1
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Romo L, Findlay SD, Burge CB. Regulatory features aid interpretation of 3'UTR variants. Am J Hum Genet 2024; 111:350-363. [PMID: 38237594 PMCID: PMC10870128 DOI: 10.1016/j.ajhg.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024] Open
Abstract
Our ability to determine the clinical impact of variants in 3' untranslated regions (UTRs) of genes remains poor. We provide a thorough analysis of 3' UTR variants from several datasets. Variants in putative regulatory elements, including RNA-binding protein motifs, eCLIP peaks, and microRNA sites, are up to 16 times more likely than variants not in these elements to have gene expression and phenotype associations. Variants in regulatory motifs result in allele-specific protein binding in cell lines and allele-specific gene expression differences in population studies. In addition, variants in shared regions of alternatively polyadenylated isoforms and those proximal to polyA sites are more likely to affect gene expression and phenotype. Finally, pathogenic 3' UTR variants in ClinVar are up to 20 times more likely than benign variants to fall in a regulatory site. We incorporated these findings into RegVar, a software tool that interprets regulatory elements and annotations for any 3' UTR variant and predicts whether the variant is likely to affect gene expression or phenotype. This tool will help prioritize variants for experimental studies and identify pathogenic variants in individuals.
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Affiliation(s)
- Lindsay Romo
- Harvard Medical Genetics Training Program, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Scott D Findlay
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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2
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Sone H, Lee TJ, Lee BR, Heo D, Oh S, Kwon SH. MicroRNA-mediated attenuation of branched-chain amino acid catabolism promotes ferroptosis in chronic kidney disease. Nat Commun 2023; 14:7814. [PMID: 38016961 PMCID: PMC10684653 DOI: 10.1038/s41467-023-43529-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Chronic kidney disease can develop from kidney injury incident to chemotherapy with cisplatin, which complicates the prognosis of cancer patients. MicroRNAs regulate gene expression by pairing with specific sets of messenger RNAs. Therefore, elucidating direct physical interactions between microRNAs and their target messenger RNAs can help decipher crucial biological processes associated with cisplatin-induced kidney injury. Through intermolecular ligation and transcriptome-wide sequencing, we here identify direct pairs of microRNAs and their target messenger RNAs in the kidney of male mice injured by cisplatin. We find that a group of cisplatin-induced microRNAs can target select messenger RNAs that affect the mitochondrial metabolic pathways in the injured kidney. Specifically, a cisplatin-induced microRNA, miR-429-3p, suppresses the pathway that catabolizes branched-chain amino acids in the proximal tubule, leading to cell death dependent on lipid peroxidation, called ferroptosis. Identification of miRNA-429-3p-mediated ferroptosis stimulation suggests therapeutic potential for modulating the branched-chain amino acid pathway in ameliorating cisplatin-induced kidney injury.
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Affiliation(s)
- Hisakatsu Sone
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, 30912, USA
| | - Byung Rho Lee
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Dan Heo
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Sekyung Oh
- Department of Medical Science, Catholic Kwandong University College of Medicine, Incheon, 22711, South Korea
| | - Sang-Ho Kwon
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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3
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Romo L, Findlay SD, Burge CB. Regulatory features aid interpretation of 3'UTR Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551549. [PMID: 37577470 PMCID: PMC10418266 DOI: 10.1101/2023.08.01.551549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Our ability to determine the clinical impact of variants in 3' untranslated regions (UTRs) of genes remains poor. We provide a thorough analysis of 3'UTR variants from several datasets. Variants in putative regulatory elements including RNA-binding protein motifs, eCLIP peaks, and microRNA sites are up to 16 times more likely than other variants to have gene expression and phenotype associations. Heterozygous variants in regulatory motifs result in allele-specific protein binding in cell lines and allele-specific gene expression differences in population studies. In addition, variants in shared regions of alternatively polyadenylated isoforms and those proximal to polyA sites are more likely to affect gene expression and phenotype. Finally, pathogenic 3'UTR variants in ClinVar are 20 times more likely than benign variants to fall in a regulatory site. We incorporated these findings into RegVar, a software tool that interprets regulatory elements and annotations for any 3'UTR variant, and predicts whether the variant is likely to affect gene expression or phenotype. This tool will help prioritize variants for experimental studies and identify pathogenic variants in patients.
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Affiliation(s)
- Lindsay Romo
- Harvard Medical Genetics Training Program, Boston Children’s Hospital, Boston, MA 02115
| | - Scott D. Findlay
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142
| | - Christopher B. Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142
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4
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Wang R, Yang YM. Identification of potential biomarkers for idiopathic pulmonary fibrosis and validation of TDO2 as a potential therapeutic target. World J Cardiol 2023; 15:293-308. [PMID: 37397828 PMCID: PMC10308271 DOI: 10.4330/wjc.v15.i6.293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/01/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with a high mortality rate. On this basis, exploring potential therapeutic targets to meet the unmet needs of IPF patients is important.
AIM To explore novel hub genes for IPF therapy.
METHODS Here, we used public datasets to identify differentially expressed genes between IPF patients and healthy donors. Potential targets were considered based on multiple bioinformatics analyses, especially the correlation between hub genes and carbon monoxide diffusing capacity of carbon monoxide, forced vital capacity, and patient survival rate. The mRNA levels of the hub genes were determined through quantitative real-time polymerase chain reaction.
RESULTS We found that TDO2 was upregulated in IPF patients and predicted poor prognosis. Surprisingly, single-cell RNA sequencing data analysis revealed significant enrichment of TDO2 in alveolar fibroblasts, indicating that TDO2 may participate in the regulation of proliferation and survival. Therefore, we verified the upregulated expression of TDO2 in an experimental mouse model of transforming growth factor-β (TGF-β)-induced pulmonary fibrosis. Furthermore, the results showed that a TDO2 inhibitor effectively suppressed TGF-β-induced fibroblast activation. These findings suggest that TDO2 may be a potential target for IPF treatment. Based on transcription factors-microRNA prediction and scRNA-seq analysis, elevated TDO2 promoted the IPF proliferation of fibroblasts and may be involved in the P53 pathway and aggravate ageing and persistent pulmonary fibrosis.
CONCLUSION We provided new target genes prediction and proposed blocking TGF-β production as a potential treatment for IPF.
