scholarly journals In silico prediction of long intergenic non-coding RNAs in sheep

Genome ◽  
2016 ◽  
Vol 59 (4) ◽  
pp. 263-275 ◽  
Author(s):  
Mohammad Reza Bakhtiarizadeh ◽  
Batool Hosseinpour ◽  
Babak Arefnezhad ◽  
Narges Shamabadi ◽  
Seyed Alireza Salami
Keyword(s):  
Limb Development ◽  
Striated Muscle ◽  
Gc Content ◽  
Ovis Aries ◽  
Specific Expression ◽  
Protein Coding ◽  
Rna Molecules ◽  
Sequencing Technologies ◽  
Non Coding Rnas ◽  
Organismal Development

Long non-coding RNAs (lncRNAs) are transcribed RNA molecules >200 nucleotides in length that do not encode proteins and serve as key regulators of diverse biological processes. Recently, thousands of long intergenic non-coding RNAs (lincRNAs), a type of lncRNAs, have been identified in mammalians using massive parallel large sequencing technologies. The availability of the genome sequence of sheep (Ovis aries) has allowed us genomic prediction of non-coding RNAs. This is the first study to identify lincRNAs using RNA-seq data of eight different tissues of sheep, including brain, heart, kidney, liver, lung, ovary, skin, and white adipose. A computational pipeline was employed to characterize 325 putative lincRNAs with high confidence from eight important tissues of sheep using different criteria such as GC content, exon number, gene length, co-expression analysis, stability, and tissue-specific scores. Sixty-four putative lincRNAs displayed tissues-specific expression. The highest number of tissues-specific lincRNAs was found in skin and brain. All novel lincRNAs that aligned to the human and mouse lincRNAs had conserved synteny. These closest protein-coding genes were enriched in 11 significant GO terms such as limb development, appendage development, striated muscle tissue development, and multicellular organismal development. The findings reported here have important implications for the study of sheep genome.

scholarly journals A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs

2020 ◽  
Vol 21 (1) ◽  
pp. 302 ◽  
Author(s):  
Enrico Alessio ◽  
Raphael Severino Bonadio ◽  
Lisa Buson ◽  
Francesco Chemello ◽  
Stefano Cagnin
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Cell Lineage ◽  
Cell Analysis ◽  
Specific Expression ◽  
Protein Coding ◽  
Rna Molecules ◽  
New Findings ◽  
Non Coding Rnas ◽  
Data Tables

In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification. The purpose of this review is to collect updated information about lncRNA classification and new findings on their function derived from single-cell analysis. We also retained useful for all researchers to describe the methods available for single-cell analysis and the databases collecting single-cell and lncRNA data. Tables are included to schematize, describe, and compare exposed concepts.

scholarly journals From Junk to Function: LncRNAs in CNS Health and Disease

2021 ◽  
Vol 14 ◽  
Author(s):  
Rafaela Policarpo ◽  
Annerieke Sierksma ◽  
Bart De Strooper ◽  
Constantin d’Ydewalle
Keyword(s):  
Potential Contribution ◽  
Protein Coding ◽  
Rna Molecules ◽  
Sequencing Technologies ◽  
Spatiotemporal Regulation ◽  
The Central Nervous System ◽  
Health And Disease ◽  
Non Coding Rnas ◽  
Neuronal Maintenance ◽  
The Brain

Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.

scholarly journals RNAsamba: coding potential assessment using ORF and whole transcript sequence information

2019 ◽  
Author(s):  
Antonio P. Camargo ◽  
Vsevolod Sourkov ◽  
Marcelo F. Carazzolle
Keyword(s):  
High Throughput Sequencing ◽  
Model Organisms ◽  
Sequence Information ◽  
Protein Coding ◽  
Rna Molecules ◽  
Coding Regions ◽  
Sequencing Technologies ◽  
Partial Length ◽  
Non Coding Rnas ◽  
Coding Potential

