Identification of miRNAs and Their Targets in C. elegans

Lima, Sarah Azoubel; Pasquinelli, Amy E.

doi:10.1007/978-1-4939-1221-6_12

Cited by 8 publications

(7 citation statements)

References 97 publications

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“…Although advances in bioinformatics algorithms have the potential to increase the confidence of miRNA target predictions, the reliability of most common algorithms (miRanda, PITA, and TargetScan) still display a relatively high false positive (46–63%) and false negative (44–82%) rate . Therefore, the experimental identification of physiological targets remains one of the crucial steps in miRNA research which is reflected in the multitude of studies and reviews on this subject . Historically, miRNA–target interactions have been inferred from genetic approaches, foremost in C. elegans (reviewed in Ref ).…”

Section: Experimental Mirna Target Identificationmentioning

confidence: 99%

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

Steinkraus

Toegel

Fulga

2016

WIREs Developmental Biology

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The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA–target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high‐throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA–target binding events in vivo drove the emergence of a slew of high‐throughput multiplex strategies, which now provide a viable prospect for elucidating genome‐wide miRNA–target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post‐transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high‐precision interference with their direct, endogenous targets. WIREs Dev Biol 2016, 5:311–362. doi: 10.1002/wdev.223For further resources related to this article, please visit the WIREs website.

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Section: Experimental Mirna Target Identificationmentioning

confidence: 99%

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

Steinkraus

Toegel

Fulga

2016

WIREs Developmental Biology

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“…miRNAs are essential in modulating several important biological pathways and cellular functions, consequently making a difference on protein expressions. Studies have shown that serum miRNAs are capable of serving as biomarkers for various diseases, including DR. miR‐365 is a potential therapeutic target for diabetes mellitus, because of its ability to act like an endocrine signaling molecule and potential disease biomarker.…”

Section: Introductionmentioning

confidence: 99%

Pro‐apoptotic effects of micro‐ribonucleic acid‐365 on retinal neurons by targeting insulin‐like growth factor‐1 in diabetic rats: An in vivo and in vitro study

Zheng

Wang

Shen

et al. 2018

J of Diabetes Invest

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Aims/ObjectiveThe present study aimed to explore the effects of micro‐ribonucleic acid‐365 (miR‐365) on apoptosis of retinal neurons by targeting insulin‐like growth factor‐1 (IGF‐1) in diabetes mellitus rats.Materials and MethodsHigh glucose‐induced retinal neurons were assigned into the blank (with no plasmid transfection), negative control (with plasmid transfection), anti‐miR‐365 (transfected miR‐365 antagomir), transfected IGF‐1 short hairpin RNA plasmid (sh‐IGF‐1) and transfected miR‐365 antagomir and IGF‐1 shRNA plasmid (anti‐miR‐365 + sh‐IGF‐1) groups. Proliferation and apoptosis of retinal neurons were detected by 5‐ethynyl‐2′‐deoxyuridine assay and Hoechst 33342 staining, respectively. Expressions of miR‐365, IGF‐1, Bcl‐2‐associated X protein (Bax) and Bcl‐2 were determined by reverse transcription quantitative polymerase chain reaction and western blotting. A control group contained 10 healthy rats. Terminal deoxynucleotidyl transferase dUTP nick‐end labeling staining was used to evaluate apoptosis of retinal neurons in rats.ResultsIn the anti‐miR‐365 group, the apoptosis rate and Bax expression were reduced in comparison with the negative control and blank groups, whereas the sh‐IGF‐1 and anti‐miR‐365 + sh‐IGF‐1 groups presented an opposite trend. Compared with the normal group, expressions of miR‐365 and Bax were increased, and expressions of IGF‐1 and Bcl‐2 were decreased, with more apoptotic cells in diabetes mellitus rat models. The sh‐IGF‐1 group had lower Bax expression, and higher expressions of IGF‐1 and Bcl‐2 with fewer apoptotic cells. Additionally, Bax expression was upregulated, expressions of IGF‐1 and Bcl‐2 were downregulated, and apoptotic cells were higher in the anti‐miR‐365 + sh‐IGF‐1 groups than the anti‐miR‐365 group.ConclusionThe results of the present study suggest that suppressed miR‐365 increases the IGF‐1 expression, leading to anti‐apoptotic effects on retinal neurons in diabetic rats.

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“…By their ability to quench gene expression, miRNAs are similar to small interfering RNAs, another class of regulatory noncoding RNA molecules, but miRNA biogenesis from maternal DNA sequences is quite different from small interfering RNA synthesis (89). While still in the nucleus, the primary long transcript of the miRNA gene, a pri-miRNA, is cleaved by the protein complex, which, in C. elegans, includes DRSH-1 RNase (Drosha in mammals) and PASH-1 (Partner of Drosha; Pasha in mammals) (90), to produce the 60-to 70-nucleotides-long intermediate called pre-miRNA (91). After its transport to the cytoplasm, the pre-miRNA is converted to functional miRNA by additional cleavage performed by Dicer endoribonuclease as well as ALG-1 and ALG-2 proteins (92,93), which belong to the argonaute (AGO) RNase family and are the only 2 AGOs in C. elegans, reported to take part in miRNA biosynthesis.…”

Section: Role Of Mirnas In Mediating Nutritional and Obesity-related Effects In C Elegans And In Other Animal Modelsmentioning

confidence: 99%

The Nematode Caenorhabditis elegans as a Model Organism to Study Metabolic Effects of ω-3 Polyunsaturated Fatty Acids in Obesity

Bouyanfif

Jayarathne

Koboziev

et al. 2019

Advances in Nutrition

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Obesity is a complex disease that is influenced by several factors, such as diet, physical activity, developmental stage, age, genes, and their interactions with the environment. Obesity develops as a result of expansion of fat mass when the intake of energy, stored as triglycerides, exceeds its expenditure. Approximately 40% of the US population suffers from obesity, which represents a worldwide public health problem associated with chronic low-grade adipose tissue and systemic inflammation (sterile inflammation), in part due to adipose tissue expansion. In patients with obesity, energy homeostasis is further impaired by inflammation, oxidative stress, dyslipidemia, and metabolic syndrome. These pathologic conditions increase the risk of developing other chronic diseases including diabetes, hypertension, coronary artery disease, and certain forms of cancer. It is well documented that several bioactive compounds such as omega-3 polyunsaturated fatty acids (ω-3 PUFAs) are able to reduce adipose and systemic inflammation and blood triglycerides and, in some cases, improve glucose intolerance and insulin resistance in vertebrate animal models of obesity. A promising model organism that is gaining tremendous interest for studies of lipid and energy metabolism is the nematode Caenorhabditis elegans. This roundworm stores fats as droplets within its hypodermal and intestinal cells. The nematode's transparent skin enables fat droplet visualization and quantification with the use of dyes that have affinity to lipids. This article provides a review of major research over the past several years on the use of C. elegans to study the effects of ω-3 PUFAs on lipid metabolism and energy homeostasis relative to metabolic diseases.

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Identification of miRNAs and Their Targets in C. elegans

Cited by 8 publications

References 97 publications

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

Pro‐apoptotic effects of micro‐ribonucleic acid‐365 on retinal neurons by targeting insulin‐like growth factor‐1 in diabetic rats: An in vivo and in vitro study

The Nematode Caenorhabditis elegans as a Model Organism to Study Metabolic Effects of ω-3 Polyunsaturated Fatty Acids in Obesity

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