Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq

Although the functional role of circular RNA (circRNA) interaction with microRNAs and proteins has been studied extensively, circRNA interactions with the protein-coding mRNAs in intact cells remain largely unknown. Here, by employing AMT-mediated proximity ligation of RNA-RNA duplexes followed by circRNA enrichment and deep sequencing, we report a novel Cross-Linking Poly(A) Pulldown RNase R Sequencing (CLiPPR-seq) technology which identified hundreds of mRNA-interacting circRNAs in three different cell types, including βTC6, C2C12 and HeLa cells. Furthermore, CLiPP-seq without RNase R treatment was also performed to identify the mRNA expression in these cells. BLAST analysis of circRNAs in CLiPPR-seq sample with the mRNAs in CLiPP-seq samples determined their potential complementary sequences for circRNA-mRNA interaction. Pulldown of circRNAs and poly(A) RNAs confirmed the direct interaction of circRNAs with target mRNAs. Silencing of mRNA-interacting circRNAs led to the altered expression of target mRNAs in βTC6 cells, suggesting the role of direct interaction of circRNAs with mRNAs in gene expression regulation. CLiPPR-seq thus represents a novel method for illuminating the myriad of uncharacterized circRNA-mRNA hybrids that may regulate gene expression.

Detecting RNA-RNA interactome

The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules, including protein, DNA, and RNA. It has been established that RNA-RNA interactions play a critical role in several biological processes by regulating the biogenesis and function of RNA molecules. Interestingly, RNA-RNA interactions regulate the biogenesis of diverse RNA molecules, including mRNAs, microRNAs, tRNAs, and circRNAs, through splicing or backsplicing. Structured RNAs like rRNA, tRNA, and snRNAs achieve their functional conformation by intramolecular RNA-RNA interactions. In addition, functional consequences of many intermolecular RNA-RNA interactions have been extensively studied in the regulation of gene expression. Hence, it is essential to understand the mechanism and functions of RNA-RNA interactions in eukaryotes. Conventionally, RNA-RNA interactions have been identified through diverse biochemical methods for decades. The advent of high-throughput RNA-sequencing technologies has revolutionized the identification of global RNA-RNA interactome in cells and their importance in RNA structure and function in gene expression regulation. Although these technologies revealed tens of thousands of intramolecular and intermolecular RNA-RNA interactions, we further look forward to future unbiased and quantitative high-throughput technologies for detecting transcriptome-wide RNA-RNA interactions. With the ability to detect RNA-RNA interactome, we expect that future studies will reveal the higher-order structures of RNA molecules and multi-RNA hybrids impacting human health and diseases. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.

Identification of Potential circRNA-microRNA-mRNA Regulatory Network in Skeletal Muscle

Circular RNAs (circRNAs) are a newly discovered family of regulatory RNAs generated through backsplicing. Genome-wide profiling of circRNAs found that circRNAs are ubiquitously expressed and regulate gene expression by acting as a sponge for RNA-binding proteins (RBPs) and microRNAs (miRNAs). To identify circRNAs expressed in mouse skeletal muscle, we performed high-throughput RNA-sequencing of circRNA-enriched gastrocnemius muscle RNA samples, which identified more than 1,200 circRNAs. In addition, we have identified more than 14,000 and 15,000 circRNAs in aging human skeletal muscle tissue and satellite cells, respectively. A subset of abundant circRNAs was analyzed by RT-PCR, Sanger sequencing, and RNase R digestion assays to validate their expression in mouse skeletal muscle tissues. Analysis of the circRNA-miRNA-mRNA regulatory network revealed that conserved circNfix might associate with miR-204-5p, a suppressor of myocyte enhancer factor 2c (Mef2c) expression. To support the hypothesis that circNfix might regulate myogenesis by controlling Mef2c expression, silencing circNfix moderately reduced Mef2c mRNA expression and inhibited C2C12 differentiation. We propose that circNfix promotes MEF2C expression during muscle cell differentiation in part by acting as a sponge for miR-204-5p.

