Systematic and computational identification of Androctonus crassicauda long non-coding RNAs

Salabi, Fatemeh; Jafari, Hedieh; Navidpour, Shahrokh; Sadr, Ayeh Sadat

doi:10.1038/s41598-021-83815-8

Cited by 4 publications

(5 citation statements)

References 54 publications

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“…The resulting assembly then underwent the lncRNA identification process using two different tools ( Figure 1 ). One of the tools, FEELnc, chosen is a high-performing program optimized for non-model organisms [ 37 ], and the second, CPC2, is a species-neutral lncRNA identification tool that has been used in non-model organisms [ 38 , 39 , 40 , 41 ]. For FEELnc, to increase the sensitivity and specificity, we used the shuffle mode of the coding potential calculation with a relaxed ORF definition, multi k-mer frequencies, and increased the mRNA and lncRNA specificity thresholds to 0.99 [ 37 ].…”

Section: Resultsmentioning

confidence: 99%

“…Non-Coding RNA 2022, 8, x FOR PEER REVIEW 3 of 12 organisms [38][39][40][41]. For FEELnc, to increase the sensitivity and specificity, we used the shuffle mode of the coding potential calculation with a relaxed ORF definition, multi kmer frequencies, and increased the mRNA and lncRNA specificity thresholds to 0.99 [37].…”

Section: Novel Lncrnas Were Identified In Both CL and Wt T Bruceimentioning

confidence: 99%

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LncRNAs Are Differentially Expressed between Wildtype and Cell Line Strains of African Trypanosomes

Kim

Jolly

2022

ncRNA

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Trypanosoma brucei is a parasitic protist that causes African sleeping sickness. The establishment of T. brucei cell lines has provided a significant advantage for the majority of T. brucei research. However, these cell lines were isolated and maintained in culture for decades, occasionally accumulating changes in gene expression. Since trypanosome strains have been maintained in culture for decades, it is possible that difference may have accumulated in fast-evolving non-coding RNAs between trypanosomes from the wild and those maintained extensively in cultures. To address this, we compared the lncRNA expression profile of trypanosomes maintained as cultured cell lines (CL) to those extracted from human patients, wildtype (WT). We identified lncRNAs from CL and WT from available transcriptomic data and demonstrate that CL and WT have unique sets of lncRNAs expressed. We further demonstrate that the unique and shared lncRNAs are differentially expressed between CL and WT parasites, and that these lncRNAs are more evenly up-regulated and down-regulated than protein-coding genes. We validated the expression of these lncRNAs using qPCR. Taken together, this study demonstrates that lncRNAs are differentially expressed between cell lines and wildtype T. brucei and provides evidence for potential evolution of lncRNAs, specifically in T. brucei maintained in culture.

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Section: Resultsmentioning

confidence: 99%

Section: Novel Lncrnas Were Identified In Both CL and Wt T Bruceimentioning

confidence: 99%

LncRNAs Are Differentially Expressed between Wildtype and Cell Line Strains of African Trypanosomes

Kim

Jolly

2022

ncRNA

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“…Another recent study investigated the poorly defined lncRNA landscape of scorpions, in particular, the venom glands of the species Androctonus crassicauda [ 227 ]. In the course of the study, authors developed a computational pipeline suitable for distinguishing protein-coding from non-protein-coding genes in arthropod species lacking a reference genome.…”

Section: Exploring the Ncrna Landscape Beyond Humansmentioning

confidence: 99%

“…The results of predicted scorpion lncRNAs showed that most did not share orthologs even with closely related species and were characterized by, e.g., lower GC content or shorter transcript length. In total, 12,642 potentially novel lncRNAs were described, highlighting the important role of ncRNAs in scorpion venom glands [ 227 ]. This study exemplifies that a surprisingly large number of ncRNAs and their function are yet to be discovered in invertebrates.…”

Section: Exploring the Ncrna Landscape Beyond Humansmentioning

confidence: 99%

Advances in Non-Coding RNA Sequencing

Micheel

Safrastyan

Wollny

2021

ncRNA

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Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.