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Affiliation(s)
- Ru Wang
- Henan University of Chinese Medicine, Collaborative Innovation Centre for Chinese Medicine and Respiratory Diseases, Zhengzhou 450046, Henan Province, China
| | - Yan-Mei Yang
- Zhengzhou University, Research Centre of Basic Medicine, Academy of Medical Sciences, Zhengzhou 450000, Henan Province, China
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5
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Xiao Y, Liu TM, MacRae IJ. A tiny loop in the Argonaute PIWI domain tunes small RNA seed strength. EMBO Rep 2023:e55806. [PMID: 37082939 DOI: 10.15252/embr.202255806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/22/2023] Open
Abstract
Argonaute (AGO) proteins use microRNAs (miRNAs) and small interfering RNAs (siRNAs) as guides to regulate gene expression in plants and animals. AGOs that use miRNAs in bilaterian animals recognize short (6-8 nt.) elements complementary to the miRNA seed region, enabling each miRNA to interact with hundreds of otherwise unrelated targets. By contrast, AGOs that use miRNAs in plants employ longer (> 13 nt.) recognition elements such that each miRNA silences a small number of physiologically related targets. Here, we show that this major functional distinction depends on a minor structural difference between plant and animal AGO proteins: a 9-amino acid loop in the PIWI domain. Swapping the PIWI loop from human Argonaute2 (HsAGO2) into Arabidopsis Argonaute10 (AtAGO10) increases seed strength, resulting in animal-like miRNA targeting. Conversely, swapping the plant PIWI loop into HsAGO2 reduces seed strength and accelerates the turnover of cleaved targets. The loop-swapped HsAGO2 silences targets more potently, with reduced miRNA-like targeting, than wild-type HsAGO2 in mammalian cells. Thus, tiny structural differences can tune the targeting properties of AGO proteins for distinct biological roles.
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Affiliation(s)
- Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - TingYu M Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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6
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Ye L, Wang J, Yi K, Wang F, Wang J, Wu H, Yang H, Yang Z, Zhang Q. Recent findings on miR‑370 expression, regulation and functions in cancer (Review). Oncol Rep 2023; 49:79. [PMID: 36866765 PMCID: PMC10018457 DOI: 10.3892/or.2023.8516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/19/2023] [Indexed: 03/04/2023] Open
Abstract
MicroRNAs (miRNAs/miRs) are a group of small non‑coding RNAs that serve as post‑transcriptional gene modulators. miRNAs have been demonstrated to serve a pivotal role in carcinogenesis and the dysregulated expression of miRNAs is a well‑understood characteristic of cancer. In recent years, miR‑370 has been established as a key miRNA in various cancers. The expression of miR‑370 is dysregulated in various types of cancer and varies markedly across different tumor types. miR‑370 can regulate multiple biological processes, including cell proliferation, apoptosis, migration, invasion, as well as cell cycle progression and cell stemness. Moreover, it has been reported that miR‑370 affects the response of tumor cells to anticancer treatments. Additionally, the expression of miR‑370 is modulated by multiple factors. The present review summarizes the role and mechanism of miR‑370 in tumors, and demonstrates its potential as a molecular marker for cancer diagnosis and prognosis.
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Affiliation(s)
- Lingling Ye
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211000, P.R. China
| | - Jinqiu Wang
- Department of Oncology, Dafeng People's Hospital, Yancheng, Jiangsu 224000, P.R. China
| | - Kui Yi
- Department of General Surgery, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211000, P.R. China
| | - Fen Wang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211000, P.R. China
| | - Jinyan Wang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211000, P.R. China
| | - Hao Wu
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211000, P.R. China
| | - Hui Yang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211000, P.R. China
| | - Zhaohui Yang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211000, P.R. China
| | - Quan'an Zhang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211000, P.R. China
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7
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miR-34c-3p Regulates Protein Kinase A Activity Independent of cAMP by Dicing prkar2b Transcripts in Theileria annulata-Infected Leukocytes. mSphere 2023; 8:e0052622. [PMID: 36847534 PMCID: PMC10117149 DOI: 10.1128/msphere.00526-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that can play critical roles in regulating various cellular processes, including during many parasitic infections. Here, we report a regulatory role for miR-34c-3p in cAMP-independent regulation of host cell protein kinase A (PKA) activity in Theileria annulata-infected bovine leukocytes. We identified prkar2b (cAMP-dependent protein kinase A type II-beta regulatory subunit) as a novel miR-34c-3p target gene and demonstrate how infection-induced upregulation of miR-34c-3p repressed PRKAR2B expression to increase PKA activity. As a result, the disseminating tumorlike phenotype of T. annulata-transformed macrophages is enhanced. Finally, we extend our observations to Plasmodium falciparum-parasitized red blood cells, where infection-induced augmentation in miR-34c-3p levels led to a drop in the amount of prkar2b mRNA and increased PKA activity. Collectively, our findings represent a novel cAMP-independent way of regulating host cell PKA activity in infections by Theileria and Plasmodium parasites. IMPORTANCE Small microRNA levels are altered in many diseases, including those caused by parasites. Here, we describe how infection by two important animal and human parasites, Theileria annulata and Plasmodium falciparum, induce changes in infected host cell miR-34c-3p levels to regulate host cell PKA kinase activity by targeting mammalian prkar2b. Infection-induced changes in miR-34c-3p levels provide a novel epigenetic mechanism for regulating host cell PKA activity independent of fluxes in cAMP to both aggravate tumor dissemination and improve parasite fitness.
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8
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Iacomino G. miRNAs: The Road from Bench to Bedside. Genes (Basel) 2023; 14:genes14020314. [PMID: 36833241 PMCID: PMC9957002 DOI: 10.3390/genes14020314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
miRNAs are small noncoding RNAs that control gene expression at the posttranscriptional level. It has been recognised that miRNA dysregulation reflects the state and function of cells and tissues, contributing to their dysfunction. The identification of hundreds of extracellular miRNAs in biological fluids has underscored their potential in the field of biomarker research. In addition, the therapeutic potential of miRNAs is receiving increasing attention in numerous conditions. On the other hand, many operative problems including stability, delivery systems, and bioavailability, still need to be solved. In this dynamic field, biopharmaceutical companies are increasingly engaged, and ongoing clinical trials point to anti-miR and miR-mimic molecules as an innovative class of molecules for upcoming therapeutic applications. This article aims to provide a comprehensive overview of current knowledge on several pending issues and new opportunities offered by miRNAs in the treatment of diseases and as early diagnostic tools in next-generation medicine.