Emerging Role of Circular RNA-Protein Interactions

Circular RNAs (circRNAs) are emerging as novel regulators of gene expression in various biological processes. CircRNAs regulate gene expression by interacting with cellular regulators such as microRNAs and RNA binding proteins (RBPs) to regulate downstream gene expression. The accumulation of high-throughput RNA-protein interaction data revealed the interaction of RBPs with the coding and noncoding RNAs, including recently discovered circRNAs. RBPs are a large family of proteins known to play a critical role in gene expression by modulating RNA splicing, nuclear export, mRNA stability, localization, and translation. However, the interaction of RBPs with circRNAs and their implications on circRNA biogenesis and function has been emerging in the last few years. Recent studies suggest that circRNA interaction with target proteins modulates the interaction of the protein with downstream target mRNAs or proteins. This review outlines the emerging mechanisms of circRNA-protein interactions and their functional role in cell physiology.

Transcriptomic analysis of crustacean molting gland (Y-organ) regulation via the mTOR signaling pathway

The intermolt crustacean Y-organ (YO) maintains a basal state mediated by pulsatile release of molt inhibiting hormone (MIH), a neuropeptide produced in the eyestalk ganglia, inhibiting YO ecdysteroidogenesis. Reduction of MIH results in YO activation and the animal enters premolt. In the crab, Gecarcinus lateralis, molting was induced by eyestalk ablation (ESA). ESA animals were injected with either rapamycin, an mTOR inhibitor, or DMSO vehicle at Day 0. YOs were harvested at 1, 3, and 7 days post-ESA and processed for high throughput RNA sequencing. ESA-induced increases in mRNA levels of mTOR signaling genes (e.g., mTOR, Rheb, TSC1/2, Raptor, Akt, and S6 kinase) declined following rapamycin treatment. In concert with mTOR inhibition, mRNA levels of ecdysteroid biosynthesis genes (e.g., Nvd, Spo, Sad, Dib, and Phm) were decreased and accompanied by a decrease in hemolymph ecdysteroid titer. By contrast, rapamycin increased the mRNA level of FKBP12, the rapamycin-binding protein, as well as the mRNA levels of genes associated with Wnt and insulin-like growth factor signaling pathways. Many MIH and transforming growth factor-β signaling genes were down regulated in ESA animals. These results indicate that mTOR activity either directly or indirectly controls transcription of genes that drive activation of the YO.

Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems

In the field of crustacean biology, usage of RNA-seq to study gene expression is rapidly growing. Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to insect and vertebrate model organisms, however, information on the organization of crustacean genomes is virtually nonexistent, making de novo transcriptome assembly, annotation and quantification problematic and challenging. We present here a summary of the methodologies and software analyses employed in 23 recent publications, which describe de novo transcriptome assembly, annotation, and differential gene expression in a variety of crustacean experimental systems. We focus on establishing a series of best practices that will allow for investigators to produce datasets that are understandable, reproducible, and of general utility for related analyses and cross-study comparisons.

Significant fluctuations in ecdysteroid receptor gene (EcR) expression in relation to seasons of molt and reproduction in the grapsid crab, Metopograpsus messor (Brachyura: Decapoda)

Metopograpsus messor, a brachyuran crab inhabiting the estuaries of North Kerala (India), is a prolific breeder releasing approximately 14-16 broods a year. The present paper reports the sequence information on the DNA binding domain (C domain, DBD), linker (D domain) and ligand binding domain (E domain, LBD) of M. messor ecdysteroid receptor (MmEcR) gene, the first grapsid brachyuran crab EcR examined. We have also measured MmEcR transcript levels in the ovary and the hepatopancreas throughout the annual cycle, with special reference to seasons of molt and reproduction. MmEcR expression in both the tissues is found to be at its peak (P<0.05) in late premolt crabs (January/May, molt/reproduction season); the expression levels are lowest (P<0.05) during June/July, when the females would neither molt nor reproduce (season for molt/reproduction repose). Intermediate levels of expression were found during the breeding season (August/December). Interestingly, this pattern of gene expression is in concordance with the fluctuating ecdysteroid levels of the hemolymph and Y organ secretory activity. The significant levels of fluctuation in the ovarian expression of MmEcR strongly suggest the ovary as a potential target for ecdysteroid action. A season-wise comparison of the gene expression reveals that ovarian MmEcR transcript levels are higher in breeding crabs (August/December) than the non-breeding animals (June/July), implicating a possible ecdysteroid role in reproduction in M. messor.

