Function of Circular RNAs in Fish and Their Potential Application as Biomarkers (original) (raw)
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A genome-wide map of circular RNAs in adult zebrafish
Scientific Reports
Circular RNAs (circRNAs) are transcript isoforms generated by back-splicing of exons and circularisation of the transcript. Recent genome-wide maps created for circular RNAs in humans and other model organisms have motivated us to explore the repertoire of circular RNAs in zebrafish, a popular model organism. We generated RNA-seq data for five major zebrafish tissues-Blood, Brain, Heart, Gills and Muscle. The repertoire RNA sequence reads left over after reference mapping to linear transcripts were used to identify unique back-spliced exons utilizing a split-mapping algorithm. Our analysis revealed 3,428 novel circRNAs in zebrafish. Further in-depth analysis suggested that majority of the circRNAs were derived from previously well-annotated protein-coding and long noncoding RNA gene loci. In addition, many of the circular RNAs showed extensive tissue specificity. We independently validated a subset of circRNAs using polymerase chain reaction (PCR) and divergent set of primers. Expression analysis using quantitative real time PCR recapitulate selected tissue specificity in the candidates studied. This study provides a comprehensive genome-wide map of circular RNAs in zebrafish tissues.
Reviews in Fish Biology and Fisheries, 2016
Current progress in high-throughput sequencing has opened up avenues to produce massive quantities of sequencing data from non-model fishes at an affordable cost. Thus, data analysis is also evolving at a rapid pace because of cutting edge computational tools. With the development and availability of experimental technologies and computational approaches, the field of MicroRNA (miRNA) biology has advanced over the last decade. MicroRNAs can play an important role in gene modulation via posttranscriptional gene regulation during acclimation and adaptation, in case of adverse conditions or climate change for example. These are useful and substantial contributors to regulatory networks of development and adaptive plasticity in fishes. Next generation sequencing technologies have extensively been used for solving biological questions in non-model fishes, where data pertaining to genome or transcriptome are either scant or totally unavailable. The data generated through this process have been used for gene discovery, variant identification, marker discovery and miRNA identification. Here, we discuss the role of miRNA in gene regulation pertaining to fish and its investigation via sequencing platforms, as well as the current use of computational algorithms for miRNA analysis. The purpose of this review is to examine the use of miRNA in aquaculture and further to investigate new technologies and advanced computational tools. However, our review also emphasizes existing challenges for miRNA investigations carried out via highthroughput sequencing and the growing demand for computationally intensive analysis software. This work along with assembled information on the known miRNAs in fish species will be useful while undertaking future studies for understanding the role of miRNAs.
Long noncoding RNAs (lncRNAs) have been recognized in recent years as key regulators of diverse cellular processes. Genome-wide large-scale projects have uncovered thousands of lncRNAs in many model organisms. Large intergenic noncoding RNAs (lincRNAs) are lncRNAs that are transcribed from intergenic regions of genomes. To date, no lincRNAs in non-model teleost fish have been reported. In this report, we present the first reference catalog of 9674 rainbow trout lincRNAs based on analysis of RNA-Seq data from 15 tissues. Systematic analysis revealed that lincRNAs in rainbow trout share many characteristics with those in other mammalian species. They are shorter and lower in exon number and expression level compared with protein-coding genes. They show tissue-specific expression pattern and are typically co-expressed with their neighboring genes. Co-expression network analysis suggested that many lincRNAs are associated with immune response, muscle differentiation, and neural development. The study provides an opportunity for future experimental and computational studies to uncover the functions of lincRNAs in rainbow trout.
Scientific reports, 2018
Muscle yield and quality traits are important for the aquaculture industry and consumers. Genetic selection for these traits is difficult because they are polygenic and result from multifactorial interactions. To study the genetic architecture of these traits, phenotypic characterization of whole body weight (WBW), muscle yield, fat content, shear force and whiteness were measured in ~500 fish representing 98 families from a growth-selected line. RNA-Seq was used to sequence the muscle transcriptome of different families exhibiting divergent phenotypes for each trait. We have identified 240 and 1,280 differentially expressed (DE) protein-coding genes and long noncoding RNAs (lncRNAs), respectively, in fish families exhibiting contrasting phenotypes. Expression of many DE lncRNAs (n = 229) was positively correlated with overlapping, neighboring or distantly located protein-coding genes (n = 1,030), resulting in 3,392 interactions. Three DE antisense lncRNAs were co-expressed with sen...
