Deep sequencing identifies new and regulated microRNAs in <i>Schmidtea mediterranea</i>

Lu, Yi-Chien; Smielewska, Magda; Palakodeti, Dasaradhi; Lovci, Michael T.; Aigner, Stefan; Yeo, G; Graveley, Brenton R.

doi:10.1261/rna.1702009

Cited by 51 publications

(58 citation statements)

References 22 publications

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“…It was previously reported that mature miRNAs from the sme-miR-71b/2d/752/13 miRNA cluster were expressed in neoblast populations (Friedländer et al 2009;Lu et al 2009). Interestingly, we found that miR-71b and miR-13 were enriched in both the X1 and X2 cell populations, while sme-miR-2d-3p was enriched in the X2 population (Fig.…”

Section: Deep Sequencing Of Small Rnas From Regenerating Tissue and Nmentioning

confidence: 95%

“…Previously, it was reported that let-7a and let-7b were enriched in neoblasts (Friedländer et al 2009;Lu et al 2009). Interestingly, our study revealed that let-7a and let-7b show fold-change enrichment in the X2 population (X1: 1.004, X2: 1.429, Xins: 0.56), which predominantly contains neoblast progeny rather than proliferating neoblasts (X1) and differentiated cells (Xins).…”

Section: Deep Sequencing Of Small Rnas From Regenerating Tissue and Nmentioning

confidence: 99%

“…Most of these studies involved comparing small RNA profiles between irradiated and nonirradiated animals or isolating a mixture of proliferating neoblasts and neoblast progeny (Friedländer et al 2009;Lu et al 2009). Thus, these studies lack information about miRNA expression in different neoblast subpopulations, which is essential to understand the function of miRNAs during proliferation and differentiation.…”

Section: Deep Sequencing Of Small Rnas From Regenerating Tissue and Nmentioning

confidence: 99%

“…These studies either compared miRNA expression between irradiated and nonirradiated animals (Lu et al 2009) or examined miRNA expression in total neoblasts, which included both the X1 and X2 cell subpopulations (Friedländer et al 2009). However, neither study provided information regarding miRNAs that are specifically enriched in the X1, X2, and Xins subpopulations.…”

Section: Deep Sequencing Of Small Rnas From Regenerating Tissue and Nmentioning

confidence: 99%

“…In a recent study, knockdown of Smed-Ago, a key factor involved in miRNA/ siRNA biogenesis in planarians, led to a drastic reduction of the neoblast population and defects in regeneration, suggesting a role of miRNAs/siRNAs in neoblast function and regeneration (Rouhana et al 2010;Li et al 2011). Previous studies have identified several miRNAs that are expressed in neoblasts (Palakodeti et al 2006;Friedländer et al 2009;Lu et al 2009), but little is known about the differential expression of miRNAs in proliferating neoblasts and neoblast progeny. Recently, Tian et al (2012) and Qin et al (2011) identified several miRNAs that are enriched in 3-d regenerating tissues.…”

Section: Introductionmentioning

confidence: 99%

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Identification of neoblast- and regeneration-specific miRNAs in the planarian Schmidtea mediterranea

Sasidharan

Bansal

et al. 2013

RNA

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In recent years, the planarian Schmidtea mediterranea has emerged as a tractable model system to study stem cell biology and regeneration. MicroRNAs are small RNA species that control gene expression by modulating translational repression and mRNA stability and have been implicated in the regulation of various cellular processes. Though recent studies have identified several miRNAs in S. mediterranea, their expression in neoblast subpopulations and during regeneration has not been examined. Here, we identify several miRNAs whose expression is enriched in different neoblast subpopulations and in regenerating tissue at different time points in S. mediterranea. Some of these miRNAs were enriched within 3 h postamputation and may, therefore, play a role in wound healing and/or neoblast migration. Our results also revealed miRNAs, such as sme-miR-2d-3p and the sme-miR-124 family, whose expression is enriched in the cephalic ganglia, are also expressed in the brain primordium during CNS regeneration. These results provide new insight into the potential biological functions of miRNAs in neoblasts and regeneration in planarians.

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Section: Deep Sequencing Of Small Rnas From Regenerating Tissue and Nmentioning

confidence: 95%

Section: Deep Sequencing Of Small Rnas From Regenerating Tissue and Nmentioning

confidence: 99%

Section: Deep Sequencing Of Small Rnas From Regenerating Tissue and Nmentioning

confidence: 99%

Section: Deep Sequencing Of Small Rnas From Regenerating Tissue and Nmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Identification of neoblast- and regeneration-specific miRNAs in the planarian Schmidtea mediterranea

Sasidharan

Bansal

et al. 2013

RNA

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Evolution of VaultRNAs

Mosig

Stadler

2011

Encyclopedia of Life Sciences

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Vault ribonucleic acids (RNAs) are small, about 100 nt long, polymerase transcripts contained in the vault particles of eukaryotic cells. Although vaults are present in many but by no means all eukaryotes, an RNA component has been described in metazoa only. The RNAs exhibit conserved regions at the 3′ and 5′ ends containing also internal promoter elements. They form a panhandle‐like well‐conserved secondary structure. Most genomes contain only one or a small number of closely related vault RNA sequences. Only eutheria exhibit two clearly distinguished paralogues at syntenically conserved genomic locations. Their phylogenetic distribution is characterised by losses in major clades, whereas lophotrochozoa have vault particles and vault RNAs, and the entire system has been deleted in all ecdysozoa. Key Concepts: Vault RNA can be traced evolutionarily along with the vault particle and its key protein components, most notably MVP . Vault RNA exhibits a concserved pan‐handle secondary structure and expression patterns that are often mistaken as a microRNA.

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MicroRNA profiling of clear cell renal cell carcinoma by whole‐genome small RNA deep sequencing of paired frozen and formalin‐fixed, paraffin‐embedded tissue specimens

Weng

Gao

et al. 2010

The Journal of Pathology

152

135

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Renal cell carcinoma (RCC) is one of the leading causes of cancer mortality. Characterization of microRNA (miRNA) expression of RCC will help disclose new pathogenic pathways in tumourigenesis and progression and may lead to the development of molecular biomarkers and target-specific therapies for diagnosis, prognostication and treatment. With limitations in test specificity and the ability to detect novel miRNA and other small non-coding RNAs (smRNAs), microarray and RT-PCR techniques are being replaced by the evolving deep-sequencing technologies, at least in the discovery phase. Until now, cancer miRNA profiling of human benign and tumour specimen sets, using smRNA deep-sequencing (smRNA-seq), has not been reported. Specifically, due to concern over possible poor RNA quality/integrity, formalin-fixed paraffin-embedded (FFPE) samples have not been used for such studies. Here, we performed whole-genome smRNA-seq analysis using a benign and RCC specimen set and have successfully profiled the miRNA expression. Studies performed on paired frozen and FFPE specimens showed very similar results. Moreover, a comparison study of microarray, deep-sequencing and RT-PCR methodologies also showed a high correlation among the three technologies. To our knowledge, this is the first study to demonstrate that FFPE specimens can be used reliably for miRNA deep-sequencing analysis, making future large-scale clinical cohort/trial-based studies possible.

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Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea

Cited by 51 publications

References 22 publications

Identification of neoblast- and regeneration-specific miRNAs in the planarian Schmidtea mediterranea

Identification of neoblast- and regeneration-specific miRNAs in the planarian Schmidtea mediterranea

Evolution of VaultRNAs

MicroRNA profiling of clear cell renal cell carcinoma by whole‐genome small RNA deep sequencing of paired frozen and formalin‐fixed, paraffin‐embedded tissue specimens

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