Hepatoprotective activity of Oxalis corniculata L. ethanolic extract against paracetamol induced hepatotoxicity in Wistar rats and its in vitro antioxidant effects

Oxalis corniculata is well known for its medicinal properties like anti-inflammatory, digestive, diuretic, antibacterial, antiseptic etc. The present study focuses on the ability of O. corniculata to alleviate liver damage caused by over dose of paracetamol. Antioxidant activity of O. corniculata was evaluated using the free radical scavenging activity of 1, 1-diphenyl-2- picrylhydrazyl radicals, total anti oxidant capacity by phosphomolybdenum method and total phenolic content was also evaluated. The ethanolic extract of whole plant of O. corniculata (OC, 500 microg/mL, po) significantly reduced 1, 1-diphenyl-2- picrylhydrazyl radicals. This dose also caused significant reduction (62.67%) in malondialdehyde levels of murine hepatic tissues. The antioxidant capacity of OC was comparable to that of standard ascorbic acid and showed 53.5 microg of phenol/mg OC. Rats pre-treated with OC for 4 days showed significant reduction in the serum enzymes such as glutamate oxaloacetate transaminase, glutamate pyruvate transaminase, alkaline phosphatase, serum bilirubin and showed almost normal histological liver architecture of the treated groups compared to paracetamol induced hepatic damage group, indicating its hepatoprotective and antioxidant potential.

The Y-organ secretory activity fluctuates in relation to seasons of molt and reproduction in the brachyuran crab, Metopograpsus messor (Grapsidae): Ultrastructural and immunohistochemical study

This paper presents a first-time report on the localization, structure and seasonal secretory activity of the Y-organ of a grapsid brachyuran crab (Metopograpsus messor). Having exhibited discrete seasonality with reference to the programming of molt and reproduction, this brachyuran crab has offered us an excellent model to obtain a clear picture of the fluctuating secretory nature of the Yorgan, all the way through the reproductive (August-December) as well as the molt-reproduction active (January-May) and inactive (June-July) seasons. Ultrastructural studies revealed that the secretion of the Y-organ was at its peak in premolt crabs during molt-reproduction season (January-May). Interestingly, the Y-organs of the intermolt females that engaged in breeding activity showed higher levels of secretion than those of the molt-reproduction inactive season (June-July), implicating the gland's involvement in reproduction. Immunohistochemical studies using the antiserum raised against 2-succinyl conjugate of ecdysone have demonstrated the ecdysteroid nature of the secretion from the Y-organ, and results of the quantitative assay of ecdysteroids (through radioimmunoassay) revealed that the hormone titer fluctuates in consonance with the Y-organ's secretory activity during seasons of molt and reproduction. Pertinently, not only that the paper gives us a comprehensive understanding on the secretory activity of the Y-organ in a season-dependent fashion, it also allows us to have a better insight into the gland's function related to molting and reproduction (for the first time) in a grapsid brachyuran crab.

Anti-inflammatory and analgesic properties of Drynaria quercifolia (L.) J. Smith

ETHNOPHARMACOLOGICAL RELEVANCE

Drynaria quercifolia (L.) J. Smith (Polypodiaceae), has been widely used by ethnic groups of India to treat inflammation, rheumatism, headache, bone fracture, jaundice, etc.

AIM OF THE STUDY

To evaluate the anti-inflammatory and analgesic properties of the ethanolic extract of rhizome of Drynaria quercifolia (DQ) and its phytochemical profile.

MATERIALS AND METHODS

DQ was used to evaluate the anti-inflammatory and analgesic effects using carrageenan-induced paw oedema/cotton pellet-induced granuloma in Wistar rats and acetic acid-induced writhing/formalin-induced paw licking test in Swiss albino mice respectively.

RESULTS

Oral administration of DQ produced significant inhibition of carrageenan-induced paw oedema and granuloma formation in rats, almost comparable to that caused by indomethacin. DQ significantly attenuated acute and delayed phases of formalin-induced pain and acetic acid-induced writhing episodes in mice. The analgesia was comparable to that produced by sodium salicylate and aspirin respectively. Phytochemical analysis gave positive tests for catechin, coumarins, flavonoids, phenolics, saponin, steroids, tannins, and triterpenes. The total phenolics in DQ was 244 mg/g and naringin content was 0.048%.

