Methods for isolation of total RNA to recover miRNAs and other small RNAs from diverse species

High quality RNA extraction protocol for polyphenolics-rich Cotton tissue

The extraction of high-quality RNA from cotton (Gossypium spp.) is challenging because of the presence of high polyphenolics, polysaccharides, quinones, and other secondary metabolites. A high-throughput RNA extraction protocol is a prerequisite. This Triton-X-100-based RNA extraction method utilizes Polyvinyl pyrrolidone polymer (PVPP) treatment which efficiently removes phenolics, and the application of Lithium chloride (LiCl) has been found that successfully precipitated the high-quality RNA from cotton tissue. Cytoplasmic male sterility (CMS) is a maternally inherited trait associated with specific mitochondrial genome rearrangements or mutations. The suitability of RNA extracted from Cotton CMS lines was assessed. cDNA was synthesized from RNA and assayed for mitochondrial genes (cox3, nad3, nad9) associated with male sterility. This paper discuss the advantages and limitation of this protocol over existing protocol for RNA extraction for polyphenolics-rich plant tissue.

Perspectives on Bulk-Tissue RNA Sequencing and Single-Cell RNA Sequencing for Cardiac Transcriptomics

The heart has been the center of numerous transcriptomic studies in the past decade. Even though our knowledge of the key organ in our cardiovascular system has significantly increased over the last years, it is still not fully understood yet. In recent years, extensive efforts were made to understand the genetic and transcriptomic contribution to cardiac function and failure in more detail. The advent of Next Generation Sequencing (NGS) technologies has brought many discoveries but it is unable to comprehend the finely orchestrated interactions between and within the various cell types of the heart. With the emergence of single-cell sequencing more than 10 years ago, researchers gained a valuable new tool to enable the exploration of new subpopulations of cells, cell-cell interactions, and integration of multi-omic approaches at a single-cell resolution. Despite this innovation, it is essential to make an informed choice regarding the appropriate technique for transcriptomic studies, especially when working with myocardial tissue. Here, we provide a primer for researchers interested in transcriptomics using NGS technologies.

On-chip miRNA extraction platforms: recent technological advances and implications for next generation point-of-care nucleic acid tests

Circulating microRNAs (or miRNAs) in bodily fluids, are increasingly being highlighted as promising diagnostic and predictive biomarkers for a broad range of pathologies. Although nucleic acid sensors have been developed that can detect minute concentrations of biomarkers with high sensitivity and sequence specificity, their robustness is often compromised by sample collection and processing prior to analysis. Such steps either (i) involve complex, multi-step procedures and toxic chemicals unsuitable for incorporation into portable devices or (ii) are inefficient and non-standardised therefore affecting the reliability/reproducibility of the test. The development of point-of-care nucleic acid tests based on the detection of miRNAs is therefore highly dependent on the development of an automated, on-chip, sample processing platform that would enable extraction or pre-purification of the biological specimen prior to reaching the sensing platform. In this review we categorise and critically discuss the most promising technologies that have been developed to facilitate the transition of nucleic acid tests based on miRNA detection from bench to bedside.

Purification of Total RNAs and Small RNAs from Fruit Tree Leaf Tissues

Perennial fruit crops are susceptible to many viral pathogens, which often lead to declines in quality and yield. For the production of good quality and virus-free propagation materials, conventional molecular detection methods combining high throughput sequencing technology have been widely applied to virus detection and discovery in fruit trees. Recovery of high-quality RNAs from fruit tree leaf tissues, the critical step for the subsequent molecular analysis, is often complicated by the presence of high levels of RNases and problematic biomolecules. Therefore, the universal extraction methods often require modification according to different properties of various tissues. In this chapter, we provide a set of methods that have been used successfully to isolate total RNAs and small RNAs from various fruit tree leaf tissues and as examples, presented in detail of a modified TRIzol method for total RNAs purification from mulberry (Morus alba L.) leaf tissues and an alternative small RNAs purification protocol using mirVana™ miRNA isolation kit (Ambion/Life Technologies) for some fruit tree leaf tissues. The protocols described here aim to provide examples of what have worked successfully for a range of fruit trees and may be successful for a given sample in the future.