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Affiliation(s)
- Giuseppe Iacomino
- Institute of Food Sciences, National Research Council, Via Roma, 64, 83100 Avellino, Italy
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9
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Castro-Mondragon JA, Aure M, Lingjærde O, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen V, Mathelier A. Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers. Nucleic Acids Res 2022; 50:12131-12148. [PMID: 36477895 PMCID: PMC9757053 DOI: 10.1093/nar/gkac1143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/03/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Most cancer alterations occur in the noncoding portion of the human genome, where regulatory regions control gene expression. The discovery of noncoding mutations altering the cells' regulatory programs has been limited to few examples with high recurrence or high functional impact. Here, we show that transcription factor binding sites (TFBSs) have similar mutation loads to those in protein-coding exons. By combining cancer somatic mutations in TFBSs and expression data for protein-coding and miRNA genes, we evaluate the combined effects of transcriptional and post-transcriptional alterations on the regulatory programs in cancers. The analysis of seven TCGA cohorts culminates with the identification of protein-coding and miRNA genes linked to mutations at TFBSs that are associated with a cascading trans-effect deregulation on the cells' regulatory programs. Our analyses of cis-regulatory mutations associated with miRNAs recurrently predict 12 mature miRNAs (derived from 7 precursors) associated with the deregulation of their target gene networks. The predictions are enriched for cancer-associated protein-coding and miRNA genes and highlight cis-regulatory mutations associated with the dysregulation of key pathways associated with carcinogenesis. By combining transcriptional and post-transcriptional regulation of gene expression, our method predicts cis-regulatory mutations related to the dysregulation of key gene regulatory networks in cancer patients.
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Affiliation(s)
- Jaime A Castro-Mondragon
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Miriam Ragle Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway,Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway,Centre for Bioinformatics, Department of Informatics, University of Oslo, Gaustadalléen 23 B, N-0373 Oslo, Norway,KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Ullernchausseen 70, N-0372 Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - John W M Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway,Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
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10
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Feitosa RM, Prieto-Oliveira P, Brentani H, Machado-Lima A. MicroRNA target prediction tools for animals: Where we are at and where we are going to - A systematic review. Comput Biol Chem 2022; 100:107729. [DOI: 10.1016/j.compbiolchem.2022.107729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/26/2022]
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11
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Mao Y, Schoenborn J, Wang Z, Chen X, Matson K, Mohan R, Zhang S, Tang X, Arunagiri A, Arvan P, Tang X. Transgenic overexpression of microRNA-30d in pancreatic beta-cells progressively regulates beta-cell function and identity. Sci Rep 2022; 12:11969. [PMID: 35831364 PMCID: PMC9279310 DOI: 10.1038/s41598-022-16174-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 07/06/2022] [Indexed: 11/15/2022] Open
Abstract
Abnormal microRNA functions are closely associated with pancreatic β-cell loss and dysfunction in type 2 diabetes. Dysregulation of miR-30d has been reported in the individuals with diabetes. To study how miR-30d affects pancreatic β-cell functions, we generated two transgenic mouse lines that specifically overexpressed miR-30d in β-cells at distinct low and high levels. Transgenic overexpressed miR-30d systemically affected β-cell function. Elevated miR-30d at low-level (TgL, 2-fold) had mild effects on signaling pathways and displayed no significant changes to metabolic homeostasis. In contrast, transgenic mice with high-level of miR-30d expression (TgH, 12-fold) exhibited significant diet-induced hyperglycemia and β-cell dysfunction. In addition, loss of β-cell identity was invariably accompanied with increased insulin/glucagon-double positive bihormonal cells and excess plasma glucagon levels. The transcriptomic analysis revealed that miR-30d overexpression inhibited β-cell-enriched gene expression and induced α-cell-enriched gene expression. These findings implicate that an appropriate miR-30d level is essential in maintaining normal β-cell identity and function.
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Affiliation(s)
- Yiping Mao
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Jacob Schoenborn
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Zhihong Wang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Xinqian Chen
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Katy Matson
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Ramkumar Mohan
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Shungang Zhang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Xiaohu Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Anoop Arunagiri
- Department of Metabolism Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter Arvan
- Department of Metabolism Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiaoqing Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA.
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12
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Sun X, Zhang T, Li L, Tu K, Yu T, Wu B, Zhou L, Tian J, Liu Z. MicroRNA expression signature in the striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis. Genomics 2022; 114:110409. [PMID: 35714827 DOI: 10.1016/j.ygeno.2022.110409] [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: 12/21/2021] [Revised: 04/25/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022]
Abstract
Increasing evidences point to the potential role of microRNAs (miRNAs) in muscle growth and development in animals. However, knowledge on the identity of miRNAs and their targets in molluscs remains largely unknown. Scallops have one large adductor muscle, composed of fast (striated) and slow (smooth) muscle types, which display great differences in muscle fibers, meat quality, cell types and molecular components. In the present study, we performed a comprehensive investigation of miRNA transcriptomes in fast and slow adductor muscles of Yesso scallop Patinopecten yessoensis. As a result, 47 differentially expressed miRNAs representing ten miRNA families were identified between the striated and smooth adductor muscles. The KEGG enrichment analysis of their target genes were mainly associated with amino acid metabolism, energy metabolism and glycan biosynthesis. The target genes of miR-133 and miR-71 were validated by the dual-luciferase reporter assays and miRNA antagomir treatment in vivo. The identification and functional validation of these different miRNAs in scallops will greatly help our understanding of miRNA regulatory mechanism that achieves the unique muscle phenotypes in scallops. The present findings provide the direct evidences for muscle-specific miRNAs involved in muscle growth and differentiation in molluscs.
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Affiliation(s)
- Xiujun Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Tianshi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Li Li
- National Oceanographic Center, Qingdao 266104, China
| | - Kang Tu
- Putian Institute of Aquaculture Science of Fujian Province, Putian 351100, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Changdao, China
| | - Biao Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Liqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Jiteng Tian
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Zhihong Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China.