CONCLUSION

The results suggest the presence of potent anti-inflammatory and analgesic principles in DQ that justifies its use for alleviating painful inflammatory conditions.

Hepatoprotective effect of three herbal extracts on aflatoxin B1-intoxicated rat liver

INTRODUCTION

Roots of Ixora coccinea (Rubiaceae), and Rhinacanthus nasuta (Acanthaceae) and whole plants of Spilanthes ciliata (Asteraceae) are extensively used by tribal communities in South India to treat liver diseases. However, the veracity of these tribal claims has not been investigated scientifically using the liver toxin, aflatoxin. This study reports on the protective effects of these three herbal ethanolic extracts on the aflatoxin B1 (AFB1)-intoxicated livers of albino male Wistar rats.

METHODS

Biochemical parameters, including serum hepatic enzymes (glutamate oxaloacetate transaminase, glutamate pyruvate transaminase and alkaline phosphatase), were studied. Hepatic tissues were processed for assay of reduced glutathione (GSH) and histological alterations.

RESULTS

Pre-treatment of the rats with oral administration of the plant ethanolic extracts, Ixora coccinea (IC), Rhinacanthus nasuta (RN), Spilanthes ciliata (SC), prior to AFB1 was found to provide significant protection against toxin-induced liver damage, determined 72 hours after the AFB1 challenge (1.5 mg/kg, intraperitoneally) as evidenced by a significant lowering of the activity of the serum enzymes and enhanced hepatic reduced GSH status. Pathological examination of the liver tissues supported the biochemical findings. The three plant extracts, IC, RN and SC, showed significant antilipid peroxidant effects in vitro.

CONCLUSION

It was concluded that the hepatoprotective effects of the three plant extracts observed in this study might result from their potent antioxidative properties.

Gastric antisecretory and antiulcer activities of Cyclea peltata (Lam.) Hook. f. & Thoms. in rats

ETHNOPHARMACOLOGICAL RELEVANCE

Cyclea peltata (Lam.) Hook. f. & Thoms. (Menispermaceae), locally called 'Padathaali/Padakizhangu' is used in Ayurvedic medicine to treat peptic ulcer.

AIM OF THE STUDY

To evaluate the gastric antisecretory and antiulcer activity of Cyclea peltata.

MATERIALS AND METHODS

The ethanolic extract of Cyclea peltata root was used to evaluate its gastric antisecretory and antiulcer effect in the pylorus-ligated rat model and gastric lesions induced by ethanol or ethanol and indomethacin respectively in rats. The levels of gastric wall mucus, non-protein sulfhydryl groups (NP-SH), malondialdehyde, protein and catalase activity in the stomach samples of Cyclea peltata treated and control groups of rats were also quantified.

RESULTS

The ethanolic extract of Cyclea peltata roots showed significant antisecretory activity as evidenced by decreased pepsin secretion, gastric juice volume and acid output in pylorus-ligated rats. Pretreatment with Cyclea peltata extract provided significant protection against the peptic ulceration caused by ethanol administered individually, or in combination with indomethacin. Our studies also revealed that pretreatment with Cyclea peltata significantly increased the gastric protein and catalase concentration of ethanol treated rats. Further, it showed significant gastroprotective effects on the stomach wall of ethanol or ethanol and indomethacin treated rats by decreasing malondialdehyde level, increasing the gastric wall mucus and non-protein sulfhydryl groups.

CONCLUSION

The present findings demonstrate that Cyclea peltata ethanolic extract has potent antisecretory and antiulcer effects and justify the traditional/ethnic usage of this herb to treat peptic ulcers and consequent stomach ache.

Hepatoprotective studies on Sida acuta Burm. f

ETHNOPHARMACOLOGICAL RELEVANCE

Sida acuta Burm. f. (Malvaceae) is used in Indian traditional medicine to treat liver disorders and is useful in treating nervous and urinary diseases and also disorders of the blood and bile.