AbstractMotivationThe advent of high-throughput sequencing technologies made it possible to obtain large volumes of genetic information, quickly and inexpensively. Thus, many efforts are devoted to unveil the biological roles of genomic elements, being one of the main tasks the identification of protein-coding and long non-coding RNAs.ResultsWe describe RNAsamba, a tool to predict the coding potential of RNA molecules from sequence information using a deep-learning model that processes both the whole sequence and the ORF to look for patterns that distinguish coding and non-coding RNAs. We evaluated the model in the classification of coding and non-coding transcripts of humans and five other model organisms and show that RNAsamba mostly outperforms other state-of-the-art methods. We also show that RNAsamba can identify coding signals in partial-length ORFs and UTR sequences, evidencing that its model is not dependent on the presence of complete coding regions. RNAsamba is a fast and easy tool that can provide valuable contributions to genome annotation pipelines.Availability and implementationThe source code of RNAsamba is freely available at:https://github.com/apcamargo/RNAsamba.

scholarly journals Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Garima Bhatia ◽  
Santosh K. Upadhyay ◽  
Anuradha Upadhyay ◽  
Kashmir Singh
Keyword(s):  
Downy Mildew ◽  
Plasmopara Viticola ◽  
Defense Responses ◽  
Protein Coding ◽  
Functional Roles ◽  
Real Time Quantitative Pcr ◽  
Transcriptional Reprogramming ◽  
Sequencing Technologies ◽  
Non Coding Rnas ◽  
Fungal Phytopathogens

Abstract Background Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide. Results Using computational approach based on RNA-seq data, 71 PM- and 83 DM-responsive V. vinifera lncRNAs were identified and comprehensively examined for their putative functional roles in plant defense response. V. vinifera protein coding sequences (CDS) were also profiled based on expression levels, and 1037 PM-responsive and 670 DM-responsive CDS were identified. Next, co-expression analysis-based functional annotation revealed their association with gene ontology (GO) terms for ‘response to stress’, ‘response to biotic stimulus’, ‘immune system process’, etc. Further investigation based on analysis of domains, enzyme classification, pathways enrichment, transcription factors (TFs), interactions with microRNAs (miRNAs), and real-time quantitative PCR of lncRNAs and co-expressing CDS pairs suggested their involvement in modulation of basal and specific defense responses such as: Ca2+-dependent signaling, cell wall reinforcement, reactive oxygen species metabolism, pathogenesis related proteins accumulation, phytohormonal signal transduction, and secondary metabolism. Conclusions Overall, the identified lncRNAs provide insights into the underlying intricacy of grapevine transcriptional reprogramming/post-transcriptional regulation to delay or seize the living cell-dependent pathogen growth. Therefore, in addition to defense-responsive genes such as TFs, the identified lncRNAs can be further examined and leveraged to candidates for biotechnological improvement/breeding to enhance fungal stress resistance in this susceptible fruit crop of economic and nutritional importance.

scholarly journals Functions and Roles of Long-Non-Coding RNAs in Human Nasopharyngeal Carcinoma

2018 ◽  
Vol 45 (3) ◽  
pp. 1191-1204 ◽  
Author(s):  
JingJing Wu ◽  
Swei Sunny Hann
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Functional Characterization ◽  
Clinical Information ◽  
Stem Cell Differentiation ◽  
Cancer Prognosis ◽  
Protein Coding ◽  
Rna Molecules ◽  
Gene Therapies ◽  
Non Coding Rnas

Nasopharyngeal carcinoma (NPC) is one of the most common cancers originating in the nasopharynx and occurring at high frequency in South-eastern Asia and North Africa. Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules and key regulators of developmental, physiological, and pathological processes in humans. Emerging studies have shown that lncRNAs play critical roles in tumorgenicity and cancer prognosis. With the development of deep sequencing analyses, an extensive amount of functional lncRNAs have been discovered in nasopharyngeal carcinoma tissues and cell lines. However, the roles and mechanisms of aberrantly expressed lncRNAs in the pathogenesis of NPC are not fully understood. In this review, we briefly illustrate the concept, identification, functional characterization, and summarize recent advancements of biological functions of lncRNAs with heterogeneous mechanistic characterization and their involvement in NPC. Then, we describe individual lncRNAs that have been associated with tumorgenesis, growth, invasion, cancer stem cell differentiation, metastasis, drug resistance and discuss the strategies of their therapeutic manipulation in NPC. We also review the emerging insights into the role of lncRNAs and their potential as biomarkers and therapeutic targets for novel treatment paradigms. Finally, we highlight the up-to-date of clinical information involving lncRNAs and future directions in the linking lncRNAs to potential gene therapies, and how modifications of lncRNAs can be exploited for prevention and treatment of NPC.

