1
|
Amaro F, González D, Gutiérrez JC. MicroRNAs in Tetrahymena thermophila: An epigenetic regulatory mechanism in the response to cadmium stress. Microbiol Res 2024; 280:127565. [PMID: 38160574 DOI: 10.1016/j.micres.2023.127565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
Among the epigenetic mechanisms based on non-coding RNA are microRNAs (miRNAs) that are involved in the post-transcriptional regulation of mRNAs. In many organisms, the expression of genes involved in the cellular response to biotic or abiotic stress depends on the regulation, generally inhibitory, performed by miRNAs. For the first time in the eukaryotic microorganism (ciliate-model) Tetrahymena thermophila, miRNAs involved in the post-transcriptional regulation of transcripts linked to the response to cadmium have been isolated and analyzed. Forty de novo miRNAs (we named tte-miRNAs) have been isolated from control and Cd-treated populations (1 or 24 h exposures). An exhaustive comparative analysis of the features of these mature tte-miRNAs and their precursor sequences (pre-tte-miRNAs) confirms that they are true miRNAs. In addition to the three types of miRNA isoforms previously described in other organisms, two new types are also described among the tte-miRNAs studied. A certain percentage of the pre-tte-miRNA sequences are in introns from genes with many introns, and have been defined as 5', 3'-tailed mirtrons. A qRT-PCR analysis of selected tte-miRNAs together with some of their targets has validated them. Cd is one of the most toxic metals for the cell, which must defend itself against its toxicity by various mechanisms, such as expulsion by membrane pumps, chelation by metallothioneins, among others. Like other toxic metals, Cd also causes a well-known series of cellular effects such as intense proteotoxicity. Many of the targets that are regulated by the tte-miRNAs are transcripts encoding proteins that fit into these defense mechanisms and toxic metal effects.
Collapse
Affiliation(s)
- Francisco Amaro
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain
| | - David González
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain
| | - Juan-Carlos Gutiérrez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain.
| |
Collapse
|
2
|
Antunes J, Salcedo-Jiménez R, Lively S, Potla P, Coté N, Dubois MS, Koenig J, Kapoor M, LaMarre J, Koch TG. microRNAs are differentially expressed in equine plasma of horses with osteoarthritis and osteochondritis dissecans versus control horses. PLoS One 2024; 19:e0297303. [PMID: 38394252 PMCID: PMC10890772 DOI: 10.1371/journal.pone.0297303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
Osteoarthritis (OA) is a leading cause of lameness in horses with no effective disease-modifying treatment and challenging early diagnosis. OA is considered a disease of the joint involving the articular cartilage, subchondral bone, synovial membrane, and ligaments. Osteochondritis dissecans (OCD) is a joint disease consisting of focal defects in the osteochondral unit which may progress to OA later in life. MicroRNAs (miRNAs) have been recognized as small non-coding RNAs that regulate a variety of biological processes and have been detected in biological fluids. MiRNAs are currently investigated for their utility as biomarkers and druggable targets for a variety of diseases. The current study hypothesizes that miRNA profiles can be used to actively monitor joint health and differences in miRNA profiles will be found in healthy vs diseased joints and that differences will be detectable in blood plasma of tested horses. Five horses with OA, OCD, and 4 controls (C) had blood plasma and synovial fluid collected. Total RNA, including miRNA was isolated before generating miRNA libraries from the plasma of the horses. Libraries were sequenced at the Schroeder Arthritis Institute (Toronto). Differential expression analysis was done using DESeq2 and validated using ddPCR. KEGG pathway analysis was done using mirPath v.3 (Diana Tools). 57 differentially expressed miRNAs were identified in OA vs C plasma, 45 differentially expressed miRNAs in OC vs C plasma, and 21 differentially expressed miRNAs in OA vs OCD plasma. Notably, miR-140-5p expression was observed to be elevated in OA synovial fluid suggesting that miR-140-5p may serve as a protective marker early on to attenuate OA progression. KEGG pathway analysis of differentially expressed plasma miRNAs showed relationships with glycan degradation, glycosaminoglycan degradation, and hippo signaling pathway. Interestingly, ddPCR was unable to validate the NGS data suggesting that isomiRs may play an integral role in miRNA expression when assessed using NGS technologies.
Collapse
Affiliation(s)
- Joshua Antunes
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Ramés Salcedo-Jiménez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Starlee Lively
- Osteoarthritis Research Program, Division of Orthopedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
| | - Pratibha Potla
- Osteoarthritis Research Program, Division of Orthopedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
| | - Nathalie Coté
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Marie-Soleil Dubois
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Judith Koenig
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Thomas Gadegaard Koch
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
3
|
Cui Y, Qi Y, Ding L, Ding S, Han Z, Wang Y, Du P. miRNA dosage control in development and human disease. Trends Cell Biol 2024; 34:31-47. [PMID: 37419737 DOI: 10.1016/j.tcb.2023.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 07/09/2023]
Abstract
In mammals, miRNAs recognize target mRNAs via base pairing, which leads to a complex 'multiple-to-multiple' regulatory network. Previous studies have focused on the regulatory mechanisms and functions of individual miRNAs, but alterations of many individual miRNAs do not strongly disturb the miRNA regulatory network. Recent studies revealed the important roles of global miRNA dosage control events in physiological processes and pathogenesis, suggesting that miRNAs can be considered as a 'cellular buffer' that controls cell fate. Here, we review the current state of research on how global miRNA dosage is tightly controlled to regulate development, tumorigenesis, neurophysiology, and immunity. We propose that methods of controlling global miRNA dosage may serve as effective therapeutic tools to cure human diseases.
Collapse
Affiliation(s)
- Yingzi Cui
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ye Qi
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Li Ding
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shuangjin Ding
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Zonglin Han
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China.
| | - Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| |
Collapse
|
4
|
Liu H, Ren N, Gao Y, Wu T, Sui B, Liu Z, Chang B, Huang M, Liu H. Sensitive detection of microRNA by dynamic light scattering based on DNAzyme walker-mediated AuNPs self-assembly. Dalton Trans 2023; 52:17340-17348. [PMID: 37937720 DOI: 10.1039/d3dt02450d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
As an important biomarker, microRNAs (miRNAs) play an important role in gene expression, and their detection has attracted increasing attention. In this study, a DNAzyme walker that could provide power to perform autonomous movement was designed. Based on the continuous mechanical motion characteristics of DNAzyme walker, a miRNA detection strategy for the self-assembly of AuNPs induced by the hairpin probe-guided DNAzyme walker "enzyme cleavage and walk" was established. In this strategy, DNAzyme walker continuously cleaved and walked on the hairpin probe on the surface of AuNPs to induce the continuous shedding of some segments of the hairpin probe. The remaining hairpin sequences on the surface of the AuNP pair with each other, causing the nanoparticles to self-assemble. This strategy uses the autonomous movement mechanism of DNAzyme walker to improve reaction efficiency and avoid the problem of using expensive and easily degradable proteases. Secondly, using dynamic light scattering technology as the signal output system, ultra-sensitive detection with a detection limit of 3.6 fM is achieved. In addition, this strategy has been successfully used to analyze target miRNAs in cancer cell samples.
Collapse
Affiliation(s)
- Haiyun Liu
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
| | - Na Ren
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
| | - Yi Gao
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
| | - Tingfan Wu
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
| | - Boren Sui
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
| | - Zhen Liu
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
| | - Bin Chang
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
| | - Man Huang
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
| | - Hong Liu
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, P.R. China.
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, PR China
| |
Collapse
|
5
|
Adhikary R, Roy A, Jolly MK, Das D. Effects of microRNA-mediated negative feedback on gene expression noise. Biophys J 2023; 122:4220-4240. [PMID: 37803829 PMCID: PMC10645566 DOI: 10.1016/j.bpj.2023.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/19/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in eukaryotes by binding with target mRNAs and preventing translation. miRNA-mediated feedback motifs are ubiquitous in various genetic networks that control cellular decision making. A key question is how such a feedback mechanism may affect gene expression noise. To answer this, we have developed a mathematical model to study the effects of a miRNA-dependent negative-feedback loop on mean expression and noise in target mRNAs. Combining analytics and simulations, we show the existence of an expression threshold demarcating repressed and expressed regimes in agreement with earlier studies. The steady-state mRNA distributions are bimodal near the threshold, where copy numbers of mRNAs and miRNAs exhibit enhanced anticorrelated fluctuations. Moreover, variation of negative-feedback strength shifts the threshold locations and modulates the noise profiles. Notably, the miRNA-mRNA binding affinity and feedback strength collectively shape the bimodality. We also compare our model with a direct auto-repression motif, where a gene produces its own repressor. Auto-repression fails to produce bimodal mRNA distributions as found in miRNA-based indirect repression, suggesting the crucial role of miRNAs in creating phenotypic diversity. Together, we demonstrate how miRNA-dependent negative feedback modifies the expression threshold and leads to a broader parameter regime of bimodality compared to the no-feedback case.