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13
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Huang S, Nishiumi S, Asaduzzaman M, Pan Y, Liu G, Yoshitake K, Maeyama K, Kinoshita S, Nagai K, Watabe S, Yoshida T, Asakawa S. Exosome-derived small non-coding RNAs reveal immune response upon grafting transplantation in Pinctada fucata (Mollusca). Open Biol 2022; 12:210317. [PMID: 35506205 PMCID: PMC9065966 DOI: 10.1098/rsob.210317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Exosomes, a subset of small extracellular vesicles, carry various nucleic acids, proteins, lipids, amino acids and metabolites. They function as a mode of intercellular communication and molecular transfer. Exosome cargo molecules, including small non-coding RNAs (sncRNAs), are involved in the immune response in various organisms. However, the role of exosome-derived sncRNAs in immune responses in molluscs remains unclear. Here, we aimed to reveal the sncRNAs involved in the immune response during grafting transplantation by the pearl oyster Pinctada fucata. Exosomes were successfully extracted from the P. fucata haemolymph during graft transplantation. Abundant microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) were simultaneously discovered in P. fucata exosomes by small RNA sequencing. The expression patterns of the miRNAs and piRNAs at the grafting and initial stages were not substantially different, but varied significantly between the initial and later stages. Target prediction and functional analysis indicate that these miRNAs and piRNAs are related to immune response upon grafting transplantation, whereas piRNAs may also be associated with transposon silencing by targeting with genome transposon elements. This work provides the basis for a functional understanding of exosome-derived sncRNAs and helps to gain further insight into the PIWI/piRNA pathway function outside of germline cells in molluscs.
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Affiliation(s)
- Songqian Huang
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shinya Nishiumi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Md Asaduzzaman
- Department of Marine Bioresources Science, Faculty of Fisheries, Chittagong Veterinary and Animal Sciences University, Khulshi 4225, Chittagong, Bangladesh
| | - Yida Pan
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Guanting Liu
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kaoru Maeyama
- Mikimoto Pharmaceutical Co., Ltd., Kurose 1425, Ise, Mie 516-8581, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyohito Nagai
- Pearl Research Laboratory, K. Mikimoto & Co., Ltd., Osaki Hazako 923, Hamajima, Shima, Mie 517-0403, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0313, Japan
| | - Tetsuhiko Yoshida
- Institute for Advanced Sciences, Toagosei Co., Ltd., Tsukuba, Ibaraki 300-2611, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
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14
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The Landscape of Circulating miRNAs in the Post-Genomic Era. Genes (Basel) 2021; 13:genes13010094. [PMID: 35052434 PMCID: PMC8774581 DOI: 10.3390/genes13010094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 02/06/2023] Open
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15
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Zhiyanov A, Nersisyan S, Tonevitsky A. Hairpin sequence and structure is associated with features of isomiR biogenesis. RNA Biol 2021; 18:430-438. [PMID: 34286662 DOI: 10.1080/15476286.2021.1952759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5'-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. In this manuscript, we analysed the distribution of miRNA cleavage positions across 31 different cancers using miRNA sequencing data of TCGA project. As a result, we found that the processing positions are not tissue specific and that all miRNAs could be correctly classified as ones exhibiting homogeneous or heterogeneous cleavage at one of the four cleavage sites. In 42% of cases (42 out of 100 miRNAs), we observed imprecise 5'-end Dicer cleavage, while this fraction was only 14% for Drosha (14 out of 99). To the contrary, almost all cleavage sites of 3'-ends (either Drosha or Dicer) were heterogeneous. With the use of only four nucleotides surrounding a 5'-end Dicer cleavage position we built a model which allowed us to distinguish between homogeneous and heterogeneous cleavage with the reliable quality (ROC AUC = 0.68). Finally, we showed the possible applications of the study by the analysis of two 5'-end isoforms originating from the same exogeneous shRNA hairpin. It turned out that the less expressed shRNA variant was functionally active, which led to the increased off-targeting. Thus, the obtained results could be applied to the design of shRNAs whose processing will result in a single 5'-variant.
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Affiliation(s)
- Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
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16
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Ye L, Wang F, Wu H, Yang H, Yang Y, Ma Y, Xue A, Zhu J, Chen M, Wang J, Zhang QA. Functions and Targets of miR-335 in Cancer. Onco Targets Ther 2021; 14:3335-3349. [PMID: 34045870 PMCID: PMC8144171 DOI: 10.2147/ott.s305098] [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: 02/03/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (18~25 nt in length) that act as master regulators of eukaryotic gene expression. They might play an oncogenic or tumor-suppressive role in multiple cancers. In recent decades, several studies have focused on the functions and mechanisms of miR-335 in cancer. The expression level of miR-335 in tissues and cells varies with cancer types, and miR-335 has been proposed as a potential biomarker for the prognosis of cancer. Besides, miR-335 may serve as an oncogene or tumor suppressor via regulating different targets or pathways in tumor initiation, development, and metastasis. Furthermore, miR-335 also influences tumor microenvironment and drug sensitivity. MiR-335 is regulated by various factors such as lncRNAs and microRNAs. In this review, we reveal the functions and targets of miR-335 in various cancers and its potential application as a possible biomarker in prognostic judgment and treatment of malignant tumors.
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Affiliation(s)
- Lingling Ye
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Fen Wang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Hao Wu
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Hui Yang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Yan Yang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Yajun Ma
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Aili Xue
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Jing Zhu
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Meili Chen
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Jinyan Wang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Quan An Zhang
- Department of Oncology, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
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17
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Arif KT, Okolicsanyi RK, Haupt LM, Griffiths LR. A combinatorial in silico approach for microRNA-target identification: Order out of chaos. Biochimie 2021; 187:121-130. [PMID: 34019954 DOI: 10.1016/j.biochi.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/17/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Contemporary computational microRNA(miRNA)-target prediction tools have been playing a vital role in pursuing putative targets for a solitary miRNA or a group of miRNAs. These tools utilise a set of probabilistic algorithms, machine learning techniques and analyse experimentally validated miRNA targets to identify the potential miRNA-target pairs. Unfortunately, current tools generate a huge number of false-positive predictions. A standardized approach with a single tool or a combination of tools is still lacking. Moreover, sensitivity, specificity and overall efficiency of any single tool are yet to be satisfactory. Therefore, a systematic combination of selective online tools combining the factors regarding miRNA-target identification would be valuable as an miRNA-target prediction scheme. The focus of this study was to develop a theoretical framework by combining six available online tools to facilitate the current understanding of miRNA-target identification.