Research hotspots and trends of microRNA in periodontology and dental implantology: a bibliometric analysis

Background

Periodontal disease is a leading cause of tooth loss, and microRNA (miRNA) has been shown to regulate various biological processes. This study aimed to quantitatively analyze the literature related to miRNA in periodontology and dental implantology and summarize the research hotspots and trends in this field.

Methods

Literature records from 1985 to 2020 were obtained from the Web of Science Core Collection database. After manual selection, the data was used for cooperative network analysis, keyword co-occurrence analysis, and reference co-citation analysis and visualized by CiteSpace.

Results

A total of 287 papers were analyzed between 2007 and 2020, and more than 95% of them were published in the past decade. The largest number of publications were from China, followed by the USA and Japan. The direct cooperation among the productive institutions was not close. At present, most of the research belongs to the discipline of dentistry, oral surgery, cell biology, and molecular biology. Literature clusters generated by reference co-citation analysis and keyword co-occurrence network showed that previous studies mainly focused on four hotspots: periodontal ligament stem cells (PDLSCs), the pathological process of periodontitis, osteogenic differentiation/bone regeneration, and the competing endogenous RNA (ceRNA) network.

Conclusions

The therapeutic potential of miRNA in promoting bone formation and how the ceRNA network contributes to miRNA regulation at a deeper level have become the two main research trends of this field.

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine

Transition of grapevine buds from paradormancy to endodormancy is coordinated by changes in gene expression, phytohormones, transcription factors, and other molecular regulators, but the mechanisms involved in transcriptional and post-transcriptional regulation of dormancy stages are not well delineated. To identify potential regulatory targets, an integrative analysis of differential gene expression profiles and their inverse relationships with miRNA abundance was performed in paradormant (long day (LD) 15 h) or endodormant (short day (SD), 13 h) Vitis riparia buds. There were 400 up- and 936 downregulated differentially expressed genes in SD relative to LD budsGene set and gene ontology enrichment analysis indicated that hormone signaling and cell cycling genes were downregulated in SD relative to LD buds. miRNA abundance and inverse expression analyses of miRNA target genes indicated increased abundance of miRNAs that negatively regulate genes involved with cell cycle and meristem development in endodormant buds and miRNAs targeting starch metabolism related genes in paradormant buds. Analysis of interactions between abundant miRNAs and transcription factors identified a network with coinciding regulation of cell cycle and epigenetic regulation related genes in SD buds. This network provides evidence for cross regulation occurring between miRNA and transcription factors both upstream and downstream of MYB3R1.

High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity

The capability to analyze small RNAs responsible for post-transcriptional regulation of genes expression is essential for characterizing cellular phenotypes. Here, we describe an intracellular biopsy technique (inCell-Biopsy) for fast, multiplexed, and highly sensitive profiling of microRNAs (miRNAs). The technique uses an array of diamond nanoneedles that are functionalized with size-dependent RNA binding proteins, working as "fishing rods" to directly pull miRNAs out of cytoplasm while keeping the cells alive, thus enabling quasi-single-cell miRNA analysis. Each nanoneedle works as a reaction chamber for parallel in situ amplification, visualization, and quantification of miRNAs as low as femtomolar, which is sufficient to detect miRNAs of a single-copy intracellular abundance with specificity to single-nucleotide variation. Using inCell-Biopsy, we analyze the temporal miRNA transcriptome over the differentiation of embryonic stem cells (ESCs). The combinatorial miRNA expression patterns derived by inCell-Biopsy identify emerging cell subpopulations differentiated from ESCs and reveal the dynamic evolution of cellular heterogeneity.

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Background

Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food industries. Although the terpenoids of P. minor have been studied thoroughly, the involvement of microRNA (miRNA) in terpenoid regulation remains poorly understood and needs to be explored. In this study, P. minor plants were inoculated with the pathogenic fungus Fusarium oxysporum for terpenoid induction.