Collapse
Affiliation(s)
- Raunak Adhikary
- Department of Biological Sciences, Indian Institute of Science Education And Research Kolkata Mohanpur, Nadia, West Bengal, India
| | - Arnab Roy
- Department of Biological Sciences, Indian Institute of Science Education And Research Kolkata Mohanpur, Nadia, West Bengal, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Dipjyoti Das
- Department of Biological Sciences, Indian Institute of Science Education And Research Kolkata Mohanpur, Nadia, West Bengal, India.
| |
Collapse
|
6
|
Orbán TI. One locus, several functional RNAs-emerging roles of the mechanisms responsible for the sequence variability of microRNAs. Biol Futur 2023:10.1007/s42977-023-00154-7. [PMID: 36847925 DOI: 10.1007/s42977-023-00154-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
With the development of modern molecular genetics, the original "one gene-one enzyme" hypothesis has been outdated. For protein coding genes, the discovery of alternative splicing and RNA editing provided the biochemical background for the RNA repertoire of a single locus, which also serves as an important pillar for the enormous protein variability of the genomes. Non-protein coding RNA genes were also revealed to produce several RNA species with distinct functions. The loci of microRNAs (miRNAs), encoding for small endogenous regulatory RNAs, were also found to produce a population of small RNAs, rather than a single defined product. This review aims to present the mechanisms contributing to the astonishing variability of miRNAs revealed by the new sequencing technologies. One important source is the careful balance of arm selection, producing sequentially different 5p- or 3p-miRNAs from the same pre-miRNA, thereby broadening the number of regulated target RNAs and the phenotypic response. In addition, the formation of 5', 3' and polymorphic isomiRs, with variable end and internal sequences also leads to a higher number of targeted sequences, and increases the regulatory output. These miRNA maturation processes, together with other known mechanisms such as RNA editing, further increase the potential outcome of this small RNA pathway. By discussing the subtle mechanisms behind the sequence diversity of miRNAs, this review intends to reveal this engaging aspect of the inherited "RNA world", how it contributes to the almost infinite molecular variability among living organisms, and how this variability can be exploited to treat human diseases.
Collapse
Affiliation(s)
- Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, Budapest, 1117, Hungary.
| |
Collapse
|
7
|
Target-Responsive Template Structure Switching-Mediated Exponential Rolling Circle Amplification for the Direct and Sensitive Detection of MicroRNA. BIOCHIP JOURNAL 2022. [DOI: 10.1007/s13206-022-00071-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
8
|
Ghorbani M, Mohamadynejad P, Moghanibashi M. Significant Association of rs77493513 Polymorphism in 3'-UTR of the NRG1 Gene with the Risk of Multiple Sclerosis Disease. Metab Brain Dis 2022; 37:1025-1030. [PMID: 35106689 DOI: 10.1007/s11011-022-00922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/27/2022] [Indexed: 10/19/2022]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory and autoimmune disease characterized by demyelination of the central nervous system (CNS). Neuregulin 1 (NRG1) is a signaling protein that plays an important role in a variety of biological processes, including potentiate oligodendrocyte differentiation and myelination in the CNS, immune response regulation, and inflammation. Single nucleotide polymorphism (SNP) rs77493513 is located in the untranslated region of the 3' mRNA (3'-UTR) of the NRG1 gene, which is predicted to be the binding site of several microRNAs and may play an important role in post-transcriptional regulation. Study aimed to investigate the association of SNP rs77493513 in the NRG1 gene with the risk of MS disease. In this study, genomic DNA was extracted from whole blood samples of 182 patients with relapsing-remitting multiple sclerosis (RRMS) and 198 controls. Different genotypes of rs77493513 polymorphism were determined using RFLP-PCR technique. Statistical analysis was performed using SPSS 21.0 software and by t, χ2 and logistic regression tests. Our data showed that genotypes AC (OR=3.63, CI= 1.93-6.81, p<0.001) and CC (OR=7.90, CI= 4.13-15.11, p<0.001) significantly increased the risk of MS disease and C allele is risk allele. Also, AC (OR=0.16, CI= 0.04-0.63, p= 0.009) and CC (OR=0.14, CI= 0.03-0.53, p=0.04) genotypes significantly decrease the age of onset of the disease. The results show that allele C of rs77493513 polymorphism in the NRG1 gene can be a risk factor for MS.
Collapse
Affiliation(s)
- Maedeh Ghorbani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Parisa Mohamadynejad
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mehdi Moghanibashi
- Department of Genetics, School of Medicine, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| |
Collapse
|
9
|
Rational design of hairpin RNA excited states reveals multi-step transitions. Nat Commun 2022; 13:1523. [PMID: 35314698 PMCID: PMC8938425 DOI: 10.1038/s41467-022-29194-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 02/01/2022] [Indexed: 11/25/2022] Open
Abstract
RNA excited states represent a class of high-energy-level and thus low-populated conformational states of RNAs that are sequestered within the free energy landscape until being activated by cellular cues. In recent years, there has been growing interest in structural and functional studies of these transient states, but the rational design of excited states remains unexplored. Here we developed a method to design small hairpin RNAs with predefined excited states that exchange with ground states through base pair reshuffling, and verified these transient states by combining NMR relaxation dispersion technique and imino chemical shift prediction. Using van’t Hoff analysis and accelerated molecular dynamics simulations, a mechanism of multi-step sequential transition has been revealed. The efforts made in this study will expand the scope of RNA rational design, and also contribute towards improved predictions of RNA secondary structure. RNA molecules exhibit conformational fluctuations between ground states and excited states. Here the authors designed and verified small hairpin RNAs with predefined secondary structure reshufflings. In light of Van’t Hoff analysis and accelerated molecular dynamics simulation, a mechanism of multistep sequential transition has been revealed.
Collapse
|
10
|
Santovito D, Weber C. Non-canonical features of microRNAs: paradigms emerging from cardiovascular disease. Nat Rev Cardiol 2022; 19:620-638. [PMID: 35304600 DOI: 10.1038/s41569-022-00680-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
Research showing that microRNAs (miRNAs) are versatile regulators of gene expression has instigated tremendous interest in cardiovascular research. The overwhelming majority of studies are predicated on the dogmatic notion that miRNAs regulate the expression of specific target mRNAs by inhibiting mRNA translation or promoting mRNA decay in the RNA-induced silencing complex (RISC). These efforts mostly identified and dissected contributions of multiple regulatory networks of miRNA-target mRNAs to cardiovascular pathogenesis. However, evidence from studies in the past decade indicates that miRNAs also operate beyond this canonical paradigm, featuring non-conventional regulatory functions and cellular localizations that have a pathophysiological role in cardiovascular disease. In this Review, we highlight the functional relevance of atypical miRNA biogenesis and localization as well as RISC heterogeneity. Moreover, we delineate remarkable non-canonical examples of miRNA functionality, including direct interactions with proteins beyond the Argonaute family and their role in transcriptional regulation in the nucleus and in mitochondria. We scrutinize the relevance of non-conventional biogenesis and non-canonical functions of miRNAs in cardiovascular homeostasis and pathology, and contextualize how uncovering these non-conventional properties can expand the scope of translational research in the cardiovascular field and beyond.
Collapse
Affiliation(s)
- Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| |
Collapse
|
11
|
Alsop E, Meechoovet B, Kitchen R, Sweeney T, Beach TG, Serrano GE, Hutchins E, Ghiran I, Reiman R, Syring M, Hsieh M, Courtright-Lim A, Valkov N, Whitsett TG, Rakela J, Pockros P, Rozowsky J, Gallego J, Huentelman MJ, Shah R, Nakaji P, Kalani MYS, Laurent L, Das S, Van Keuren-Jensen K. A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids. Front Cell Dev Biol 2022; 10:804164. [PMID: 35317387 PMCID: PMC8934391 DOI: 10.3389/fcell.2022.804164] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/28/2022] [Indexed: 12/20/2022] Open
Abstract
One promising goal for utilizing the molecular information circulating in biofluids is the discovery of clinically useful biomarkers. Extracellular RNAs (exRNAs) are one of the most diverse classes of molecular cargo, easily assayed by sequencing and with expressions that rapidly change in response to subject status. Despite diverse exRNA cargo, most evaluations from biofluids have focused on small RNA sequencing and analysis, specifically on microRNAs (miRNAs). Another goal of characterizing circulating molecular information, is to correlate expression to injuries associated with specific tissues of origin. Biomarker candidates are often described as being specific, enriched in a particular tissue or associated with a disease process. Likewise, miRNA data is often reported to be specific, enriched for a tissue, without rigorous testing to support the claim. Here we provide a tissue atlas of small RNAs from 30 different tissues and three different blood cell types. We analyzed the tissues for enrichment of small RNA sequences and assessed their expression in biofluids: plasma, cerebrospinal fluid, urine, and saliva. We employed published data sets representing physiological (resting vs. acute exercise) and pathologic states (early- vs. late-stage liver fibrosis, and differential subtypes of stroke) to determine differential tissue-enriched small RNAs. We also developed an online tool that provides information about exRNA sequences found in different biofluids and tissues. The data can be used to better understand the various types of small RNA sequences in different tissues as well as their potential release into biofluids, which should help in the validation or design of biomarker studies.
Collapse
Affiliation(s)
- Eric Alsop
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Bessie Meechoovet
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Robert Kitchen
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Thadryan Sweeney
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Geidy E. Serrano
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Elizabeth Hutchins
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ionita Ghiran
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
| | - Rebecca Reiman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Michael Syring
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Michael Hsieh
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Amanda Courtright-Lim
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Nedyalka Valkov
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Timothy G. Whitsett
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | | | - Paul Pockros
- Division of Gastroenterology/Hepatology, Scripps Clinic, La Jolla, CA, United States
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Juan Gallego
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, NY, United States
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, United States
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
| | - Matthew J. Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ravi Shah
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Peter Nakaji
- Department of Neurosurgery, Banner Health, Phoenix, AZ, United States
| | - M. Yashar S. Kalani
- Department of Neurosurgery, St. John Medical Center, Tulsa, OK, United States
| | - Louise Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, San Diego, CA, United States
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | | |
Collapse
|
12
|
A comparative analysis of single cell small RNA sequencing data reveals heterogeneous isomiR expression and regulation. Sci Rep 2022; 12:2834. [PMID: 35181712 PMCID: PMC8857176 DOI: 10.1038/s41598-022-06876-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs which play a critical role in the regulation of gene expression in cells. It is known that miRNAs are often expressed as multiple isoforms, called isomiRs, which may have alternative regulatory functions. Despite the recent development of several single cell small RNA sequencing protocols, these methods have not been leveraged to investigate isomiR expression and regulation to better understand their role on a single cell level. Here we integrate sequencing data from three independent studies and find substantial differences in isomiR composition that suggest that cell autonomous mechanisms may drive isomiR processing. We also find evidence of altered regulatory functions of different classes of isomiRs, when compared to their respective wild-type miRNA, which supports a biological role for many of the isomiRs that are expressed.