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“…Non-protein-coding RNAs (ncRNAs) are among the small molecules that have increasingly gained attention in various cellular processes. ncRNA is a functional RNA molecule that is transcribed from DNA, but is not translated into proteins and has been shown to be involved in regulating gene expression and inhibiting the translation and degradation of messenger RNAs (mRNAs) [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

ncRNAs and polyphenols: new therapeutic strategies for hypertension

et al. 2022

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Polyphenols have gained significant attention in protecting several chronic diseases, such as cardiovascular diseases (CVDs). Accumulating evidence indicates that polyphenols have potential protective roles for various CVDs. Hypertension (HTN) is among the hazardous CVDs accounting for nearly 8.5 million deaths worldwide. HTN is a complex and multifactorial disease and a combination of genetic susceptibility and environmental factors play major roles in its development. However, the underlying regulatory mechanisms are still elusive. Polyphenols have shown to cause favourable and beneficial effects in the management of HTN. Noncoding RNAs (ncRNAs) as influential mediators in modulating the biological properties of polyphenols, have shown significant footprints in CVDs. ncRNAs control basic functions in virtually all cell types relevant to the cardiovascular system and, thus, a direct link with blood pressure (BP) regulation is highly probable. Recent evidence suggests that a number of ncRNAs, including main small ncRNAs, microRNAs (miRNAs) and long ncRNAs (lncRNAs), play crucial roles with respect to the antihypertensive effects of polyphenols. Indeed, targeting lncRNAs by polyphenols will be a novel and promising strategy in the management of HTN. Herein, we reviewed the effects of polyphenols in HTN. Additionally, we emphasized on the potential effects of polyphenols on regulations of main ncRNAs, which imply the role of polyphenols in regulating ncRNAs in order to exert protective effects and thus proposing them as new targets for HTN treatment. Abbreviations : CVD: cardiovascular disease; BP: blood pressure; HTN: hypertension, lncRNAs: long noncoding RNAs; p38-MAPK: p38-mitogenactivated protein kinase; OPCs: oligomeric procyanidins; GTP: guanosine triphosphate; ROS: reactive oxygen species; cGMP: cyclic guanosine monophosphate; SGC: soluble guanylate cyclase; PI3K: phosphatidylinositol 3-kinase; cGMP: Cyclic GMP; eNOS: endothelial NO synthase; ERK ½: extracellular signal-regulated kinase ½; L-Arg: L-Arginine; MAPK: mitogen-activated protein kinases; NO: Nitric oxide; P: Phosphorus; PDK1: Phosphoinositide-dependent kinase 1; PI3-K: Phosphatidylinositol 3-kinase; PIP2: Phosphatidylinositol diphosphate; ncRNAs: non-protein-coding RNA; miRNAs: microRNAs; OPCs: oligomeric procyanidins; RES: resveratrol; GE: grape extract; T2DM: type 2 diabetes mellitus; IL: interleukin; TNF-α: tumour necrosis factor-alpha; NF-κB: nuclear factor NF-kappa-B; ALP: alkaline phosphatase; PARP1: poly [ADP-ribose] polymerase 1; HIF1a: Hypoxia-inducible-factor 1A; NFATc2: nuclear factor of activated T cells 2; PAD: peripheral artery disease; SHR: spontaneously hypertensive rat; RAAS: renin-angiotensin-aldosterone system; AT 1 R: angiotensin type-1 receptor; Nox: NADPH oxidase; HO-1: haem oxygenase-1; JAK/STAT: Janus kinase/signal transducers/activators of the transcription; PNS: panax notoginseng saponin; snoRNA: small nucleolar RNA; hnRNA: heterogeneous nuclear RNA;...

show abstract

Systematic and computational identification of Androctonus crassicauda long non-coding RNAs

Cited by 4 publications

References 54 publications

LncRNAs Are Differentially Expressed between Wildtype and Cell Line Strains of African Trypanosomes

LncRNAs Are Differentially Expressed between Wildtype and Cell Line Strains of African Trypanosomes

Advances in Non-Coding RNA Sequencing

ncRNAs and polyphenols: new therapeutic strategies for hypertension

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