Result

SPME GC-MS analysis showed the highest terpenoid accumulation on the 6th day post-inoculation (dpi) compared to the other treatment time points (0 dpi, 3 dpi, and 9 dpi). Among the increased terpenoid compounds, α-cedrene, valencene and β-bisabolene were prominent. P. minor inoculated for 6 days was selected for miRNA library construction using next generation sequencing. Differential gene expression analysis showed that 58 miRNAs belonging to 30 families had significantly altered regulation. Among these 58 differentially expressed genes (DEGs), 33 miRNAs were upregulated, whereas 25 miRNAs were downregulated. Two putative novel pre-miRNAs were identified and validated through reverse transcriptase PCR. Prediction of target transcripts potentially involved in the mevalonate pathway (MVA) was carried out by psRobot software, resulting in four miRNAs: pmi-miR530, pmi-miR6173, pmi-miR6300 and a novel miRNA, pmi-Nov_13. In addition, two miRNAs, miR396a and miR398f/g, were predicted to have their target transcripts in the non-mevalonate pathway (MEP). In addition, a novel miRNA, pmi-Nov_12, was identified to have a target gene involved in green leaf volatile (GLV) biosynthesis. RT-qPCR analysis showed that pmi-miR6173, pmi-miR6300 and pmi-nov_13 were downregulated, while miR396a and miR398f/g were upregulated. Pmi-miR530 showed upregulation at 9 dpi, and dynamic expression was observed for pmi-nov_12. Pmi-6300 and pmi-miR396a cleavage sites were detected through degradome sequence analysis. Furthermore, the relationship between miRNA metabolites and mRNA metabolites was validated using correlation analysis.

Conclusion

Our findings suggest that six studied miRNAs post-transcriptionally regulate terpenoid biosynthesis in P. minor. This regulatory behaviour of miRNAs has potential as a genetic tool to regulate terpenoid biosynthesis in P. minor.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5954-0) contains supplementary material, which is available to authorized users.

MicroRNA Signature of Traumatic Brain Injury: From the Biomarker Discovery to the Point-of-Care

Traumatic brain injury (TBI) is a serious problem that causes high morbidity and mortality around the world. Currently, no reliable biomarkers are used to assess the severity and predict the recovery. Many protein biomarkers were extensively studied for diagnosis and prognosis of different TBI severities such as S-100β, glial fibrillary acidic protein (GFAP), neuron-specific enolase (NSE), neurofilament light chain (NFL), cleaved tau protein (C-tau), and ubiquitin C-terminal hydrolase-L1 (UCH-L1). However, none of these candidates is currently used in the clinical practice, due to relatively low sensitivity, for the diagnosis of mild TBI (mTBI) or mild to moderate TBI (MMTBI) patients who are clinically well and do not have a detectable intracranial pathology on the scans. MicroRNAs (miRNAs or miRs) are a class of small endogenous molecular regulators, which showed to be altered in different pathologies, including TBI and for this reason, their potential role in diagnosis, prognosis and therapeutic applications, is explored. Promising miRNAs such as miR-21, miR-16 or let-7i were identified as suitable candidate biomarkers for TBI and can differentiate mild from severe TBI. Also, they might represent new potential therapeutic targets. Identification of miRNA signature in tissue or biofluids, for several pathological conditions, is now possible thanks to the introduction of new high-throughput technologies such as microarray platform, Nanostring technologies or Next Generation Sequencing. This review has the aim to describe the role of microRNA in TBI and to explore the most commonly used techniques to identify microRNA profile. Understanding the strengths and limitations of the different methods can aid in the practical use of miRNA profiling for diverse clinical applications, including the development of a point-of-care device.

The Stability of Medicinal Plant microRNAs in the Herb Preparation Process

Herbal medicine is now globally accepted as a valid alternative system of pharmaceutical therapies. Various studies around the world have been initiated to develop scientific evidence-based herbal therapies. Recently, the therapeutic potential of medicinal plant derived miRNAs has attracted great attraction. MicroRNAs have been indicated as new bioactive ingredients in medicinal plants. However, the stability of miRNAs during the herbal preparation process and their bioavailability in humans remain unclear. Viscum album L. (European mistletoe) has been widely used in folk medicine for the treatment of cancer and cardiovascular diseases. Our previous study has indicated the therapeutic potential of mistletoe miRNAs by using bioinformatics tools. To evaluate the stability of these miRNAs, various mistletoe extracts that mimic the clinical medicinal use as well as traditional folk medicinal use were prepared. The mistletoe miRNAs including miR166a-3p, miR159a, miR831-5p, val-miR218 and val-miR11 were quantified by stem-loop qRT-PCR. As a result, miRNAs were detectable in the majority of the extracts, indicating that consumption of medicinal plant preparations might introduce miRNAs into mammals. The factors that might cause miRNA degradation include ultrasonic treatment, extreme heat, especially RNase treatment, while to be associated with plant molecules (e.g., proteins, exosomes) might be an efficient way to protect miRNAs against degradation. Our study confirmed the stability of plant derived miRNAs during herb preparations, suggesting the possibility of functionally intact medicinal plant miRNAs in mammals.

Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica

Deep sequencing of small RNAs (sRNAs) in developing male strobili of second-generation offspring originating from a nuclear genic male sterile tree of Cryptomeria japonica were performed to characterize sRNA populations in the male strobili at early pollen developmental stages. Comparing to sequences of microRNA (miRNA) families of plant species and sRNAs expressed in the reproductive organs of representative vascular plants, 37 conserved miRNA families were detected, of which eight were ubiquitously expressed in the reproductive organs of land plant species. In contrast, miR1083 was common in male reproductive organs of gymnosperm species but absent in angiosperm species. In addition to conserved miRNAs, 199 novel miRNAs candidates were predicted. The expression patterns of the obtained sRNAs were further investigated to detect the differentially expressed (DE) sRNAs between genic male sterile and fertile individuals. A total of 969 DE sRNAs were obtained and only three known miRNA families were included among them. These results suggest that both conserved and species-specific sRNAs contribute to the development of male strobili in C. japonica.

Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species

The role of non-coding RNAs in different biological processes and diseases is continuously expanding. Next-generation sequencing together with the parallel improvement of bioinformatics analyses allows the accurate detection and quantification of an increasing number of RNA species. With the aim of exploring new potential biomarkers for disease classification, a clear overview of the expression levels of common/unique small RNA species among different biospecimens is necessary. However, except for miRNAs in plasma, there are no substantial indications about the pattern of expression of various small RNAs in multiple specimens among healthy humans. By analysing small RNA-sequencing data from 243 samples, we have identified and compared the most abundantly and uniformly expressed miRNAs and non-miRNA species of comparable size with the library preparation in four different specimens (plasma exosomes, stool, urine, and cervical scrapes). Eleven miRNAs were commonly detected among all different specimens while 231 miRNAs were globally unique across them. Classification analysis using these miRNAs provided an accuracy of 99.6% to recognize the sample types. piRNAs and tRNAs were the most represented non-miRNA small RNAs detected in all specimen types that were analysed, particularly in urine samples. With the present data, the most uniformly expressed small RNAs in each sample type were also identified. A signature of small RNAs for each specimen could represent a reference gene set in validation studies by RT-qPCR. Overall, the data reported hereby provide an insight of the constitution of the human miRNome and of other small non-coding RNAs in various specimens of healthy individuals.

Comparative assessment of four RNA extraction methods and modification to obtain high-quality RNA from Parthenium hysterophorus leaf

Isolation of high-quality RNA from weed plants such as Parthenium hysterophorus is a difficult task due to the hindrance caused by numerous secondary metabolites. Such metabolites not only affect the quality and yield of RNA, but also limit the quality of downstream applications. Therefore, the present study was undertaken to design a protocol for yielding RNA with better quality and quantity from P. hysterophorus leaf which could be suitable for functional genomics. To achieve the objective, four different important RNA extraction protocols, viz. acid guanidinium thiocyanate-phenol-chloroform, phenol-LiCl precipitation, TRIzol®, and PVP-ethanol were tested. The PVP-ethanol method proved to be best among the tested protocols. This method was further modified for obtaining improved quality and yield of RNA. The modified method successfully enhanced the yield of RNA from 280 to 334 µg g-1 fresh weight. The absorbance ratio (A260/A280) was in the purity range of 1.9 that indicated the good quality of RNA. To prove the feasibility of the extracted RNA in PCR-based cDNA synthesis, actin transcripts were targeted and successfully amplified using suitable primers. The improved protocol thus not only improved the yield and quality of RNA, but also gave better results in reverse transcriptase PCR.