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Affiliation(s)
- Km Taufiqul Arif
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
| | - Rachel K Okolicsanyi
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
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18
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Wang Z, Mohan R, Chen X, Matson K, Waugh J, Mao Y, Zhang S, Li W, Tang X, Satin LS, Tang X. microRNA-483 Protects Pancreatic β-Cells by Targeting ALDH1A3. Endocrinology 2021; 162:6132087. [PMID: 33564883 PMCID: PMC7951052 DOI: 10.1210/endocr/bqab031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Indexed: 12/14/2022]
Abstract
Pancreatic β-cell dysfunction is central to the development and progression of type 2 diabetes. Dysregulation of microRNAs (miRNAs) has been associated with pancreatic islet dysfunction in type 2 diabetes. Previous study has shown that miR-483 is expressed relatively higher in β-cells than in α-cells. To explore the physiological function of miR-483, we generated a β-cell-specific knockout mouse model of miR-483. Loss of miR-483 enhances high-fat diet-induced hyperglycemia and glucose intolerance by the attenuation of diet-induced insulin release. Intriguingly, mice with miR-483 deletion exhibited loss of β-cell features, as indicated by elevated expression of aldehyde dehydrogenase family 1, subfamily A3 (Aldh1a3), a marker of β-cell dedifferentiation. Moreover, Aldh1a3 was validated as a direct target of miR-483 and overexpression of miR-483 repressed Aldh1a3 expression. Genetic ablation of miR-483 also induced alterations in blood lipid profile. Collectively, these data suggest that miR-483 is critical in protecting β-cell function by repressing the β-cell disallowed gene Aldh1a3. The dysregulated miR-483 may impair insulin secretion and initiate β-cell dedifferentiation during the development of type 2 diabetes.
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Affiliation(s)
- Zhihong Wang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Ramkumar Mohan
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Xinqian Chen
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Katy Matson
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Jackson Waugh
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Yiping Mao
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Shungang Zhang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Wanzhen Li
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Xiaohu Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Leslie S Satin
- Department of Pharmacology, Brehm Center for Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoqing Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
- Correspondence: Xiaoqing Tang, PhD, Michigan Technological University, 1400 Townsend Dr., Houghton, MI 49931, USA.
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19
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Tian J, Adams MJ, Tay JWT, James I, Powell S, Hughes QW, Gilmore G, Baker RI, Tiao JYH. Estradiol-Responsive miR-365a-3p Interacts with Tissue Factor 3'UTR to Modulate Tissue Factor-Initiated Thrombin Generation. Thromb Haemost 2021; 121:1483-1496. [PMID: 33540457 DOI: 10.1055/a-1382-9983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND High estradiol (E2) levels are linked to an increased risk of venous thromboembolism; however, the underlying molecular mechanism(s) remain poorly understood. We previously identified an E2-responsive microRNA (miR), miR-494-3p, that downregulates protein S expression, and posited additional coagulation factors, such as tissue factor, may be regulated in a similar manner via miRs. OBJECTIVES To evaluate the coagulation capacity of cohorts with high physiological E2, and to further characterize novel E2-responsive miR and miR regulation on tissue factor in E2-related hypercoagulability. METHODS Ceveron Alpha thrombin generation assay (TGA) was used to assess plasma coagulation profile of three cohorts. The effect of physiological levels of E2, 10 nM, on miR expression in HuH-7 cells was compared using NanoString nCounter and validated with independent assays. The effect of tissue factor-interacting miR was confirmed by dual-luciferase reporter assays, immunoblotting, flow cytometry, biochemistry assays, and TGA. RESULTS Plasma samples from pregnant women and women on the contraceptive pill were confirmed to be hypercoagulable (compared with sex-matched controls). At equivalent and high physiological levels of E2, miR-365a-3p displayed concordant E2 downregulation in two independent miR quantification platforms, and tissue factor protein was upregulated by E2 treatment. Direct interaction between miR-365a-3p and F3-3'UTR was confirmed and overexpression of miR-365a-3p led to a decrease of (1) tissue factor mRNA transcripts, (2) protein levels, (3) activity, and (4) tissue factor-initiated thrombin generation. CONCLUSION miR-365a-3p is a novel tissue factor regulator. High E2 concentrations induce a hypercoagulable state via a miR network specific for coagulation factors.
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Affiliation(s)
- Jiayin Tian
- Western Australian Centre for Thrombosis and Haemostasis, Murdoch University, Murdoch, Perth, Australia.,Perth Blood Institute, West Perth, Perth, Australia.,College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Perth, Australia
| | - Murray J Adams
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, Australia
| | - Jasmine Wee Ting Tay
- Western Australian Centre for Thrombosis and Haemostasis, Murdoch University, Murdoch, Perth, Australia.,Perth Blood Institute, West Perth, Perth, Australia
| | - Ian James
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Perth, Australia
| | - Suzanne Powell
- Western Australian Centre for Thrombosis and Haemostasis, Murdoch University, Murdoch, Perth, Australia
| | - Quintin W Hughes
- Western Australian Centre for Thrombosis and Haemostasis, Murdoch University, Murdoch, Perth, Australia.,Perth Blood Institute, West Perth, Perth, Australia
| | - Grace Gilmore
- Western Australian Centre for Thrombosis and Haemostasis, Murdoch University, Murdoch, Perth, Australia.,Perth Blood Institute, West Perth, Perth, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Perth, Australia
| | - Ross I Baker
- Western Australian Centre for Thrombosis and Haemostasis, Murdoch University, Murdoch, Perth, Australia.,Perth Blood Institute, West Perth, Perth, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Perth, Australia
| | - Jim Yu-Hsiang Tiao
- Western Australian Centre for Thrombosis and Haemostasis, Murdoch University, Murdoch, Perth, Australia.,Perth Blood Institute, West Perth, Perth, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Perth, Australia
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20
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Grigaitis P, Starkuviene V, Rost U, Serva A, Pucholt P, Kummer U. miRNA target identification and prediction as a function of time in gene expression data. RNA Biol 2020; 17:990-1000. [PMID: 32249661 PMCID: PMC7549638 DOI: 10.1080/15476286.2020.1748921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/01/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
The understanding of miRNA target interactions is still limited due to conflicting data and the fact that high-quality validation of targets is a time-consuming process. Faster methods like high-throughput screens and bioinformatics predictions are employed but suffer from several problems. One of these, namely the potential occurrence of downstream (i.e. secondary) effects in high-throughput screens has been only little discussed so far. However, such effects limit usage for both the identification of interactions and for the training of bioinformatics tools. In order to analyse this problem more closely, we performed time-dependent microarray screening experiments overexpressing human miR-517a-3p, and, together with published time-dependent datasets of human miR-17-5p, miR-135b and miR-124 overexpression, we analysed the dynamics of deregulated genes. We show that the number of deregulated targets increases over time, whereas seed sequence content and performance of several miRNA target prediction algorithms actually decrease over time. Bioinformatics recognition success of validated miR-17 targets was comparable to that of data gained only 12 h post-transfection. We therefore argue that the timing of microarray experiments is of critical importance for detecting direct targets with high confidence and for the usability of these data for the training of bioinformatics prediction tools.