Collapse
|
13
|
Relevance of miR-223 as Potential Diagnostic and Prognostic Markers in Cancer. BIOLOGY 2022; 11:biology11020249. [PMID: 35205115 PMCID: PMC8869096 DOI: 10.3390/biology11020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
In 1993, the discovery of microRNAs in Caenorhabditis elegans (C. elegans) altered the paradigmatic view of RNA biology and post-transcriptional gene regulation. Further study revealed the role of microRNAs in disease development and progression. In particular, this review highlights microRNA-223 (miR-223 or miRNA-223) expression in malignant neoplastic disorders. miR-223 expression controls aspects of hematopoiesis and apoptosis, and cell proliferation, migration, and invasion. miR-223 regulates a number of gene targets, including cytoplasmic activation/proliferation-associated protein-1 (Caprin-1), insulin-like growth factor-1 receptor (IGF-1R), and other cell proliferation- and cell cycle-associated genes. Several studies have proposed miR-223 as a novel biomarker for early cancer diagnosis. Here, we emphasize miR-223′s role in the development and progression of cancer.
Collapse
|
14
|
Schmauch E, Levonen AL, Linna-Kuosmanen S. Global MicroRNA Profiling of Vascular Endothelial Cells. Methods Mol Biol 2022; 2475:157-186. [PMID: 35451756 DOI: 10.1007/978-1-0716-2217-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
MicroRNA sequencing (miRNA-seq) enables the detection and characterization of the cell miRNome, including miRNA isoforms (isomiRs) and novel miRNA species. In roughly half of the cases, the most abundant isomiR in the cells is not the reference miRNA given in miRBase, which highlights the importance of isomiR-specific analysis. Here, we describe a gel-free protocol for global miRNA profiling in vascular endothelial cells and the main steps of the subsequent data analysis with two alternative analysis methods. In addition to endothelial cells, the protocol is suitable for other cell and tissue types and has been successfully used to obtain miRNA-seq data from human cardiac tissue, plasma, pericardial fluid, and biofluid exosomes.
Collapse
Affiliation(s)
- Eloi Schmauch
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna-Liisa Levonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Suvi Linna-Kuosmanen
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
15
|
Zhang X, Ping P, Hutvagner G, Blumenstein M, Li J. Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach. Nucleic Acids Res 2021; 49:e106. [PMID: 34291293 PMCID: PMC8631080 DOI: 10.1093/nar/gkab610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/21/2022] Open
Abstract
Raw sequencing reads of miRNAs contain machine-made substitution errors, or even insertions and deletions (indels). Although the error rate can be low at 0.1%, precise rectification of these errors is critically important because isoform variation analysis at single-base resolution such as novel isomiR discovery, editing events understanding, differential expression analysis, or tissue-specific isoform identification is very sensitive to base positions and copy counts of the reads. Existing error correction methods do not work for miRNA sequencing data attributed to miRNAs’ length and per-read-coverage properties distinct from DNA or mRNA sequencing reads. We present a novel lattice structure combining kmers, (k – 1)mers and (k + 1)mers to address this problem. The method is particularly effective for the correction of indel errors. Extensive tests on datasets having known ground truth of errors demonstrate that the method is able to remove almost all of the errors, without introducing any new error, to improve the data quality from every-50-reads containing one error to every-1300-reads containing one error. Studies on experimental miRNA sequencing datasets show that the errors are often rectified at the 5′ ends and the seed regions of the reads, and that there are remarkable changes after the correction in miRNA isoform abundance, volume of singleton reads, overall entropy, isomiR families, tissue-specific miRNAs, and rare-miRNA quantities.
Collapse
Affiliation(s)
- Xuan Zhang
- Data Science Institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Pengyao Ping
- Data Science Institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Michael Blumenstein
- Faculty of Engineering and IT, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Jinyan Li
- To whom correspondence should be addressed. Tel: +61 295149264; Fax: +61 295149264;
| |
Collapse
|
16
|
Role of SNPs in the Biogenesis of Mature miRNAs. BIOMED RESEARCH INTERNATIONAL 2021; 2021:2403418. [PMID: 34239922 PMCID: PMC8233088 DOI: 10.1155/2021/2403418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022]
Abstract
Single nucleotide polymorphisms (SNPs) play a significant role in microRNA (miRNA) generation, processing, and function and contribute to multiple phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect miRNA maturation mechanisms is important for precision medicine. The present study established an SNP-associated pre-miRNA (SNP-pre-miRNA) database, named miRSNPBase, and constructed SNP-pre-miRNA sequences. We also identified phenotypes and disease biomarker-associated isoform miRNA (isomiR) based on miRFind, which was developed in our previous study. We identified functional SNPs and isomiRs. We analyzed the biological characteristics of functional SNPs and isomiRs and studied their distribution in different ethnic groups using whole-genome analysis. Notably, we used individuals from Great Britain (GBR) as examples and identified isomiRs and isomiR-associated SNPs (iso-SNPs). We performed sequence alignments of isomiRs and miRNA sequencing data to verify the identified isomiRs and further revealed GBR ethnographic epigenetic dominant biomarkers. The SNP-pre-miRNA database consisted of 886 pre-miRNAs and 2640 SNPs. We analyzed the effects of SNP type, SNP location, and SNP-mediated free energy change during mature miRNA biogenesis and found that these factors were closely associated to mature miRNA biogenesis. Remarkably, 158 isomiRs were verified in the miRNA sequencing data for the 18 GBR samples. Our results indicated that SNPs affected the mature miRNA processing mechanism and contributed to the production of isomiRs. This mechanism may have important significance for epigenetic changes and diseases.
Collapse
|
17
|
Bryzgunova O, Konoshenko M, Zaporozhchenko I, Yakovlev A, Laktionov P. Isolation of Cell-Free miRNA from Biological Fluids: Influencing Factors and Methods. Diagnostics (Basel) 2021; 11:865. [PMID: 34064927 PMCID: PMC8151063 DOI: 10.3390/diagnostics11050865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
A vast wealth of recent research has seen attempts of using microRNA (miRNA) found in biological fluids in clinical research and medicine. One of the reasons behind this trend is the apparent their high stability of cell-free miRNA conferred by small size and packaging in supramolecular complexes. However, researchers in both basic and clinical settings often face the problem of selecting adequate methods to extract appropriate quality miRNA preparations for use in specific downstream analysis pipelines. This review outlines the variety of different methods of miRNA isolation from biofluids and examines the key determinants of their efficiency, including, but not limited to, the structural properties of miRNA and factors defining their stability in the extracellular environment.
Collapse
Affiliation(s)
- Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Ivan Zaporozhchenko
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Alexey Yakovlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| |
Collapse
|
18
|
Perdiguero P, Rodrigues AS, Chaves I, Costa B, Alves A, de María N, Vélez MD, Díaz-Sala C, Cervera MT, Miguel CM. Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability. PLANT, CELL & ENVIRONMENT 2021; 44:706-728. [PMID: 33314160 DOI: 10.1111/pce.13976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
An increasing number of microRNAs (miRNAs) and miRNA-related sequences produced during miRNA biogenesis, comprising the isomiRome, have been recently highlighted in different species as critical mediators of environmental stress responses. Conifers have some of the largest known genomes but an extensive characterization of the isomiRome from any conifer species has been lacking. We provide here a comprehensive overview of the Pinus pinaster isomiRome expressed in roots, stem and needles under well-watered and drought conditions. From the 13,441 unique small RNA sequences identified, 2,980 were annotated as canonical miRNAs or miRNA* and the remaining were classified as isomiRNA or miRNA-like sequences. A survey of their expression patterns highlighted roots as the most responsive organ under drought, where specific sequences of which a 24-nt novel miRNA stood out, were strongly down-regulated. Given the putative roles of the miRNA-targeted transcripts validated specifically in root tissues, some of the miRNAs, conserved and novel, are shortlisted as potential regulators of drought response. These results provide a valuable resource for comparative studies between gymnosperms and angiosperms. Furthermore, it evidences high transferability of the isomiRome between pine species being a useful basis for further molecular regulation and physiological studies, and especially those focused on adaptation to drought conditions.
Collapse
Affiliation(s)
- Pedro Perdiguero
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Centro de Investigación en Sanidad Animal (CISA-INIA), Madrid, Spain
| | - Andreia Santos Rodrigues
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês Chaves
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Bruno Costa
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Alves
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Nuria de María
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - María Dolores Vélez
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Carmen Díaz-Sala
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain
| | - María Teresa Cervera
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Célia Maria Miguel
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
19
|
Heydarzadeh S, Ranjbar M, Karimi F, Seif F, Alivand MR. Overview of host miRNA properties and their association with epigenetics, long non-coding RNAs, and Xeno-infectious factors. Cell Biosci 2021; 11:43. [PMID: 33632341 PMCID: PMC7905430 DOI: 10.1186/s13578-021-00552-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/06/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-derived structures play impressive roles in various biological processes. So dysregulation of miRNAs can lead to different human diseases. Recent studies have extended our comprehension of the control of miRNA function and features. Here, we overview some remarkable miRNA properties that have potential implications for the miRNA functions, including different variants of a miRNA called isomiRs, miRNA arm selection/arm switching, and the effect of these factors on miRNA target selection. Besides, we review some aspects of miRNA interactions such as the interaction between epigenetics and miRNA (different miRNAs and their related processing enzymes are epigenetically regulated by multiple DNA methylation enzymes. moreover, DNA methylation could be controlled by diverse mechanisms related to miRNAs), direct and indirect crosstalk between miRNA and lnc (Long Non-Coding) RNAs as a further approach to conduct intercellular regulation called "competing endogenous RNA" (ceRNA) that is involved in the pathogenesis of different diseases, and the interaction of miRNA activities and some Xeno-infectious (virus/bacteria/parasite) factors, which result in modulation of the pathogenesis of infections. This review provides some related studies to a better understanding of miRNA involvement mechanisms and overcoming the complexity of related diseases that may be applicable and useful to prognostic, diagnostic, therapeutic purposes and personalized medicine in the future.