Non-coding RNAs as a new dawn in tumor diagnosis

The current knowledge about non-coding RNAs (ncRNAs) as important regulators of gene expression in both physiological and pathological conditions, has been the main engine for the design of innovative platforms to finalize the pharmacological application of ncRNAs as either therapeutic tools or as molecular biomarkers in cancer. Biochemical alterations of cancer cells are, in fact, largely supported by ncRNA disregulation in the tumor site, which, in turn, reflects the cancer-associated specific modification of circulating ncRNA expression pattern. The aim of this review is to describe the state of the art of pre-clinical and clinical studies that analyze the involvement of miRNAs and lncRNAs in cancer-related processes, such as proliferation, invasion and metastases, giving emphasis to their functional role. A central node of our work has been also the examination of advantages and criticisms correlated with the clinical use of ncRNAs, taking into account the pressing need to refine the profiling methods aimed at identify novel diagnostic and prognostic markers and the request to optimize the delivery of such nucleic acids for a therapeutic use in an imminent future.

miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects

microRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression in eukaryotes. Their differential abundance is indicative or even causative for a variety of pathological processes including cancer or cardiovascular disorders. Due to their important biological function, miRNAs represent a promising class of novel biomarkers that may be used to diagnose life-threatening diseases, and to monitor disease progression. Further, they may guide treatment selection or dosage of drugs. miRNAs from blood or derived fractions are particularly interesting candidates for routine laboratory applications, as they can be measured in most clinical laboratories already today. This assures a good accessibility of respective tests. Albeit their great potential, miRNA-based diagnostic tests have not made their way yet into the clinical routine, and hence no standardized workflows have been established to measure miRNAs for patients' benefit. In this review we summarize the detection technologies and workflow options that exist to measure miRNAs, and we describe the advantages and disadvantages of each of these options. Moreover, we also provide a perspective on data analysis aspects that are vital for translation of raw data into actionable diagnostic test results.

Systematic Review of Micro-RNA Expression in Pre-Eclampsia Identifies a Number of Common Pathways Associated with the Disease

Background

Pre-eclampsia (PE) is a complex, multi-systemic condition of pregnancy which greatly impacts maternal and perinatal morbidity and mortality. MicroRNAs (miRs) are differentially expressed in PE and may be important in helping to understand the condition and its pathogenesis.

Methods

Case-control studies investigating expression of miRs in PE were collected through a systematic literature search. Data was extracted and compared from 58 studies to identify the most promising miRs associated with PE pathogenesis and identify areas of methodology which could account for often conflicting results.

Results

Some of the most frequently differentially expressed miRs in PE include miR-210, miR-223 and miR-126/126* which associate strongly with the etiological domains of hypoxia, immunology and angiogenesis. Members of the miR-515 family belonging to the imprinted chromosome 19 miR cluster with putative roles in trophoblast invasion were also found to be differentially expressed. Certain miRs appear to associate with more severe forms of PE such as miR-210 and the immune-related miR-181a and miR-15 families. Patterns of miR expression may help pinpoint key pathways (e.g. IL-6/miR-223/STAT3) and aid in untangling the heterogeneous nature of PE. The detectable presence of many PE-associated miRs in antenatal circulatory samples suggests their usefulness as predictive biomarkers. Further progress in ascertaining the clinical value of miRs and in understanding how they might contribute to pathogenesis is predicated upon resolving current methodological challenges in studies. These include differences in diagnostic criteria, cohort characteristics, sampling technique, RNA isolation and platform-dependent variation in miR profiling.

Conclusion

Reviewing studies of PE-associated miRs has revealed their potential as informants of underlying target genes and pathways relating to PE pathogenesis. However, the incongruity in results across current studies hampers their capacity to be useful biomarkers of the condition.

Investigating the effect of drought stress on expression of WRKY1 and EREBP1 genes and antioxidant enzyme activities in lemon balm (Melissa Officinalis L.)