scholarly journals Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

2020 ◽  
Vol 21 (10) ◽  
pp. 3711
Author(s):  
Melina J. Sedano ◽  
Alana L. Harrison ◽  
Mina Zilaie ◽  
Chandrima Das ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Biological Significance ◽  
Rna Seq ◽  
Biological Functions ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

scholarly journals Characterization and identification of long non-coding RNAs based on feature relationship

2018 ◽  
Author(s):  
Guangyu Wang ◽  
Hongyan Yin ◽  
Boyang Li ◽  
Chunlei Yu ◽  
Fan Wang ◽  
...  
Keyword(s):  
Prior Knowledge ◽  
Large Scale ◽  
Gc Content ◽  
Training Data ◽  
Significant Advance ◽  
Protein Coding ◽  
Reading Frame ◽  
Wide Range ◽  
Non Coding Rnas ◽  
Computational Identification

ABSTRACTThe significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations. Here we first characterize lncRNAs by contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between ORF (open reading frame) length and GC content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.

scholarly journals Non-coding RNAs: emerging players in cardiomyocyte proliferation and cardiac regeneration

2020 ◽  
Vol 115 (5) ◽  
Author(s):  
Naisam Abbas ◽  
Filippo Perbellini ◽  
Thomas Thum
Keyword(s):  
Cell Cycle ◽  
Molecular Mechanisms ◽  
Contractile Function ◽  
Cardiac Regeneration ◽  
Therapeutic Interventions ◽  
Circular Rnas ◽  
Cardiomyocyte Proliferation ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rnas

Abstract Soon after birth, the regenerative capacity of the mammalian heart is lost, cardiomyocytes withdraw from the cell cycle and demonstrate a minimal proliferation rate. Despite improved treatment and reperfusion strategies, the uncompensated cardiomyocyte loss during injury and disease results in cardiac remodeling and subsequent heart failure. The promising field of regenerative medicine aims to restore both the structure and function of damaged tissue through modulation of cellular processes and regulatory mechanisms involved in cardiac cell cycle arrest to boost cardiomyocyte proliferation. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) are functional RNA molecules with no protein-coding function that have been reported to engage in cardiac regeneration and repair. In this review, we summarize the current understanding of both the biological functions and molecular mechanisms of ncRNAs involved in cardiomyocyte proliferation. Furthermore, we discuss their impact on the structure and contractile function of the heart in health and disease and their application for therapeutic interventions.

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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fatemeh Salabi ◽  
Hedieh Jafari ◽  
Shahrokh Navidpour ◽  
Ayeh Sadat Sadr
Keyword(s):  
Gc Content ◽  
Sequencing Data ◽  
Closely Related Species ◽  
Protein Coding ◽  
Model Animal ◽  
Lower Protein ◽  
Non Coding Rnas ◽  
Reference Genomes ◽  
Per Gene

AbstractThe potential function of long non-coding RNAs in regulating neighbor protein-coding genes has attracted scientists’ attention. Despite the important role of lncRNAs in biological processes, a limited number of studies focus on non-model animal lncRNAs. In this study, we used a stringent step-by-step filtering pipeline and machine learning-based tools to identify the specific Androctonus crassicauda lncRNAs and analyze the features of predicted scorpion lncRNAs. 13,401 lncRNAs were detected using pipeline in A. crassicauda transcriptome. The blast results indicated that the majority of these lncRNAs sequences (12,642) have no identifiable orthologs even in closely related species and those considered as novel lncRNAs. Compared to lncRNA prediction tools indicated that our pipeline is a helpful approach to distinguish protein-coding and non-coding transcripts from RNA sequencing data of species without reference genomes. Moreover, analyzing lncRNA characteristics in A. crassicauda uncovered that lower protein-coding potential, lower GC content, shorter transcript length, and less number of isoform per gene are outstanding features of A. crassicauda lncRNAs transcripts.

scholarly journals LncRNAs in domesticated animals: from dog to livestock species

2021 ◽  
Author(s):  
Sandrine Lagarrigue ◽  
Matthias Lorthiois ◽  
Fabien Degalez ◽  
David Gilot ◽  
Thomas Derrien
Keyword(s):  
Current Knowledge ◽  
Domestic Animals ◽  
Genetic Studies ◽  
Protein Coding ◽  
Domesticated Animals ◽  
Case Examples ◽  
Rna Molecules ◽  
Livestock Species ◽  
Functional Characterisation ◽  
Non Coding Rnas

AbstractAnimal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

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