Collapse
Affiliation(s)
- Samaneh Heydarzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Ranjbar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farokh Karimi
- Department of Biotechnology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Farhad Seif
- Department of Immunology and Allergy, Academic Center for Education, Culture, and Research (ACECR), Tehran, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
20
|
Pommier A, Varilh J, Bleuse S, Delétang K, Bonini J, Bergougnoux A, Brochiero E, Koenig M, Claustres M, Taulan-Cadars M. miRNA repertoires of cystic fibrosis ex vivo models highlight miR-181a and miR-101 that regulate WISP1 expression. J Pathol 2020; 253:186-197. [PMID: 33095908 DOI: 10.1002/path.5571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/24/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022]
Abstract
Cystic fibrosis (CF), a genetic disorder, is characterized by chronic lung disease. Small non-coding RNAs are key regulators of gene expression and participate in various processes, which are dysregulated in CF; however, they remain poorly studied. Here, we determined the complete microRNAs (miRNAs) expression pattern in three CF ex vivo models. The miRNA profiles of air-liquid interface cultures of airway epithelia (bronchi, nasal cells, and nasal polyps) samples from patients with CF and non-CF controls were obtained by deep sequencing. Compared with non-CF controls, several miRNAs were deregulated in CF samples; for instance, miR-181a-5p and the miR-449 family were upregulated. Moreover, mature miRNAs often showed variations (i.e. isomiRs) relative to their reference sequence, such as miR-101, suggesting that miRNAs consist of heterogeneous repertoires of multiple isoforms with different effects on gene expression. Analysis of miR-181a-5p and miR-101-3p roles indicated that they regulate the expression of WISP1, a key component of cell proliferation/migration programs. We showed that miR-101 and miR-181a-5p participated in aberrant recapitulation of wound healing programs by controlling WISP1 mRNA and protein level. Our miRNA expression data bring new insights into CF physiopathology and define new potential therapeutic targets in CF. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Alexandra Pommier
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France
| | - Jessica Varilh
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France
| | - Solenne Bleuse
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France
| | - Karine Delétang
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France
| | - Jennifer Bonini
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France
| | - Anne Bergougnoux
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France.,CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - Emmanuelle Brochiero
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Michel Koenig
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France.,CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - Mireille Claustres
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France
| | - Magali Taulan-Cadars
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares EA7402, Montpellier, France
| |
Collapse
|
21
|
Ishii H, Kaneko S, Yanai K, Aomatsu A, Hirai K, Ookawara S, Ishibashi K, Morishita Y. MicroRNAs in Podocyte Injury in Diabetic Nephropathy. Front Genet 2020; 11:993. [PMID: 33193581 PMCID: PMC7477342 DOI: 10.3389/fgene.2020.00993] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022] Open
Abstract
Diabetic nephropathy is one of the major complications of diabetes mellitus and is the leading cause of end-stage renal disease worldwide. Podocyte injury contributes to the development of diabetic nephropathy. However, the molecules that regulate podocyte injury in diabetic nephropathy have not been fully clarified. MicroRNAs (miRNAs) are small non-coding RNAs that can inhibit the translation of target messenger RNAs. Previous reports have described alteration of the expression levels of many miRNAs in cultured podocyte cells stimulated with a high glucose concentration and podocytes in rodent models of diabetic nephropathy. The associations between podocyte injury and miRNA expression levels in blood, urine, and kidney in patients with diabetic nephropathy have also been reported. Moreover, modulation of the expression of several miRNAs has been shown to have protective effects against podocyte injury in diabetic nephropathy in cultured podocyte cells in vitro and in rodent models of diabetic nephropathy in vivo. Therefore, this review focuses on miRNAs in podocyte injury in diabetic nephropathy, with regard to their potential as biomarkers and miRNA modulation as a therapeutic option.
Collapse
Affiliation(s)
- Hiroki Ishii
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Shohei Kaneko
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Katsunori Yanai
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Akinori Aomatsu
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Keiji Hirai
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Susumu Ookawara
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Kenichi Ishibashi
- Department of Medical Physiology, Meiji Pharmaceutical University, Kiyose, Japan
| | - Yoshiyuki Morishita
- Division of Nephrology, First Department of Integrated Medicine, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| |
Collapse
|
22
|
Koi Y, Tsutani Y, Nishiyama Y, Ueda D, Ibuki Y, Sasada S, Akita T, Masumoto N, Kadoya T, Yamamoto Y, Takahashi RU, Tanaka J, Okada M, Tahara H. Predicting the presence of breast cancer using circulating small RNAs, including those in the extracellular vesicles. Cancer Sci 2020; 111:2104-2115. [PMID: 32215990 PMCID: PMC7293081 DOI: 10.1111/cas.14393] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 12/26/2022] Open
Abstract
Emerging evidence indicates that small RNAs, including microRNAs (miRNAs) and their isoforms (isomiRs), and transfer RNA fragments (tRFs), are differently expressed in breast cancer (BC) and can be detected in blood circulation. Circulating small RNAs and small RNAs in extracellular vesicles (EVs) have emerged as ideal markers in small RNA‐based applications for cancer detection. In this study, we first undertook small RNA sequencing to assess the expression of circulating small RNAs in the serum of BC patients and cancer‐free individuals (controls). Expression of 3 small RNAs, namely isomiR of miR‐21‐5p (3′ addition C), miR‐23a‐3p and tRF‐Lys (TTT), was significantly higher in BC samples and was validated by small RNA sequencing in an independent cohort. Our constructed model using 3 small RNAs showed high diagnostic accuracy with an area under the receiver operating characteristic curve of 0.92 and discriminated early‐stage BCs at stage 0 from control. To test the possibility that these small RNAs are released from cancer cells, we next examined EVs from the serum of BC patients and controls. Two of the 3 candidate small RNAs were identified, and shown to be abundant in EVs of BC patients. Interestingly, these 2 small RNAs are also more abundantly detected in culture media of breast cancer cell lines (MCF‐7 and MDA‐MB‐231). The same tendency in selective elevation seen in total serum, serum EV, and EV derived from cell culture media could indicate the efficiency of this model using total serum of patients. These findings indicate that small RNAs serve as significant biomarkers for BC detection.
Collapse
Affiliation(s)
- Yumiko Koi
- Surgical Oncology, Division of Radiation Biology and Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yasuhiro Tsutani
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yukie Nishiyama
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Daisuke Ueda
- Surgical Oncology, Division of Radiation Biology and Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yuta Ibuki
- Surgical Oncology, Division of Radiation Biology and Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Shinsuke Sasada
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Tomoyuki Akita
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Norio Masumoto
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takayuki Kadoya
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yuki Yamamoto
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ryou-U Takahashi
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Junko Tanaka
- Department of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Center for Radiation Casualty Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Collaborative laboratory of Liquid Biopsy, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
23
|
Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
|
24
|
Zaporozhchenko IA, Rykova EY, Laktionov PP. The Fundamentals of miRNA Biology: Structure, Biogenesis, and Regulatory Functions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s106816202001015x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
25
|
Bjerke GA, Yi R. Integrated analysis of directly captured microRNA targets reveals the impact of microRNAs on mammalian transcriptome. RNA (NEW YORK, N.Y.) 2020; 26:306-323. [PMID: 31900330 PMCID: PMC7025510 DOI: 10.1261/rna.073635.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/27/2019] [Indexed: 05/16/2023]
Abstract
MicroRNA (miRNA)-mediated regulation is widespread, relatively mild but functionally important. It remains challenging to unequivocally identify miRNA targeted RNAs at a genomic scale and determine how changes in miRNA levels affect the transcriptome. Here, we captured individual miRNAs and their targeted RNA sites in wild-type, miR-200 family knockout and induced epithelial cells. We detected 1797 miRNAs interacting with 13,830 transcripts at 616,127 sites by sequencing 1,230,019 unique miRNA:RNA chimeras. Although mRNA sites that are bound by miRNAs and contain matches to seed sequences confer the strongest regulation, ∼40%-60% of miRNA bound regions do not contain seed matches. Different miRNAs have different preferences to seed matches and 3' end base-pairing. For individual miRNAs, the effectiveness of mRNA regulation is highly correlated with the number of captured miRNA:mRNA chimeras. Notably, elevated miR-200 expression robustly represses existing targets with little impact on newly recognized targets. Global analysis of directly captured mRNA targets reveals pathways that are involved in cancer and cell adhesion and signaling pathways that are highly regulated by many different miRNAs in epithelial cells. Comparison between experimentally captured and TargetScan predicted targets indicates that our approach is more effective in identifying bona fide targets by reducing false positive and negative predictions. This study reveals the global binding landscape and impact of miRNAs on the mammalian transcriptome.