Drought stress is a severe environmental constraint to plant productivity. In this study, gene expression of WRKY1 and EREBP1 genes and activity of two enzymes were investigated in two genotypes, G9 (as resistance) and G12 (as susceptible) of 10 days-old lemon balm seedlings. Experiments were done according to factorial design on the base of completely randomized design with three replications for expression analysis and enzyme assays. Seedlings were cultured in MS medium suspensions, including 0, 3, 6, 12 and 15 % w/v PEG 6000. Leaf samples were subsequently collected at 0, 3, 6, 24, 48, 72 h after culture. According to the results of the enzyme assay, SOD activity in resistant genotype was more than in sensitive one. POD activity was high in G9 in severe drought condition and in G12 this activity was increased at initial times of drought stress. The survey results revealed that the expression levels of both genes, EREBP1 and WRKY1, in G9 variety were more than G12, and in this respect we can say that the G9 variety is more resistant to drought.

Mini but mighty: microRNAs in the pathobiology of periodontal disease

MicroRNAs (miRNAs) are a family of small, noncoding RNA molecules that negatively regulate protein expression either by inhibiting initiation of the translation of mRNA or by inducing the degradation of mRNA molecules. Accumulating evidence suggests that miRNA-mediated repression of protein expression is of paramount importance in a broad range of physiologic and pathologic conditions. In particular, miRNA-induced dysregulation of molecular processes involved in inflammatory pathways has been shown to contribute to the development of chronic inflammatory diseases. In this review, first of all we provide an overview of miRNA biogenesis, the main mechanisms of action and the miRNA profiling tools currently available. Then, we summarize the available evidence supporting a specific role for miRNAs in the pathobiology of periodontitis. Based on a review of available data on the differential expression of miRNAs in gingival tissues in states of periodontal health and disease, we address specific roles for miRNAs in molecular and cellular pathways causally linked to periodontitis. Our review points to several lines of evidence suggesting the involvement of miRNAs in periodontal tissue homeostasis and pathology. Although the intricate regulatory networks affected by miRNA function are still incompletely mapped, further utilization of systems biology tools is expected to enhance our understanding of the pathobiology of periodontitis.

Circulating microRNAs and long non-coding RNAs in gastric cancer diagnosis: An update and review

Gastric cancer (GC) is the fourth most common cancer and the third leading cause of cancer mortality worldwide. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are the most popular non-coding RNAs in cancer research. To date, the roles of miRNAs and lncRNAs have been extensively studied in GC, suggesting that miRNAs and lncRNAs represent a vital component of tumor biology. Furthermore, circulating miRNAs and lncRNAs are found to be dysregulated in patients with GC compared with healthy individuals. Circulating miRNAs and lncRNAs may function as promising biomarkers to improve the early detection of GC. Multiple possibilities for miRNA secretion have been elucidated, including active secretion by microvesicles, exosomes, apoptotic bodies, high-density lipoproteins and protein complexes as well as passive leakage from cells. However, the mechanism underlying lncRNA secretion and the functions of circulating miRNAs and lncRNAs have not been fully illuminated. Concurrently, to standardize results of global investigations of circulating miRNAs and lncRNAs biomarker studies, several recommendations for pre-analytic considerations are put forward. In this review, we summarize the known circulating miRNAs and lncRNAs for GC diagnosis. The possible mechanism of miRNA and lncRNA secretion as well as methodologies for identification of circulating miRNAs and lncRNAs are also discussed. The topics covered here highlight new insights into GC diagnosis and screening.

Forensic miRNA: potential biomarker for body fluids?

In forensic investigation, body fluids represent an important support to professionals when detected, collected and correctly identified. Through many years, various approaches were used, namely serology-based methodologies however, their lack of sensitivity and specificity became difficult to set aside. In order to sidetrack the problem, miRNA profiling surged with a real potential to be used to identify evidences like urine, blood, menstrual blood, saliva, semen and vaginal secretions. MiRNAs are small RNA structures with 20-25 nt whose proprieties makes them less prone to degradation processes when compared to mRNA which is extremely important once, in a crime scene, biological evidences might be exposed to several unfavorable environmental factors. Recently, published studies were able to identify some specific miRNAs, however their results were not always reproducible by others which can possibly be the reflection of different workflow strategies for their profiling studies. Given the current blast of interest in miRNAs, it is important to acknowledge potential limitations of miRNA profiling, yet, the lack of such studies are evident. This review pretends to gather all the information to date and assessed a multitude of factors that have a potential aptitude to discrediting miRNA profiling, such as: methodological approaches, environmental factors, physiological conditions, gender, pathologies and samples storage. It can be asserted that much has yet to be made, but we pretend to highlight a potential answer for the ultimate question: Can miRNA profiling be used as the forensic biomarker for body fluids identification?