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Affiliation(s)
- Pranas Grigaitis
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Vytaute Starkuviene
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
- Institute of Biosciences, Vilnius University Life Sciences Centre, Vilnius, Lithuania
| | - Ursula Rost
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Andrius Serva
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Pascal Pucholt
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Ursula Kummer
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
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21
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Wiebe KF, Elebute OO, LeMoine CMR, Cassone BJ. A Day in the Life: Identification of Developmentally Regulated MicroRNAs in the Colorado Potato Beetle (Leptinotarsa decemlineata; Coleoptera: Chrysomelidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:1445-1454. [PMID: 32150604 DOI: 10.1093/jee/toaa020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 06/10/2023]
Abstract
The Colorado potato beetle (Leptinotarsa decemlineata (Say)) is an important pest of the cultivated potato (Solanum tuberosum (L.) [Solanales: Solanaceae]). With its broad resistance toward commonly used insecticides, it is clear that more sophisticated control strategies are needed. Due to their importance in insect development, microRNAs (miRNAs) represent a potential tool to employ in insect control strategies. However, most studies conducted in this area have focused on model species with well-annotated genomes. In this study, next-generation sequencing was used to catalogue the miRNAs produced by L. decemlineata across all eight stages of its development, from eggs to adults. For most stages, the length of miRNAs peaked between 21 and 22 nt, though it was considerably longer for the egg stage (26 nt). Global profiling of miRNAs revealed three distinct developmental clusters: 1) egg stage; 2) early stage (first, second, and third instar); and 3) late stage (fourth instar, prepupae, pupae, and adult). We identified 86 conserved miRNAs and 33 bonafide novel miRNAs, including stage-specific miRNAs and those not previously identified in L. decemlineata. Most of the conserved miRNAs were found in multiple developmental stages, whereas the novel miRNAs were often stage specific with the bulk identified in the egg stage. The identified miRNAs have a myriad of putative functions, including growth, reproduction, and insecticide resistance. We discuss the putative roles of some of the most notable miRNAs in the regulation of L. decemlineata development, as well as the potential applications of this research in Colorado potato beetle management.
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Affiliation(s)
- K F Wiebe
- Department of Biology, Brandon University, Brandon, Canada
| | - O O Elebute
- Department of Biology, Brandon University, Brandon, Canada
| | - C M R LeMoine
- Department of Biology, Brandon University, Brandon, Canada
| | - B J Cassone
- Department of Biology, Brandon University, Brandon, Canada
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22
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Bautista-Sánchez D, Arriaga-Canon C, Pedroza-Torres A, De La Rosa-Velázquez IA, González-Barrios R, Contreras-Espinosa L, Montiel-Manríquez R, Castro-Hernández C, Fragoso-Ontiveros V, Álvarez-Gómez RM, Herrera LA. The Promising Role of miR-21 as a Cancer Biomarker and Its Importance in RNA-Based Therapeutics. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:409-420. [PMID: 32244168 PMCID: PMC7118281 DOI: 10.1016/j.omtn.2020.03.003] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs are small noncoding transcripts that posttranscriptionally regulate gene expression via base-pairing complementarity. Their role in cancer can be related to tumor suppression or oncogenic function. Moreover, they have been linked to processes recognized as hallmarks of cancer, such as apoptosis, invasion, metastasis, and proliferation. Particularly, one of the first oncomiRs found upregulated in a variety of cancers, such as gliomas, breast cancer, and colorectal cancer, was microRNA-21 (miR-21). Some of its target genes associated with cancer are PTEN (phosphatase and tensin homolog), PDCD4 (programmed cell death protein 4), RECK (reversion-inducing cysteine-rich protein with Kazal motifs), and STAT3 (signal transducer activator of transcription 3). As a result, miR-21 has been proposed as a plausible diagnostic and prognostic biomarker, as well as a therapeutic target for several types of cancer. Currently, research and clinical trials to inhibit miR-21 through anti-miR-21 oligonucleotides and ADM-21 are being conducted. As all of the evidence suggests, miR-21 is involved in carcinogenic processes; therefore, inhibiting it could have effects on more than one type of cancer. However, whether miR-21 can be used as a tissue-specific biomarker should be analyzed with caution. Consequently, the purpose of this review is to outline the available information and recent advances regarding miR-21 as a potential biomarker in the clinical setting and as a therapeutic target in cancer to highlight its importance in the era of precision medicine.
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Affiliation(s)
- Diana Bautista-Sánchez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Abraham Pedroza-Torres
- CONACYT-Instituto Nacional de Cancerología, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | | | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Verónica Fragoso-Ontiveros
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Rosa María Álvarez-Gómez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22, Colonia Sección XVI, Tlalpan, CP 14080, Mexico City, Mexico; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Tlalpan, CP 14610, Mexico City, Mexico.