Collapse
Affiliation(s)
- Glen A Bjerke
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Rui Yi
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
| |
Collapse
|
26
|
Ma M, Yin Z, Zhong H, Liang T, Guo L. Analysis of the expression, function, and evolution of miR-27 isoforms and their responses in metabolic processes. Genomics 2019; 111:1249-1257. [DOI: 10.1016/j.ygeno.2018.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 12/13/2022]
|
27
|
MicroRNAs in Daphnia magna identified and characterized by deep sequencing, genome mapping and manual curation. Sci Rep 2019; 9:15945. [PMID: 31685896 PMCID: PMC6828783 DOI: 10.1038/s41598-019-52387-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 10/11/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression in most organisms. The water flea, Daphnia magna is a key model to study phenotypic, physiological and genomic responses to environmental cues and miRNAs can potentially mediate these responses. By using deep sequencing, genome mapping and manual curations, we have characterised the miRNAome of D. magna. We identified 66 conserved miRNAs and 13 novel miRNAs; all of these were found in the three studied life stages of D. magna (juveniles, subadults, adults), but with variation in expression levels between stages. Forty-one of the miRNAs were clustered into 13 genome clusters also present in the D. pulex genome. Most miRNAs contained sequence variants (isomiRs). The highest expressed isomiRs were 3′ template variants with one nucleotide deletion or 3′ non-template variants with addition of A or U at the 3′ end. We also identified offset RNAs (moRs) and loop RNAs (loRs). Our work extends the base for further work on all species (miRNA, isomiRs, moRNAs, loRNAs) of the miRNAome of Daphnia as biomarkers in response to chemical substances and environment cues, and underline age dependency.
Collapse
|
28
|
Benmoussa A, Laugier J, Beauparlant CJ, Lambert M, Droit A, Provost P. Complexity of the microRNA transcriptome of cow milk and milk-derived extracellular vesicles isolated via differential ultracentrifugation. J Dairy Sci 2019; 103:16-29. [PMID: 31677838 DOI: 10.3168/jds.2019-16880] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/11/2019] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are small gene-regulatory noncoding RNA that are highly enriched in cow milk. They are encapsulated in different extracellular vesicle (EV) subsets that protect them from the extracellular milieu and the harsh conditions of the gastrointestinal tract during digestion. Here, we isolated pellets enriched in 4 different EV subsets, via differential ultracentrifugation of commercial cow milk: 12,000 × g (P12K), 35,000 × g (P35K), 70,000 × g (P70K), and 100,000 × g (P100K). Small RNA sequencing (sRNA-Seq) analyses revealed an unprecedented level of diversity in the complete miRNA repertoire and features of unfractionated cow milk and derived EV subsets. Although 5 miRNA sequences represented more than 50% of all miRNAs, milk EV exhibited heterogeneous content of miRNAs and isomeric variants (termed isomiR): P100K EV were enriched in reference miRNA sequences, and P12K and P35K EV in related isomiR. Incubation of milk EV with human cultured HeLa cells led to cellular enrichment in miRNA miR-223, which was concomitant with decreased expression of a reporter gene placed under the control of miR-223, thereby demonstrating the functionality of miR-223. These results suggest that cow milk EV may transfer their miRNAs to human cells and regulate recipient cell gene expression programming in a manner as complex as that of their miRNA transcriptome. The biological activity and relevance of the different milk EV subsets and bioactive mediators, including small noncoding RNA, in health and disease, warrants further investigation.
Collapse
Affiliation(s)
- Abderrahim Benmoussa
- Centre Hospitalier Universitaire de Québec Research Center/Centre Hospitalier de l'Université Laval, Quebec G1V 4G2, Canada; Department of Microbiology, Infectious Diseases and Immunology and Faculty of Medicine, Université Laval, Quebec G1V 0A6, Canada
| | - Jonathan Laugier
- Centre Hospitalier Universitaire de Québec Research Center/Centre Hospitalier de l'Université Laval, Quebec G1V 4G2, Canada; Department of Microbiology, Infectious Diseases and Immunology and Faculty of Medicine, Université Laval, Quebec G1V 0A6, Canada
| | - Charles Joly Beauparlant
- Centre Hospitalier Universitaire de Québec Research Center/Centre Hospitalier de l'Université Laval, Quebec G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Université Laval, Axe Endocrinologie - Néphrologie du Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec City, Québec, Canada
| | - Marine Lambert
- Centre Hospitalier Universitaire de Québec Research Center/Centre Hospitalier de l'Université Laval, Quebec G1V 4G2, Canada; Department of Microbiology, Infectious Diseases and Immunology and Faculty of Medicine, Université Laval, Quebec G1V 0A6, Canada
| | - Arnaud Droit
- Centre Hospitalier Universitaire de Québec Research Center/Centre Hospitalier de l'Université Laval, Quebec G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Université Laval, Axe Endocrinologie - Néphrologie du Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec City, Québec, Canada
| | - Patrick Provost
- Centre Hospitalier Universitaire de Québec Research Center/Centre Hospitalier de l'Université Laval, Quebec G1V 4G2, Canada; Department of Microbiology, Infectious Diseases and Immunology and Faculty of Medicine, Université Laval, Quebec G1V 0A6, Canada.
| |
Collapse
|
29
|
Forero DA, González-Giraldo Y, Castro-Vega LJ, Barreto GE. qPCR-based methods for expression analysis of miRNAs. Biotechniques 2019; 67:192-199. [PMID: 31560239 DOI: 10.2144/btn-2019-0065] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem-loop reverse transcriptase-PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.
Collapse
Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis J Castro-Vega
- INSERM, UMR970, Paris-Cardiovascular Research Center, Equipe Labellisée par la Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| |
Collapse
|
30
|
An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6193673. [PMID: 31467902 PMCID: PMC6699389 DOI: 10.1155/2019/6193673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/28/2019] [Accepted: 06/24/2019] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease/phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual's samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs. Using matpred2, we identified isomiRs and then verified them by searching within individual miRNA sequencing data. Our approach yielded biomarkers for biological experiments, mined functions of miRNAs and SNPs, improved disease risk assessment, and provided a way to achieve individualized precision medicine.
Collapse
|
31
|
Yang M, Lu H, Xue F, Ma L. Identifying High Confidence microRNAs in the Developing Seeds of Jatropha curcas. Sci Rep 2019; 9:4510. [PMID: 30872797 PMCID: PMC6418140 DOI: 10.1038/s41598-019-41189-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/01/2019] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenously short noncoding regulatory RNAs implicated in plant development and physiology. Nine small RNA (sRNA) libraries from three typical seed developmental stages (young, intermediate, and mature) were generated by deep sequencing to identify the miRNAs of J. curcas, a potential oilseed crop for the production of renewable oil. Strict criteria were adopted to identify 93 high confidence miRNAs including 48 conserved miRNAs and 45 novel miRNAs. Target genes of these miRNAs were involved in a broad range of physiological functions, including gene expression regulation, primary & secondary metabolism, growth & development, signal transduction, and stress response. About one third (29 out of 93) miRNAs showed significant changes in expression levels during the seed developmental process, indicating that the miRNAs might regulate its targets by their changes of transcription levels in seed development. However, most miRNAs were found differentially expressed in the late stage of seed development, suggesting that miRNAs play more important roles in the stage when seed accumulating organic matters and suffering dehydration stress. This study presents the first large scale identification of high confidence miRNAs in the developing seeds of J. curcas.
Collapse
Affiliation(s)
- Mingfeng Yang
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Heshu Lu
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Feiyan Xue
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Lanqing Ma
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China.
| |
Collapse
|
32
|
Benmoussa A, Provost P. Milk MicroRNAs in Health and Disease. Compr Rev Food Sci Food Saf 2019; 18:703-722. [PMID: 33336926 DOI: 10.1111/1541-4337.12424] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 02/06/2023]
Abstract
MicroRNAs are small noncoding RNAs responsible for regulating 40% to 60% of gene expression at the posttranscriptional level. The discovery of circulating microRNAs in several biological fluids opened the path for their study as biomarkers and long-range cell-to-cell communication mediators. Their transfer between individuals in the case of blood transfusion, for example, and their high enrichment in milk have sparked the interest for microRNA transfer through diet, especially from mothers to infants during breastfeeding. The extension of such paradigm led to the study of milk microRNAs in the case of cow or goat milk consumption in adults. Here we provide a comprehensive critical review of the key findings surrounding milk microRNAs in human, cow, and goat milk among other species. We discuss the data on their biological properties, their use as disease biomarkers, their transfer between individuals or species, and their putative or verified functions in health and disease of infants and adult consumers. This work is based on all the literature available and integrates all the results, theories, debates, and validation studies available so far on milk microRNAs and related areas of investigations. We critically discuss the limitations and outline future aspects and avenues to explore in this rapidly growing field of research that could impact public health through infant milk formulations or new therapies. We hope that this comprehensive review of the literature will provide insight for all teams investigating milk RNAs' biological activities and help ensure the quality of future reports.
Collapse
Affiliation(s)
- Abderrahim Benmoussa
- CHUQ Research Center/CHUL, 2705 Blvd Laurier, Quebec, QC, G1V 4G2, Canada.,Dept. of Microbiology-Infectious Disease and Immunity and Faculty of Medicine, Univ. Laval, Quebec, QC, G1V 0A6, Canada
| | - Patrick Provost
- CHUQ Research Center/CHUL, 2705 Blvd Laurier, Quebec, QC, G1V 4G2, Canada.,Dept. of Microbiology-Infectious Disease and Immunity and Faculty of Medicine, Univ. Laval, Quebec, QC, G1V 0A6, Canada
| |
Collapse
|
33
|
Desvignes T, Batzel P, Sydes J, Eames BF, Postlethwait JH. miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish. Sci Rep 2019; 9:3913. [PMID: 30850632 PMCID: PMC6408482 DOI: 10.1038/s41598-019-40361-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/15/2019] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) can have organ-specific expression and functions; they can originate from dedicated miRNA genes, from non-canonical miRNA genes, or from mirror-miRNA genes and can also experience post-transcriptional variation. It remains unclear, however, which mechanisms of miRNA production or modification are organ-specific and the extent of their evolutionary conservation. To address these issues, we developed the software Prost! (PRocessing Of Short Transcripts), which, among other features, helps quantify mature miRNAs, accounts for post-transcriptional processing, such as nucleotide editing, and identifies mirror-miRNAs. Here, we applied Prost! to annotate and analyze miRNAs in three-spined stickleback (Gasterosteus aculeatus), a model fish for evolutionary biology reported to have a miRNome larger than most teleost fish. Zebrafish (Danio rerio), a distantly related teleost with a well-known miRNome, served as comparator. Our results provided evidence for the existence of 286 miRNA genes and 382 unique mature miRNAs (excluding mir430 gene duplicates and the vaultRNA-derived mir733), which doesn't represent a miRNAome larger than other teleost miRNomes. In addition, small RNA sequencing data from brain, heart, testis, and ovary in both stickleback and zebrafish identified suites of mature miRNAs that display organ-specific enrichment, many of which are evolutionarily-conserved in the brain and heart in both species. These data also supported the hypothesis that evolutionarily-conserved, organ-specific mechanisms may regulate post-transcriptional variations in miRNA sequence. In both stickleback and zebrafish, miR2188-5p was edited frequently with similar nucleotide changes in the seed sequence with organ specific editing rates, highest in the brain. In summary, Prost! is a new tool to identify and understand small RNAs, to help clarify a species' miRNA biology as shown here for an important model for the evolution of developmental mechanisms, and to provide insight into organ-enriched expression and the evolutionary conservation of miRNA post-transcriptional modifications.