A MicroRNA Repertoire for Functional Genome Research in Rainbow Trout ( Oncorhynchus mykiss
Marine Biotechnology, 2010
MicroRNAs (miRNAs) are small, highly conserved, non-coding RNAs that regulate gene expression of target mRNAs through cleavage or translational inhibition. miRNAs are most often identified through computational prediction from genome sequences. The rainbow trout genome sequence is not available yet, which does not allow miRNA prediction for this species which is of great economic interest for aquaculture and sport fisheries, and is a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. To identify miRNAs from rainbow trout, we constructed a miRNA library from a pool of nine somatic tissues. Analysis of the library identified 210 unique sequences representing 54 distinct miRNAs; 50 with conserved sequences matching previously identified miRNAs and four novel miRNAs. In addition, 13 miRNAs were computationally predicted from the rainbow trout transcriptome. Real-time PCR was used to measure miRNA expression patterns in adult somatic tissues and unfertilized eggs. The majority of the miRNAs showed characteristic tissue-specific expression patterns suggesting potential roles in maintaining tissue identity. Potential miRNA-target interactions were computationally predicted and single nucleotide polymorphisms (SNPs) were identified in the miRNAs and their target sites in the rainbow trout transcripts. The rainbow trout miRNAs identified and characterized in this study provide a new tool for functional genome research in salmonids. Tissue-specific miRNAs may serve as molecular markers, predictive of specific functional and diagnostic implications. The data on genetic polymorphisms in miRNA-target interactions is particularly useful for rainbow trout breeding programs.
Identification and characterization of circular RNAs in zebrafish
FEBS Letters, 2016
Circular RNAs (circRNAs) play critical roles in signal transduction during cell proliferation, differentiation, and apoptosis in a posttranscriptional manner. Recently, circRNAs have been proved to be a large class of animal RNAs with regulatory potency. However, whether circRNAs can respond to mechanical force (MF) and impact on human periodontal ligament stem cells (PDLSCs) and the orthodontic tooth movement (OTM) process remain unknown. Here, we investigated the circRNAs expression patterns in PDLSCs induced by MF and found that circRNAs were responsive to the MF in PDLSCs. Through the valid reads' distribution analysis, we found that the majority of reads in both the control PDLSCs and the MF-induced PDLSCs were distributed in exons. Then we analyzed Gene Ontology terms of genes that overlap with or are neighbors of the stress-responsive circRNAs and found unique enrichment patterns in biological processes, molecular function, and cellular component of PDLSCs. Next, we predicted the possible functions of circRNAs through circRNAs-miRNAs networks. We found that one circRNA may regulate one or several miRNA/miRNAs and one miRNA may interact with one or multiple circRNA/circRNAs. Importantly, a number of circRNAs were predicted to directly or indirectly regulate miRNAs-mediated osteogenic differentiation in mesenchymal stem cells. For instance, circRNA3140 was highly and widely associated with microRNA-21, which plays a critical role in MF-induced osteogenic differentiation of PDLSCs. Taken together, these findings reveal a previously unrecognized mechanism that MF can induce the expression changes of circRNAs in PDLSCs, which may modulate the OTM process and the alveolar bone remodeling.
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2019
Fish respond to increasing stocking density as a stressor, adjusting physiological functions to increase energy supply for coping with deleterious effects and adapting. These responses are complex and systemic, and the molecular mechanisms involved remain undetermined. One of the most sensitive organs to environmental and homeostatic disruptions is the intestine, and since it plays several vital functions, understanding the molecular underpinnings of this organ under deleterious conditions is imperative for health improvement in aquaculture systems. This study aimed to understand how different stocking densities of rainbow trout (Oncorhynchus mykiss) modulates the coding and non-coding RNAs profiling, that in turn, play key roles to maintain the fish homeostasis. For this, the intestine tissue of juvenile trout stocked for 30 days either at low (LD: 3 kg m −3) or high density (HD: 40 kg m −3) were sampled to isolate total RNA and then construct cDNA libraries for an illumina sequencing platform. Differential gene expression analysis revealed a generalized downregulation of transcripts, including coding and long non-coding RNAs (lncRNAs). Notably, significant differences in transcripts involved in metabolic pathways, as well as immune and epithelium integrity and stability related pathways were found. A high number of downregulated transcripts enriched these pathways, and a strong correlation was observed between the most differentially expressed transcripts and the highly expressed lncRNAs. This study suggests a cross-talk between coding and non-coding RNAs in the intestine of fish exposed to suboptimal conditions, providing new insights into the regulatory role of the lncRNAs on fish response to stressors.
Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire
PLoS ONE, 2013
Atlantic salmon (Salmo salar L.), a member of the family Salmonidae, is a totemic species of ecological and cultural significance that is also economically important in terms of both sports fisheries and aquaculture. These factors have promoted the continuous development of genomic resources for this species, furthering both fundamental and applied research. MicroRNAs (miRNA) are small endogenous non-coding RNA molecules that control spatial and temporal expression of targeted genes through post-transcriptional regulation. While miRNA have been characterised in detail for many other species, this is not yet the case for Atlantic salmon. To identify miRNAs from Atlantic salmon, we constructed whole fish miRNA libraries for 18 individual juveniles (fry, four months post hatch) and characterised them by Illumina high-throughput sequencing (total of 354,505,167 paired-ended reads). We report an extensive and partly novel repertoire of miRNA sequences, comprising 888 miRNA genes (547 unique mature miRNA sequences), quantify their expression levels in basal conditions, examine their homology to miRNAs from other species and identify their predicted target genes. We also identify the location and putative copy number of the miRNA genes in the draft Atlantic salmon reference genome sequence. The Atlantic salmon miRNAs experimentally identified in this study provide a robust large-scale resource for functional genome research in salmonids. There is an opportunity to explore the evolution of salmonid miRNAs following the relatively recent whole genome duplication event in salmonid species and to investigate the role of miRNAs in the regulation of gene expression in particular their contribution to variation in economically and ecologically important traits.
Scientific Reports, 2016
Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with high mortalities in salmonid aquaculture. Using next-generation sequencing, whole-transcriptome analysis of the Salmo salar response to ISAV infection was performed, identifying 5,636 putative lncRNAs with a mean length of 695 base pairs. The transcriptional modulation evidenced a similar number of differentially expressed lncRNAs in the gills (3,294), head-kidney (3,275), and liver (3,325) over the course of the infection. Moreover, analysis of a subset of these lncRNAs showed the following: (i) Most were similarly regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection. Large-scale transcriptomic studies have led to surprising discoveries, including that <10% of the mammalian genome is dedicated to protein coding and that the genome contains a vast amount of non-protein coding transcripts, which has resulted in debate about the role of non-coding RNAs (ncRNAs) in cell biology 1,2. In contrast to protein coding genes, it is possible that the non-coding portion of the genome is related to organism complexity and crucial regulatory processes 3,4. Traditionally, the regulatory functions of RNA were thought limited to roles as ribosomal, messenger, and transfer RNAs. However, ncRNAs have been classified as housekeeping RNAs, microRNAs, small interfering RNAs, PIWI-interacting RNAs, small ncRNAs (< 200 nucleotides [nt] in length), and long ncRNAs (lncRNAs, > 200 nt in length) 5. Specifically, lncRNAs are endogenous cellular RNAs that are mRNA-like in length but with an absent or reduced coding potential (open reading frames (ORF) > 30 amino acids). These RNAs include tens of thousands of polyadenylated and non-polyadenylated lncRNAs that are anti-sense, intronic, intergenic, and that overlap with protein coding loci 5. Once thought to be transcriptional noise, lncRNAs have been shown to regulate a variety of biological processes. While the complex paradigm of RNA-based gene regulation is slowly being revealed, there is a growing body of evidence for a central role of lncRNAs in controlling gene regulation 6,7. A recent review estimated that the total number of lncRNAs is likely ~20,000 transcripts, but, to date, only ~200 lncRNAs have been characterized 8 .
BMC Developmental Biology, 2008
Background Current literature and our previous results on expression patterns of oocyte-specific genes and transcription factors suggest a global but highly regulated maternal mRNA degradation at the time of embryonic genome activation (EGA). MicroRNAs (miRNAs) are small, non-coding regulatory RNAs (19–23 nucleotides) that regulate gene expression by guiding target mRNA cleavage or translational inhibition. These regulatory RNAs are potentially involved in the degradation of maternally inherited mRNAs during early embryogenesis. Results To identify miRNAs that might be important for early embryogenesis in rainbow trout, we constructed a miRNA library from a pool of unfertilized eggs and early stage embryos. Sequence analysis of random clones from the library identified 14 miRNAs, 4 of which are novel to rainbow trout. Real-time PCR was used to measure the expression of all cloned miRNAs during embryonic development. Four distinct expression patterns were observed and some miRNAs sho...