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23
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Posner R, Laubenbacher R. The contribution of microRNA-mediated regulation to short- and long-term gene expression predictability. J Theor Biol 2020; 486:110055. [PMID: 31647935 DOI: 10.1016/j.jtbi.2019.110055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/14/2019] [Accepted: 10/20/2019] [Indexed: 11/28/2022]
Abstract
MicroRNAs are a class of short, noncoding RNAs which are essential for the coordination and timing of cell differentiation and embryonic development. However, despite their guiding role in development, microRNAs are dysregulated in many pathologies, including nearly all cases of cancer. While both development and oncogenesis can be thought of as extremes of phenotypic plasticity, they characteristically manifest on much different time scales: one taking place over a matter of weeks, the other typically requiring decades. Because microRNAs are believed to support this plasticity, a critically important question is how microRNAs affect phenotypic stability on different time scales, and what dynamical characteristics shift the balance between these two roles. To address this question, we extend a well-established mathematical model of transcriptional gene regulation to include translational regulation by microRNAs, and examine their effects on both short- and long-term gene expression predictability. Our findings show that microRNAs greatly improve short-term predictability for earlier, developmental phenotypes while causing a small decrease in long-term predictability, and that these effects are difficult to separate. In addition to providing a theoretical explanation for this seemingly duplicitous behavior, we describe some of the properties which determine the cost-benefit balance between short-term stabilization and long-term destabilization.
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Affiliation(s)
- Russell Posner
- Center for Quantitative Medicine, UConn Health, 263 Farmington Avenue Farmington, CT 06030, USA.
| | - Reinhard Laubenbacher
- Center for Quantitative Medicine, UConn Health, 263 Farmington Avenue Farmington, CT 06030, USA; The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington, CT 06032, USA
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24
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Piragasam RS, Hussain SF, Chaulk SG, Siddiqi ZA, Fahlman RP. Label-free proteomic analysis reveals large dynamic changes to the cellular proteome upon expression of the miRNA-23a-27a-24-2 microRNA cluster. Biochem Cell Biol 2020; 98:61-69. [DOI: 10.1139/bcb-2019-0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In deciphering the regulatory networks of gene expression controlled by the small non-coding RNAs known as microRNAs (miRNAs), a major challenge has been with the identification of the true mRNA targets by these RNAs within the context of the enormous numbers of predicted targets for each of these small RNAs. To facilitate the system-wide identification of miRNA targets, a variety of system wide methods, such as proteomics, have been implemented. Here we describe the utilization of quantitative label-free proteomics and bioinformatics to identify the most significant changes to the proteome upon expression of the miR-23a-27a-24-2 miRNA cluster. In light of recent work leading to the hypothesis that only the most pronounced regulatory events by miRNAs may be physiologically relevant, our data reveal that label-free analysis circumvents the limitations of proteomic labeling techniques that limit the maximum differences that can be quantified. The result of our analysis identifies a series of novel candidate targets that are reduced in abundance by more than an order of magnitude upon the expression of the miR-23a-27a-24-2 cluster.
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Affiliation(s)
- Ramanaguru S. Piragasam
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - S. Faraz Hussain
- Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Steven G. Chaulk
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Zaeem A. Siddiqi
- Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Richard P. Fahlman
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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25
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Reynolds JA. Noncoding RNA Regulation of Dormant States in Evolutionarily Diverse Animals. THE BIOLOGICAL BULLETIN 2019; 237:192-209. [PMID: 31714856 DOI: 10.1086/705484] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dormancy is evolutionarily widespread and can take many forms, including diapause, dauer formation, estivation, and hibernation. Each type of dormancy is characterized by distinct features; but accumulating evidence suggests that each is regulated by some common processes, often referred to as a common "toolkit" of regulatory mechanisms, that likely include noncoding RNAs that regulate gene expression. Noncoding RNAs, especially microRNAs, are well-known regulators of biological processes associated with numerous dormancy-related processes, including cell cycle progression, cell growth and proliferation, developmental timing, metabolism, and environmental stress tolerance. This review provides a summary of our current understanding of noncoding RNAs and their involvement in regulating dormancy.
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Not Only Mutations Matter: Molecular Picture of Acute Myeloid Leukemia Emerging from Transcriptome Studies. JOURNAL OF ONCOLOGY 2019; 2019:7239206. [PMID: 31467542 PMCID: PMC6699387 DOI: 10.1155/2019/7239206] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023]
Abstract
The last two decades of genome-scale research revealed a complex molecular picture of acute myeloid leukemia (AML). On the one hand, a number of mutations were discovered and associated with AML diagnosis and prognosis; some of them were introduced into diagnostic tests. On the other hand, transcriptome studies, which preceded AML exome and genome sequencing, remained poorly translated into clinics. Nevertheless, gene expression studies significantly contributed to the elucidation of AML pathogenesis and indicated potential therapeutic directions. The power of transcriptomic approach lies in its comprehensiveness; we can observe how genome manifests its function in a particular type of cells and follow many genes in one test. Moreover, gene expression measurement can be combined with mutation detection, as high-impact mutations are often present in transcripts. This review sums up 20 years of transcriptome research devoted to AML. Gene expression profiling (GEP) revealed signatures distinctive for selected AML subtypes and uncovered the additional within-subtype heterogeneity. The results were particularly valuable in the case of AML with normal karyotype which concerns up to 50% of AML cases. With the use of GEP, new classes of the disease were identified and prognostic predictors were proposed. A plenty of genes were detected as overexpressed in AML when compared to healthy control, including KIT, BAALC, ERG, MN1, CDX2, WT1, PRAME, and HOX genes. High expression of these genes constitutes usually an unfavorable prognostic factor. Upregulation of FLT3 and NPM1 genes, independent on their mutation status, was also reported in AML and correlated with poor outcome. However, transcriptome is not limited to the protein-coding genes; other types of RNA molecules exist in a cell and regulate genome function. It was shown that microRNA (miRNA) profiles differentiated AML groups and predicted outcome not worse than protein-coding gene profiles. For example, upregulation of miR-10a, miR-10b, and miR-196b and downregulation of miR-192 were found as typical of AML with NPM1 mutation whereas overexpression of miR-155 was associated with FLT3-internal tandem duplication (FLT3-ITD). Development of high-throughput technologies and microarray replacement by next generation sequencing (RNA-seq) enabled uncovering a real variety of leukemic cell transcriptomes, reflected by gene fusions, chimeric RNAs, alternatively spliced transcripts, miRNAs, piRNAs, long noncoding RNAs (lncRNAs), and their special type, circular RNAs. Many of them can be considered as AML biomarkers and potential therapeutic targets. The relations between particular RNA puzzles and other components of leukemic cells and their microenvironment, such as exosomes, are now under investigation. Hopefully, the results of this research will shed the light on these aspects of AML pathogenesis which are still not completely understood.