Collapse
Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA.
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | - B Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | | |
Collapse
|
34
|
Expanding the miRNA Repertoire in Atlantic Salmon; Discovery of IsomiRs and miRNAs Highly Expressed in Different Tissues and Developmental Stages. Cells 2019; 8:cells8010042. [PMID: 30641951 PMCID: PMC6356880 DOI: 10.3390/cells8010042] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional gene expression regulators. Here, 448 different miRNA genes, including 17 novel miRNAs, encoding for 589 mature Atlantic salmon miRNAs were identified after sequencing 111 samples (fry, pathogen challenged fry, various developmental and adult tissues). This increased the reference miRNAome with almost one hundred genes. Prior to isomiR characterization (mature miRNA variants), the proportion of erroneous sequence variants (ESVs) arising in the analysis pipeline was assessed. The ESVs were biased towards 5’ and 3’ end of reads in unexpectedly high proportions indicating that measurements of ESVs rather than Phred score should be used to avoid misinterpreting ESVs as isomiRs. Forty-three isomiRs were subsequently discovered. The biological effect of the isomiRs measured as increases in target diversity was small (<3%). Five miRNA genes showed allelic variation that had a large impact on target gene diversity if present in the seed. Twenty-one miRNAs were ubiquitously expressed while 31 miRNAs showed predominant expression in one or few tissues, indicating housekeeping or tissue specific functions, respectively. The miR-10 family, known to target Hox genes, were highly expressed in the developmental stages. The proportion of miR-430 family members, participating in maternal RNA clearance, was high at the earliest developmental stage.
Collapse
|
35
|
Saliminejad K, Khorram Khorshid HR, Soleymani Fard S, Ghaffari SH. An overview of microRNAs: Biology, functions, therapeutics, and analysis methods. J Cell Physiol 2018; 234:5451-5465. [PMID: 30471116 DOI: 10.1002/jcp.27486] [Citation(s) in RCA: 1016] [Impact Index Per Article: 169.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/06/2018] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs, which function in posttranscriptional regulation of gene expression. They are powerful regulators of various cellular activities including cell growth, differentiation, development, and apoptosis. They have been linked to many diseases, and currently miRNA-mediated clinical trial has shown promising results for treatment of cancer and viral infection. This review provides an overview and update on miRNAs biogenesis, regulation of miRNAs expression, their biological functions, and role of miRNAs in epigenetics and cell-cell communication. In addition, alteration of miRNAs following exercise, their association with diseases, and therapeutic potential will be explained. Finally, miRNA bioinformatics tools and conventional methods for miRNA detection and quantification will be discussed.
Collapse
Affiliation(s)
- Kioomars Saliminejad
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Shahrzad Soleymani Fard
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Hamidollah Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
36
|
Yu T, Li X, Coates BS, Zhang Q, Siegfried BD, Zhou X. microRNA profiling between Bacillus thuringiensis Cry1Ab-susceptible and -resistant European corn borer, Ostrinia nubilalis (Hübner). INSECT MOLECULAR BIOLOGY 2018; 27:279-294. [PMID: 29451334 DOI: 10.1111/imb.12376] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transgenic maize hybrids that express insecticidal Bacillus thuringiensis (Bt) crystalline (Cry) protein toxins effectively protect against the European corn borer, Ostrinia nubilalis, a devastating maize pest. Field monitoring and laboratory selections have detected varying levels of O. nubilalis resistance to Cry1Ab toxin. MicroRNAs (miRNAs) are short noncoding RNAs that are involved in post-transcriptional gene regulation. Their potential roles in the evolution of Bt resistance, however, remain largely unknown. Sequencing of small RNA libraries from the midgut of Cry1Ab-susceptible and resistant O. nubilalis larvae resulted in the discovery of 277 miRNAs, including 248 conserved and 29 novel. Comparative analyses of miRNA expression profiles between the laboratory strains predicted 26 and nine significantly up- and down-regulated transcripts, respectively, in the midgut of Cry1Ab resistant larvae. Amongst 15 differentially regulated miRNAs examined by quantitative real-time PCR, nine (60%) were validated as cosegregating with Cry1Ab resistance in a backcross progeny. Differentially expressed miRNAs were predicted to affect transcripts involved in cell membrane components with functions in metabolism and binding, and the putative Bt-resistance genes aminopeptidase N and cadherin. These results lay the foundation for future investigation of the potential role of miRNAs in the evolution of Bt resistance.
Collapse
Affiliation(s)
- T Yu
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - X Li
- Department of Entomology, University of Kentucky, Lexington, KY, USA
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - B-S Coates
- Corn Insects & Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Q Zhang
- Department of Entomology, University of Kentucky, Lexington, KY, USA
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - B-D Siegfried
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - X Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
37
|
Identification of the miRNAome of early mesoderm progenitor cells and cardiomyocytes derived from human pluripotent stem cells. Sci Rep 2018; 8:8072. [PMID: 29795287 PMCID: PMC5966391 DOI: 10.1038/s41598-018-26156-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/01/2018] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are small non-coding RNAs involved in post-transcriptional regulation of gene expression related to many cellular functions. We performed a small-RNAseq analysis of cardiac differentiation from pluripotent stem cells. Our analyses identified some new aspects about microRNA expression in this differentiation process. First, we described a dynamic expression profile of microRNAs where some of them are clustered according to their expression level. Second, we described the extensive network of isomiRs and ADAR modifications. Third, we identified the microRNAs families and clusters involved in the establishment of cardiac lineage and define the mirRNAome based on these groups. Finally, we were able to determine a more accurate miRNAome associated with cardiomyocytes by comparing the expressed microRNAs with other mature cells. MicroRNAs exert their effect in a complex and interconnected way, making necessary a global analysis to better understand their role. Our data expands the knowledge of microRNAs and their implications in cardiomyogenesis.
Collapse
|
38
|
Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8518563. [PMID: 29682564 PMCID: PMC5845524 DOI: 10.1155/2018/8518563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/01/2018] [Indexed: 11/23/2022]
Abstract
As a novel class of noncoding RNAs, circular RNAs (circRNAs) have been reported to play a role in various biological processes. Some circRNAs may serve as microRNA (miRNA) sponges, regulating transcription or splicing. Herein, we investigated the expression profiles and interactions of miRNAs/isomiRs and circRNAs in male patients with esophageal cancer. We found that some miRNA genes generated two deregulated miRNA products (miR-#-5p and miR-#-3p), and these products were consistently abnormally expressed. Some circRNAs were predicted to be miRNA sponges for specific miRNAs. Some of these typically showed opposing expression patterns in cancer tissues: one upregulated and the other downregulated. Although fewer miRNAs were predicted to interact with circRNAs, the number of predicted interactions would be substantially increased if detailed isomiRs were involved. High sequence similarity across multiple isomiRs suggested that they might interact with circRNAs, similar to the interaction of homologous miRNAs with circRNAs. At the isomiR level, due to the characteristics of the sequences and expression patterns involved, the cross-talk between different ncRNAs is complicated despite simplification of the isomiRs involved through clustering. We expect that our results may provide methods for further study of the cross-talk among ncRNAs and elucidate their biological roles in human diseases.
Collapse
|
39
|
Fehlmann T, Backes C, Alles J, Fischer U, Hart M, Kern F, Langseth H, Rounge T, Umu SU, Kahraman M, Laufer T, Haas J, Staehler C, Ludwig N, Hübenthal M, Meder B, Franke A, Lenhof HP, Meese E, Keller A. A high-resolution map of the human small non-coding transcriptome. Bioinformatics 2017; 34:1621-1628. [DOI: 10.1093/bioinformatics/btx814] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/20/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Julia Alles
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Ulrike Fischer
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Martin Hart
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Hilde Langseth
- Cancer Registry of Norway, Institute of Population-based Cancer Research, Oslo, Norway
| | - Trine Rounge
- Cancer Registry of Norway, Institute of Population-based Cancer Research, Oslo, Norway
| | - Sinan Ugur Umu
- Cancer Registry of Norway, Institute of Population-based Cancer Research, Oslo, Norway
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Hummingbird Diagnostics GmbH, Heidelberg, Germany
| | | | - Jan Haas
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Cord Staehler
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| |
Collapse
|
40
|
Seow N, Fenati RA, Connolly AR, Ellis AV. Hi-fidelity discrimination of isomiRs using G-quadruplex gatekeepers. PLoS One 2017; 12:e0188163. [PMID: 29145502 PMCID: PMC5690596 DOI: 10.1371/journal.pone.0188163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/01/2017] [Indexed: 11/17/2022] Open
Abstract
Core microRNA (miRNA) sequences exist as populations of variants called isomiRs made up of different lengths and nucleotide compositions. In particular, the short sequences of miRNA make single-base isomiR mismatches very difficult to be discriminated. Non-specific hybridizations often arise when DNA probe-miRNA target hybridization is the primary, or initial, mode of detection. These errors then become exacerbated through subsequent amplification steps. Here, we present the design of DNA probes modified with poly-guanine (PG) tracts that were induced to form G-quadruplexes (G4) for hi-fidelity discrimination of miRNA core target sequence from single-base mismatched isomiRs. We demonstrate that, when compared to unmodified probes, this G4 'gate-keeping' function within the G4-modified probes enables more stringent hybridization of complementary core miRNA target transcripts while limiting non-specific hybridizations. This increased discriminatory power of the G4-modified probes over unmodified probes is maintained even after further reverse transcriptase extension of probe-target hybrids. Enzymatic extension also enhanced the clarity and sensitivity of readouts and allows different isomiRs to be distinguished from one another via the relative positions of the mismatches.