AIM OF THE STUDY

Evaluation of the hepatoprotective properties of the methanolic extract of the root of Sida acuta (SA) and the phytochemical analysis of SA.

MATERIALS AND METHODS

The model of paracetamol-induced hepatotoxicity in Wistar rats, liver histopathological observations, hexobarbitone-induced narcosis and in vitro anti-lipid peroxidation studies were employed to assess the hepatoprotective efficacy of SA. Phytochemical assay of SA was conducted following standard protocols.

RESULTS

Significant hepatoprotective effects were obtained against liver damage induced by paracetamol overdose as evident from decreased serum levels of glutamate pyruvate transaminase, glutamate oxaloacetate transaminase, alkaline phosphatase and bilirubin in the SA treated groups (50, 100, 200mg/kg) compared to the intoxicated controls. The hepatoprotective effect was further verified by histopathology of the liver. Pretreatment with Sida acuta extract significantly shortened the duration of hexobarbitone-induced narcosis in mice indicating its hepatoprotective potential. Phytochemical studies confirmed the presence of the phenolic compound, ferulic acid in the root of Sida acuta, which accounts for the significant hepatoprotective effects observed in the present study.

CONCLUSION

The present study thus provides a scientific rationale for the traditional use of this plant in the management of liver disorders.

Hepatoprotective effect of Hibiscus hispidissimus Griffith, ethanolic extract in paracetamol and CCl4 induced hepatotoxicity in Wistar rats

Hibiscus hispidissimus Griff. is used in tribal medicine of Kerala, the southern most state of India, to treat liver diseases. In the present study, the effect of the ethanolic extract of Hibiscus hispidissimus whole plant on paracetamol (PCM)-induced and carbon tetrachloride (CCl4)-induced liver damage in healthy Wistar albino rats was studied. The results showed that significant hepatoprotective effects were obtained against liver damage induced by PCM and CCl4 as evidenced by decreased levels of serum enzymes, glutamate oxaloacetate transaminase (SGOT), glutamate pyruvate transaminase (SGPT), serum alkaline phosphatase (SAKP), serum bilirubin (SB) and an almost normal histological architecture of the liver of the treated groups compared to the toxin controls. The extract also showed significant antilipid peroxidant effects in vitro, besides exhibiting significant activity in quenching 1, 1-diphenyl-2-picryl hydrazyl (DPPH) radical, indicating its potent antioxidant effects.

Hepatoprotective effects of Pittosporum neelgherrense Wight&Arn., a popular Indian ethnomedicine

The stem bark of Pittosporum neelgherrense Wight&Arn. is used by the Kani and Malapandaram tribes of Kerala as an effective antidote to snake bite and for the treatment of various hepatic disorders. In the present study, the effect of the methanolic extract of the stem bark of Pittosporum neelgherrense was studied against carbon tetrachloride (CCl(4))-, d-galactosamine (D-GalN)- and acetaminophen (APAP)-induced acute hepatotoxicity in Wistar rats. Significant hepatoprotective effects were obtained against liver damage induced by all the three liver toxins, as evident from decreased levels of serum enzymes, glutamate oxaloacetate transaminase (SGOT), glutamate pyruvate transaminase (SGPT) and an almost normal architecture of the liver in the treated groups, compared to the toxin controls. Thus the present study provides a scientific rationale for the traditional use of this plant in the management of liver diseases.

Hepatoprotective studies on Hedyotis corymbosa (L.) Lam

Hedyotis corymbosa is used in traditional medicine of India and China to treat various hepatic disorders. In the present study, the hepatoprotective effect of the methanolic extract of the whole plant of Hedyotis corymbosa against paracetamol overdose-induced liver damage in Wistar rats was studied. The methanolic extract of the plant produced significant hepatoprotective effects as evidenced by decreased serum enzyme activities, SGPT, SGOT, SAKP and serum bilirubin and an almost normal histological architecture of the liver, in treated groups, compared to the controls. Hedyotis corymbosa shortened hexobarbitone-induced sleeping time in mice, besides showing significant antilipid peroxidant effect in vitro. The results thus support the use of Hedyotis corymbosa as a hepatoprotective agent.