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.

A simple and efficient protocol for isolation of high quality functional RNA from different tissues of turmeric (Curcuma longa L.)

Many experiments in plant molecular biology require processing of a large number of RNA samples and in some cases large quantities are required for a single application. In turmeric, a major spice and medicinal plant, a protocol for RNA isolation is not available. The major difficulty encountered while using other popular protocols is the low yield and quality of RNA which hampers the downstream applications like qRT-PCR, cDNA synthesis and micro RNA isolation. Commercial kits though available are costly and were found to be unsuccessful in case of rhizomes and root tissues that are rich in polyphenols, polysaccharides and alkaloids. It was thus felt that a quick, handy and cheap protocol of total RNA isolation from different tissues of turmeric was required for day to day working in our lab. The new protocol utilizes SDS based extraction buffer including β-mercaptoethanol and PVP with sequential acid phenol:chloroform extraction to remove polyphenols and proteins, followed by the purification with sodium acetate to eliminate polysaccharides. The protocol is simple and can be completed in less than 3 h. The RNA yield from rhizome was higher by more than fivefold with both A260/280 and A260/230 ratio in the range of 1.8-2.0. The protocol worked well with leaf, rhizome, pseudostem and root tissues with RIN >7.0 and the isolated RNA could be successfully used for cDNA synthesis, RT-PCR, qRT-PCR and small RNA isolation including microRNA.

A method for extracting high-quality RNA from diverse plants for next-generation sequencing and gene expression analyses

PREMISE OF THE STUDY

To study gene expression in plants, high-quality RNA must be extracted in quantities sufficient for subsequent cDNA library construction. Field-based collections are often limited in quantity and quality of tissue and are typically preserved in RNAlater. Obtaining sufficient and high-quality yield from variously preserved samples is essential to studies of comparative biology. We present a protocol for the extraction of high-quality RNA from even the most recalcitrant plant tissues. •

METHODS AND RESULTS

Tissues from mosses, cycads, and angiosperm floral organs and leaves were preserved in RNAlater or frozen fresh at -80°C. Extractions were performed and quality was measured for yield and purity. •

CONCLUSIONS

This protocol results in the extraction of high-quality RNA from a variety of plant tissues representing vascular and nonvascular plants. RNA was used for cDNA synthesis to generate libraries for next-generation sequencing and for expression studies using quantitative PCR (qPCR) and semiquantitative reverse transcription PCR (RT-PCR).

microRNAs in breast cancer development and treatment

microRNAs (herein after miRNAs) represent a recently uncovered class of small and endogenous non-coding RNAs. miRNAs play a well conserved and crucial role in normal biological processes, such as cell differentiation, proliferation and apoptosis through a complicated gene regulation networking. The recent rise of interest in miRNAs in cancer research is ascribed to the breakthrough of their role in many pathological processes, including malignant transformation. miRNAs signatures have been clearly defined for certain types of cancer, with correlation to tumor aggressiveness, therapy response and patient outcome. Furthermore, the use of miRNAs as therapeutic targets for cancer is currently under investigation. The aim of this review is to focus on the role of miRNAs in breast cancer development and to summarize the evidence for their potential diagnostic and therapeutic applications in clinical practice.

Identification and validation of reference genes for transcript normalization in strawberry (Fragaria × ananassa) defense responses

Strawberry (Fragaria spp) is an emerging model for the development of basic genomics and recombinant DNA studies among rosaceous crops. Functional genomic and molecular studies involve relative quantification of gene expression under experimental conditions of interest. Accuracy and reliability are dependent upon the choice of an optimal reference control transcript. There is no information available on validated endogenous reference genes for use in studies testing strawberry-pathogen interactions. Thirteen potential pre-selected strawberry reference genes were tested against different tissues, strawberry cultivars, biotic stresses, ripening and senescent conditions, and SA/JA treatments. Evaluation of reference candidate's suitability was analyzed by five different methodologies, and information was merged to identify best reference transcripts. A combination of all five methods was used for selective classification of reference genes. The resulting superior reference genes, FaRIB413, FaACTIN, FaEF1α and FaGAPDH2 are strongly recommended as control genes for relative quantification of gene expression in strawberry. This report constitutes the first systematic study to identify and validate optimal reference genes for accurate normalization of gene expression in strawberry plant defense response studies.