Collapse
Affiliation(s)
- Nianjia Seow
- Flinders Centre for Nanoscale Science and Technology, Flinders University, Bedford Park, SA, Australia
| | - Renzo A Fenati
- Flinders Centre for Nanoscale Science and Technology, Flinders University, Bedford Park, SA, Australia.,School of Chemical and Biomedical Engineering, The University of Melbourne, Parkville, Victoria, Australia
| | - Ashley R Connolly
- Flinders Centre for Nanoscale Science and Technology, Flinders University, Bedford Park, SA, Australia
| | - Amanda V Ellis
- Flinders Centre for Nanoscale Science and Technology, Flinders University, Bedford Park, SA, Australia.,School of Chemical and Biomedical Engineering, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
41
|
Androvic P, Valihrach L, Elling J, Sjoback R, Kubista M. Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification. Nucleic Acids Res 2017; 45:e144. [PMID: 28911110 PMCID: PMC5587787 DOI: 10.1093/nar/gkx588] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/28/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on two-step RT-qPCR with SYBR-green detection chemistry called Two-tailed RT-qPCR. It takes advantage of novel, target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of seven logs and a sensitivity sufficient to detect down to ten target miRNA molecules. It is capable to capture the full isomiR repertoire, leading to accurate representation of the complete miRNA content in a sample. The reverse transcription step can be multiplexed and the miRNA profiles measured with Two-tailed RT-qPCR show excellent correlation with the industry standard TaqMan miRNA assays (r2 = 0.985). Moreover, Two-tailed RT-qPCR allows for rapid testing with a total analysis time of less than 2.5 hours.
Collapse
Affiliation(s)
- Peter Androvic
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic.,Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc 783 71, Czech Republic
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic
| | | | | | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic.,TATAA Biocenter AB, Gothenburg 411 03, Sweden
| |
Collapse
|
42
|
Bortolomeazzi M, Gaffo E, Bortoluzzi S. A survey of software tools for microRNA discovery and characterization using RNA-seq. Brief Bioinform 2017; 20:918-930. [DOI: 10.1093/bib/bbx148] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/12/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | |
Collapse
|
43
|
Stachowiak M, Flisikowska T, Bauersachs S, Perleberg C, Pausch H, Switonski M, Kind A, Saur D, Schnieke A, Flisikowski K. Altered microRNA profiles during early colon adenoma progression in a porcine model of familial adenomatous polyposis. Oncotarget 2017; 8:96154-96160. [PMID: 29221194 PMCID: PMC5707088 DOI: 10.18632/oncotarget.21774] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/23/2017] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs are dysregulated in various cancers including colorectal cancer, and are potential useful biomarkers of disease development. We used next generation sequencing to investigate miRNA expression profiles in low- and high-grade intraepithelial dysplastic polyps from pigs carrying a mutation in the adenomatous polyposis coli tumour suppressor (APC1311 , orthologous to human APC1309 ) that model an inherited predisposition to colorectal cancer, familial adenomatous polyposis. We identified several miRNAs and their isomiRs significantly (P < 0.05) differentially expressed between low and high-grade intraepithelial dysplastic polyps. Of these, ssc-let-7e, ssc-miR-98, ssc-miR-146a-5p, ssc-miR-146b, ssc-miR-183 and ssc-miR-196a were expressed at higher level and ssc-miR-126-3p at lower level in high-grade intraepithelial dysplastic polyps. Functional miRNA target analysis revealed significant (P < 0.001) over-representation of cancer-related pathways, including 'microRNAs in cancer', 'proteoglycans in cancer', 'pathways in cancer' and 'colorectal cancer'. This is the first study to reveal miRNAs associated with premalignant transformation of colon polyps.
Collapse
Affiliation(s)
- Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637 Poznan, Poland
| | - Tatiana Flisikowska
- Chair of Livestock Biotechnology, Technische Universität München, 85354 Freising, Germany
| | - Stefan Bauersachs
- Institute of Agricultural Sciences, Animal Physiology, ETH Zurich, CH-8092 Zurich, Switzerland.,Current address: University of Zurich, Clinic for Animal Reproduction Medicine, Genetics and Functional Genomics Group, CH-8092 Zurich, Switzerland
| | - Carolin Perleberg
- Chair of Livestock Biotechnology, Technische Universität München, 85354 Freising, Germany
| | - Hubert Pausch
- Institute of Agricultural Sciences, Animal Genomics, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637 Poznan, Poland
| | - Alexander Kind
- Chair of Livestock Biotechnology, Technische Universität München, 85354 Freising, Germany
| | - Dieter Saur
- Klinikum Rechts der Isar II, Technische Universität München, 81675 Munich, Germany
| | - Angelika Schnieke
- Chair of Livestock Biotechnology, Technische Universität München, 85354 Freising, Germany
| | - Krzysztof Flisikowski
- Chair of Livestock Biotechnology, Technische Universität München, 85354 Freising, Germany
| |
Collapse
|
44
|
Berardocco M, Radeghieri A, Busatto S, Gallorini M, Raggi C, Gissi C, D'Agnano I, Bergese P, Felsani A, Berardi AC. RNA-seq reveals distinctive RNA profiles of small extracellular vesicles from different human liver cancer cell lines. Oncotarget 2017; 8:82920-82939. [PMID: 29137313 PMCID: PMC5669939 DOI: 10.18632/oncotarget.20503] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/29/2017] [Indexed: 12/20/2022] Open
Abstract
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome. Here are reported genome wide data of the expression level of coding and non-coding transcripts, microRNAs, isomiRs and snoRNAs providing the first comprehensive overview of the extracellular-vesicle RNA cargo released from LC cell lines. The EV-RNA expression profiles of the four liver cancer cell lines share a similar background, but cell-specific features clearly emerge showing the marked heterogeneity of the EV-cargo among the individual cell lines, evident both for the coding and non-coding RNA species.
Collapse
Affiliation(s)
- Martina Berardocco
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
| | - Annalisa Radeghieri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sara Busatto
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Chiara Raggi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Clarissa Gissi
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
| | - Igea D'Agnano
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Armando Felsani
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Italy.,Genomnia Srl, Bresso, Italy
| | - Anna C Berardi
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
| |
Collapse
|
45
|
Snyman MC, Solofoharivelo MC, Souza-Richards R, Stephan D, Murray S, Burger JT. The use of high-throughput small RNA sequencing reveals differentially expressed microRNAs in response to aster yellows phytoplasma-infection in Vitis vinifera cv. 'Chardonnay'. PLoS One 2017; 12:e0182629. [PMID: 28813447 PMCID: PMC5558978 DOI: 10.1371/journal.pone.0182629] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 07/22/2017] [Indexed: 11/19/2022] Open
Abstract
Phytoplasmas are cell wall-less plant pathogenic bacteria responsible for major crop losses throughout the world. In grapevine they cause grapevine yellows, a detrimental disease associated with a variety of symptoms. The high economic impact of this disease has sparked considerable interest among researchers to understand molecular mechanisms related to pathogenesis. Increasing evidence exist that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation during plant development and responses to biotic and abiotic stresses. Thus, we aimed to dissect complex high-throughput small RNA sequencing data for the genome-wide identification of known and novel differentially expressed miRNAs, using read libraries constructed from healthy and phytoplasma-infected Chardonnay leaf material. Furthermore, we utilised computational resources to predict putative miRNA targets to explore the involvement of possible pathogen response pathways. We identified multiple known miRNA sequence variants (isomiRs), likely generated through post-transcriptional modifications. Sequences of 13 known, canonical miRNAs were shown to be differentially expressed. A total of 175 novel miRNA precursor sequences, each derived from a unique genomic location, were predicted, of which 23 were differentially expressed. A homology search revealed that some of these novel miRNAs shared high sequence similarity with conserved miRNAs from other plant species, as well as known grapevine miRNAs. The relative expression of randomly selected known and novel miRNAs was determined with real-time RT-qPCR analysis, thereby validating the trend of expression seen in the normalised small RNA sequencing read count data. Among the putative miRNA targets, we identified genes involved in plant morphology, hormone signalling, nutrient homeostasis, as well as plant stress. Our results may assist in understanding the role that miRNA pathways play during plant pathogenesis, and may be crucial in understanding disease symptom development in aster yellows phytoplasma-infected grapevines.
