Megel

et al. 2016

Nucleic Acids Research

122

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In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19–26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed. Depending on the tRNA, either tRF-5D (due to a cleavage in the D region) or tRF-3T (via a cleavage in the T region) were found and hot spots of tRNA cleavages have been identified. Interestingly, up to 25% of the tRFs originate from plastid tRNAs and we provide evidence that mitochondrial tRNAs can also be a source of tRFs. Very specific tRF-5D deriving not only from nucleus-encoded but also from plastid-encoded tRNAs are strongly enriched in AGO1 immunoprecipitates. We demonstrate that the organellar tRFs are not found within chloroplasts or mitochondria but rather accumulate outside the organelles. These observations suggest that some organellar tRFs could play regulatory functions within the plant cell and may be part of a signaling pathway.

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Section: Introductionmentioning

confidence: 99%

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

Cognat

Morelle

Megel

et al. 2016

Nucleic Acids Research

122

View full text Add to dashboard Cite

show abstract

“…tRFs have been reported in viruses (Herpesvirus and human immunodeficiency virus-1 (HIV-1)) [40, 42], archaea ( Haloferax volcanii ) [43], bacteria [15, 22], protozoa ( Tetrahymena ) [12, 44], plants ( Hordeum vulgare L. & rice embryogenic callus) [45, 46], chickens [14], mice [23, 47] and humans [4, 15, 22]. This class of small RNAs thus spans the entire evolutionary tree, and biological roles have been identified for some tRFs in subsets of organisms [4, 26, 28, 40, 48].…”

Section: Biological Function Of Trfsmentioning

confidence: 99%

Biogenesis and Function of Transfer RNA-Related Fragments (tRFs)

Kumar

Kuscu

Dutta

2016

Trends in Biochemical Sciences

383

443

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Non-coding small RNAs arise from the various un-annotated and annotated regions of the genome. When they arise from annotated genes, the non-coding small RNAs are functionally different from the parent genes. This is a brief review of one class of non-coding small RNAs, tRNA related fragments (tRFs), which are generated from tRNA. tRFs have been suggested to play roles in cell proliferation, priming of viral reverse transcriptases, regulation of gene expression, RNA processing, modulation of the DNA damage response, tumor suppression, and neurodegeneration.

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“…Somatic embryogenesis-related genes has been extensively characterised in many plant species including Arabidopsis (Gliwicka et al 2013;Wickramasuriya and Dunwell 2015), maize (Salvo et al 2014), longan (Lai and Lin 2013), rice (Chen et al 2011;Xu et al 2012), soybean (Thibaud-Nissen et al 2003), potato (Sharma et al 2008) and oil palm (Lin et al 2009). A number of genes playing important roles in somatic embryogenesis have been reported such as late embryogenesis abundant (LEA) protein (Wickramasuriya and Dunwell 2015), somatic embryogenesis receptor-like kinase (SERK) (Salvo et al 2014), WUSCHEL (Gliwicka et al 2013), AGAMOUS (Gliwicka et al 2013) and MYB transcription factor (Xu et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus

Jamaluddin

Noor

Goh

2017

Physiol Mol Biol Plants

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Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. By using 3 0 mRNA-sequencing, we generated 6,190,687 processed reads and 47.0% were aligned to papaya genome reference, in which 21,170 (75.4%) of 27,082 annotated genes were found to be expressed but only 41% was expressed at functionally high levels. The top 10% of genes with high transcript abundance were significantly enriched in biological processes related to cell proliferation, stress response, and metabolism. Genes functioning in somatic embryogenesis such as SERK and LEA, hormone-related genes, stress-related genes, and genes involved in secondary metabolite biosynthesis pathways were highly expressed. Transcription factors such as NAC, WRKY, MYB, WUSCHEL, Agamous-like MADS-box protein and bHLH important in somatic embryos of other plants species were found to be expressed in papaya embryogenic callus. Abundant expression of enolase and ADH is consistent with proteome study of papaya somatic embryo. Our study highlights that some genes related to secondary metabolite biosynthesis, especially phenylpropanoid biosynthesis, were highly expressed in papaya embryogenic callus, which might have implication for cell factory applications. The discovery of all genes expressed in papaya embryogenic callus provides an important information into early biological processes during the induction of embryogenesis and useful for future research in other plant species.

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Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus

Cited by 114 publications

References 70 publications

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

Biogenesis and Function of Transfer RNA-Related Fragments (tRFs)

Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus

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