Circulating miRNAs as sensitive and specific biomarkers for the diagnosis and monitoring of human diseases: promises and challenges

The regulation and modulation of gene expression has been a central focus of modern biomedical research ever since the first molecular elucidation of DNA. The cellular mechanisms by which genes are expressed and repressed hold valuable insight for maintaining tissue homeostasis or conversely provide mechanistic understanding of disease progression. Hence, the discovery of the first miRNA in humans roughly a decade ago profoundly shook the previously established dogmas of gene regulation. Since, these small RNAs of around 20 nucleotides have unquestionably influenced almost every area of medical research. This momentum has now spread to the clinical arena. Hundreds of papers have already been published shedding light on the mechanisms of action of miRNAs, their profound stability in almost every bodily fluid and relating their presence to disease state and severity of disease progression. In this review, we explore the diagnostic potential of miRNAs in the clinical laboratory with a focus on studies reporting the detection of miRNAs in blood and urine for investigation of human disease. Sensitivities, specificities, areas under the curve, group descriptions and miRNAs of interest for 69 studies covering a broad range of diseases are provided. We discuss the practicality of miRNAs in the screening, diagnosis and prognosis of a range of pathologies. Characteristics and pitfalls of miRNA detection in blood are also discussed. The topics covered here are pertinent in the design of future miRNA-based detection strategies for use in clinical biochemistry laboratory settings.

MicroRNA profiling: approaches and considerations

MicroRNAs (miRNAs) are small RNAs that post-transcriptionally regulate the expression of thousands of genes in a broad range of organisms in both normal physiological contexts and in disease contexts. miRNA expression profiling is gaining popularity because miRNAs, as key regulators in gene expression networks, can influence many biological processes and also show promise as biomarkers for disease. Technological advances have spawned a multitude of platforms for miRNA profiling, and an understanding of the strengths and pitfalls of different approaches can aid in their effective use. Here, we review the major considerations for carrying out and interpreting results of miRNA-profiling studies.

Construction of small RNA cDNA libraries for high-throughput sequencing

Small RNAs (smRNAs) play an essential role in virtually every aspect of growth and development, by regulating gene expression at the post-transcriptional and/or transcriptional level. New high-throughput sequencing technology allows for a comprehensive coverage of smRNAs in any given biological sample, and has been widely used for profiling smRNA populations in various developmental stages, tissue and cell types, or normal and disease states. In this article, we describe the method used in our laboratory to construct smRNA cDNA libraries for high-throughput sequencing.

Identification and testing of superior reference genes for a starting pool of transcript normalization in Arabidopsis

Genes that are stably expressed during development or in response to environmental changes are essential for accurate normalization in qRT-PCR experiments. To prevent possible misinterpretation caused by the use of unstable housekeeping genes, such as UBQ10, ACT, TUB and EF-1α, as a reference, the use of 20 stably expressed genes identified from microarray analyses was proposed. Furthermore, it was recommended that at least four genes among them be tested to identify suitable reference genes under different experimental conditions. However, testing the 20 potential reference genes under any condition is inefficient. Furthermore, since their stability still varies, there is a need to identify a subset of genes that are more stable than others, which can be used as a starting pool for testing. Here, we validated the expression stability of the potential candidate genes together with the above-mentioned conventional reference genes under six experimental conditions commonly used in plant developmental biology. To increase fidelity, three independent validation experiments were carried out for each experimental condition. A hypothetical normalization factor, which is the geometric mean of genes that were identified as stably expressed genes in each experiment, was used to exclude unstable genes under a given condition. We identified a subset of genes showing higher expression stability under specific experimental conditions. We recommend the use of these genes as a starting pool for the identification of suitable reference genes under given experimental conditions to ensure accurate normalization in qRT-PCR analysis.