Collapse
Affiliation(s)
- Marius C. Snyman
- The Vitis Laboratory, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Rose Souza-Richards
- The Vitis Laboratory, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Dirk Stephan
- The Vitis Laboratory, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Shane Murray
- Centre for Proteomic and Genomic Research, Observatory, Cape Town, South Africa
| | - Johan T. Burger
- The Vitis Laboratory, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
46
|
Jackowiak P, Hojka-Osinska A, Philips A, Zmienko A, Budzko L, Maillard P, Budkowska A, Figlerowicz M. Small RNA fragments derived from multiple RNA classes - the missing element of multi-omics characteristics of the hepatitis C virus cell culture model. BMC Genomics 2017; 18:502. [PMID: 28666407 PMCID: PMC5493846 DOI: 10.1186/s12864-017-3891-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/21/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A pool of small RNA fragments (RFs) derived from diverse cellular RNAs has recently emerged as a rich source of functionally relevant molecules. Although their formation and accumulation has been connected to various stress conditions, the knowledge on RFs produced upon viral infections is very limited. Here, we applied the next generation sequencing (NGS) to characterize RFs generated in the hepatitis C virus (HCV) cell culture model (HCV-permissive Huh-7.5 cell line). RESULTS We found that both infected and non-infected cells contained a wide spectrum of RFs derived from virtually all RNA classes. A significant fraction of identified RFs accumulated to similar levels as miRNAs. Our analysis, focused on RFs originating from constitutively expressed non-coding RNAs, revealed three major patterns of parental RNA cleavage. We found that HCV infection induced significant changes in the accumulation of low copy number RFs, while subtly altered the levels of high copy number ones. Finally, the candidate RFs potentially relevant for host-virus interactions were identified. CONCLUSIONS Our results indicate that RFs should be considered an important component of the Huh-7.5 transcriptome and suggest that the main factors influencing the RF biogenesis are the RNA structure and RNA protection by interacting proteins. The data presented here significantly complement the existing transcriptomic, miRnomic, proteomic and metabolomic characteristics of the HCV cell culture model.
Collapse
Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Hojka-Osinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965, Poznan, Poland
| | - Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Patrick Maillard
- Institut Pasteur, Hepacivirus and Innate Immunity, CNRS, UMR3569, 75724, Paris, France
| | - Agata Budkowska
- Institut Pasteur, Hepacivirus and Innate Immunity, CNRS, UMR3569, 75724, Paris, France.,Scientific Advisor for the Department of International Affairs, Institut Pasteur, 75724, Paris, France
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965, Poznan, Poland.
| |
Collapse
|
47
|
Buñay J, Larriba E, Moreno RD, Del Mazo J. Chronic low-dose exposure to a mixture of environmental endocrine disruptors induces microRNAs/isomiRs deregulation in mouse concomitant with intratesticular estradiol reduction. Sci Rep 2017; 7:3373. [PMID: 28611354 PMCID: PMC5469815 DOI: 10.1038/s41598-017-02752-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/18/2017] [Indexed: 12/31/2022] Open
Abstract
Humans are environmentally exposed not only to single endocrine-disrupting chemicals (EDCs) but to mixtures that affect their reproductive health. In reproductive tissues, microRNAs (miRNAs) are emerging as key targets of EDCs. Here, we analysed changes in the testis "miRNome" (and their biogenesis mechanism) in chronically exposed adult mice to a cocktail of five EDCs containing 0.3 mg/kg-body weight (BW)/day of each phthalate (DEHP, DBP, BBP) and 0.05 mg/kg-BW/day of each alkylphenol (NP, OP), from conception to adulthood. The testis "miRNome" was characterised using next-generation sequencing (NGS). Expression levels of genes involved in miRNA biogenesis were measured by RT-qPCR, as well as several physiological and cytological parameters. We found two up-regulated, and eight down-regulated miRNAs and thirty-six differentially expressed isomiRs along with an over-expression of Drosha, Adar and Zcchc11. A significant decrease of intratesticular estradiol but not testosterone was detected. Functional analysis showed altered spermatogenesis, germ cell apoptosis and negative correlation of miR-18a-5p with Nr1h2 involved in the deregulation of the steroidogenesis pathway. Here, we present the first association between miRNA/isomiRs deregulation, their mechanisms of biogenesis and histopathological and hormonal alterations in testes of adult mice exposed to a mixture of low-dose EDCs, which can play a role in male infertility.
Collapse
Affiliation(s)
- Julio Buñay
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo Larriba
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Ricardo D Moreno
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Jesús Del Mazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain.
| |
Collapse
|
48
|
Megiorni F, Colaiacovo M, Cialfi S, McDowell HP, Guffanti A, Camero S, Felsani A, Losty PD, Pizer B, Shukla R, Cappelli C, Ferrara E, Pizzuti A, Moles A, Dominici C. A sketch of known and novel MYCN-associated miRNA networks in neuroblastoma. Oncol Rep 2017; 38:3-20. [PMID: 28586032 PMCID: PMC5492854 DOI: 10.3892/or.2017.5701] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 04/27/2017] [Indexed: 12/12/2022] Open
Abstract
Neuroblastoma (NB) originates from neural crest-derived precursors and represents the most common childhood extracranial solid tumour. MicroRNAs (miRNAs), a class of small non-coding RNAs that participate in a wide variety of biological processes by regulating gene expression, appear to play an essential role within the NB context. High-throughput next generation sequencing (NGS) was applied to study the miRNA transcriptome in a cohort of NB tumours with and without MYCN-amplification (MNA and MNnA, respectively) and in dorsal root ganglia (DRG), as a control. Out of the 128 miRNAs differentially expressed in the NB vs. DRG comparison, 47 were expressed at higher levels, while 81 were expressed at lower levels in the NB tumours. We also found that 23 miRNAs were differentially expressed in NB with or without MYCN-amplification, with 17 miRNAs being upregulated and 6 being downregulated in the MNA subtypes. Functional annotation analysis of the target genes of these differentially expressed miRNAs demonstrated that many mRNAs were involved in cancer-related pathways, such as DNA-repair and apoptosis as well as FGFR and EGFR signalling. In particular, we found that miR-628-3p negatively affects MYCN gene expression. Furthermore, we identified a novel miRNA candidate with variable expression in MNA vs. MNnA tumours, whose putative target genes are implicated in the mTOR pathway. The present study provides further insight into the molecular mechanisms that correlate miRNA dysregulation to NB development and progression.
Collapse
Affiliation(s)
- Francesca Megiorni
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, I-00161 Rome, Italy
| | | | - Samantha Cialfi
- Department of Molecular Medicine, Sapienza University of Rome, I-00161 Rome, Italy
| | - Heather P McDowell
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, I-00161 Rome, Italy
| | | | - Simona Camero
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, I-00161 Rome, Italy
| | | | - Paul D Losty
- Department of Paediatric Surgery, Alder Hey Children's NHS Foundation Trust, L12 2AP Liverpool, UK
| | - Barry Pizer
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, L12 2AP Liverpool, UK
| | - Rajeev Shukla
- Department of Perinatal and Paediatric Pathology, Alder Hey Children's NHS Foundation Trust, L12 2AP Liverpool, UK
| | - Carlo Cappelli
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, I-00161 Rome, Italy
| | - Eva Ferrara
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, I-00161 Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, I-00161 Rome, Italy
| | - Anna Moles
- Genomnia s.r.l., I-20091 Bresso, MI, Italy
| | - Carlo Dominici
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, I-00161 Rome, Italy
| |
Collapse
|
49
|
Correia CN, Nalpas NC, McLoughlin KE, Browne JA, Gordon SV, MacHugh DE, Shaughnessy RG. Circulating microRNAs as Potential Biomarkers of Infectious Disease. Front Immunol 2017; 8:118. [PMID: 28261201 PMCID: PMC5311051 DOI: 10.3389/fimmu.2017.00118] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/25/2017] [Indexed: 12/12/2022] Open
Abstract
microRNAs (miRNAs) are a class of small non-coding endogenous RNA molecules that regulate a wide range of biological processes by post-transcriptionally regulating gene expression. Thousands of these molecules have been discovered to date, and multiple miRNAs have been shown to coordinately fine-tune cellular processes key to organismal development, homeostasis, neurobiology, immunobiology, and control of infection. The fundamental regulatory role of miRNAs in a variety of biological processes suggests that differential expression of these transcripts may be exploited as a novel source of molecular biomarkers for many different disease pathologies or abnormalities. This has been emphasized by the recent discovery of remarkably stable miRNAs in mammalian biofluids, which may originate from intracellular processes elsewhere in the body. The potential of circulating miRNAs as biomarkers of disease has mainly been demonstrated for various types of cancer. More recently, however, attention has focused on the use of circulating miRNAs as diagnostic/prognostic biomarkers of infectious disease; for example, human tuberculosis caused by infection with Mycobacterium tuberculosis, sepsis caused by multiple infectious agents, and viral hepatitis. Here, we review these developments and discuss prospects and challenges for translating circulating miRNA into novel diagnostics for infectious disease.
Collapse
Affiliation(s)
- Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland; University College Dublin, UCD Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland; University College Dublin, UCD Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - Ronan G Shaughnessy
- UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland
| |
Collapse
|
50
|
Liang T, Yu J, Liu C, Guo L. IsomiR expression patterns in canonical and Dicer‑independent microRNAs. Mol Med Rep 2017; 15:1071-1078. [PMID: 28098889 PMCID: PMC5367367 DOI: 10.3892/mmr.2017.6117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/11/2016] [Indexed: 11/23/2022] Open
Abstract
Multiple microRNA (miRNA) variants, known as isomiRs, are extensively distributed in miRNA loci and predominantly derive from the alternative cleavage of Drosha/Dicer and 3′addition events. The present study aimed to investigate the expression patterns of multiple isomiRs in typical miRNA and Dicer-independent miRNA loci by conducting evolutionary and expression analysis using public datasets. Although different miRNA maturation processes exist, multiple isomiRs can be detected by similar expression distributions. However, isomiR expression in Dicer-independent miRNA loci tends to be at a moderate level, particularly for random distribution in the ends that are split by Dicer in the typical miRNA loci. Compared with the mature miRNA locus (dominant miRNA locus), the non-dominant miRNA locus indicates an expression distribution similar to that of the Dicer-independent miRNA locus. These results increase the understanding of multiple isomiRs in the progression of diseases.
Collapse
Affiliation(s)
- Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong 253023, P.R. China
| | - Chang Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu 210023, P.R. China
| | - Li Guo
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210023, P.R. China
| |
Collapse
|