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Phillips JO, Butt LE, Henderson CA, Devonshire M, Healy J, Conway SJ, Locker N, Pickford AR, Vincent HA, Callaghan AJ. High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions. Nucleic Acids Res 2019; 46:e86. [PMID: 29846708 PMCID: PMC6101487 DOI: 10.1093/nar/gky410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/02/2018] [Indexed: 12/13/2022] Open
Abstract
We are just beginning to unravel the myriad of interactions in which non-coding RNAs participate. The intricate RNA interactome is the foundation of many biological processes, including bacterial virulence and human disease, and represents unexploited resources for the development of potential therapeutic interventions. However, identifying specific associations of a given RNA from the multitude of possible binding partners within the cell requires robust high-throughput systems for their rapid screening. Here, we present the first demonstration of functional-RNA arrays as a novel platform technology designed for the study of such interactions using immobilized, active RNAs. We have generated high-density RNA arrays by an innovative method involving surface-capture of in vitro transcribed RNAs. This approach has significant advantages over existing technologies, particularly in its versatility in regards to binding partner character. Indeed, proof-of-principle application of RNA arrays to both RNA–small molecule and RNA–RNA pairings is demonstrated, highlighting their potential as a platform technology for mapping RNA-based networks and for pharmaceutical screening. Furthermore, the simplicity of the method supports greater user-accessibility over currently available technologies. We anticipate that functional-RNA arrays will find broad utility in the expanding field of RNA characterization.
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Affiliation(s)
- Jack O Phillips
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Louise E Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Charlotte A Henderson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Martin Devonshire
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Jess Healy
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7HX, UK
| | - Andrew R Pickford
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Helen A Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Anastasia J Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
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Ravichandran S, Ragupathy R, Edwards T, Domaratzki M, Cloutier S. MicroRNA-guided regulation of heat stress response in wheat. BMC Genomics 2019; 20:488. [PMID: 31195958 PMCID: PMC6567507 DOI: 10.1186/s12864-019-5799-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022] Open
Abstract
Background With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post-transcriptional level. In this study, small RNAs and the degradome (parallel analysis of RNA ends) of leaf tissues collected from control and heat-stressed wheat plants immediately at the end of the stress period and 1 and 4 days later were analysed. Results Sequencing of 24 small RNA libraries produced 55.2 M reads while 404 M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins. Conclusion The interlaced data set generated in this study identified and validated heat stress regulated miRNAs and their target genes associated with thermotolerance. Such accurate identification and validation of miRNAs and their target genes are essential to develop novel regulatory gene-based breeding strategies. Electronic supplementary material The online version of this article (10.1186/s12864-019-5799-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sridhar Ravichandran
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Raja Ragupathy
- Plant Science Department, University of Manitoba, Winnipeg, Manitoba, Canada.,Present address: Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Tara Edwards
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Michael Domaratzki
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada.
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29
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Mockly S, Seitz H. Inconsistencies and Limitations of Current MicroRNA Target Identification Methods. Methods Mol Biol 2019; 1970:291-314. [PMID: 30963499 DOI: 10.1007/978-1-4939-9207-2_16] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
MicroRNAs and their Argonaute protein partners constitute the RISC complex, which can repress specific target mRNAs. The identification of microRNA targets is of central importance, and various experimental and computational methods have been developed over the last 15 years. Most experimental methods are based on the assumption that mRNAs which interact physically with the RISC complex constitute regulatory targets and, similarly, some computational methods only aim at predicting physical interactors for RISC. Besides specific limitations, which we discuss for each method, the mere concept of assuming a functional role for every detected molecular event is likely to identify many deceptive interactions (i.e., interactions that really exist at the molecular scale, but without controlling any biological function at the macroscopic scale).In order to select biologically important interactions, some computational tools interrogate the phylogenetic conservation of microRNA/mRNA interactions, thus theoretically selecting only biologically relevant targets. Yet even comparative genomics can yield false positives.Conceptual and technical limitations for all these techniques tend to be overlooked by the scientific community. This review sums them up, emphasizing on the implications of these issues on our understanding of microRNA biology.
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Affiliation(s)
- Sophie Mockly
- IGH (CNRS and University of Montpellier), Montpellier, France
| | - Hervé Seitz
- IGH (CNRS and University of Montpellier), Montpellier, France.
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30
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Abstract
miRNAs, ∼20 to 22 nucleotide single-stranded RNA species that play a pivotal role in the regulation of protein-coding genes, are emerging as robust biomarkers for assessing allograft status. Herein, the authors briefly review the biogenesis and function of the miRNAs and provide an overview of the tools to quantify miRNAs in tissues and body fluids. They then review their studies of discovery and validation of alterations in miRNA expression within kidney allografts with or without acute rejection, as well as with or without fibrosis, and summarize published data on miRNA expression patterns in kidney transplant recipients.
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Affiliation(s)
- Zahraa Khan
- Division of Nephrology and Hypertension, Department of Medicine, New York-Presbyterian-Weill Cornell Medicine, 525 East 68th Street, Box 3, New York, NY 10065, USA; Division of Nephrology and Hypertension, Department of Transplantation Medicine, New York-Presbyterian-Weill Cornell Medicine, 525 East 68th Street, Box 3, New York, NY 10065, USA
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, New York-Presbyterian-Weill Cornell Medicine, 525 East 68th Street, Box 3, New York, NY 10065, USA; Division of Nephrology and Hypertension, Department of Transplantation Medicine, New York-Presbyterian-Weill Cornell Medicine, 525 East 68th Street, Box 3, New York, NY 10065, USA
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension, Department of Medicine, New York-Presbyterian-Weill Cornell Medicine, 525 East 68th Street, Box 3, New York, NY 10065, USA; Division of Nephrology and Hypertension, Department of Transplantation Medicine, New York-Presbyterian-Weill Cornell Medicine, 525 East 68th Street, Box 3, New York, NY 10065, USA.
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Fuchs Wightman F, Giono LE, Fededa JP, de la Mata M. Target RNAs Strike Back on MicroRNAs. Front Genet 2018; 9:435. [PMID: 30333855 PMCID: PMC6175985 DOI: 10.3389/fgene.2018.00435] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are extensively studied regulatory non-coding small RNAs that silence animal genes throughout most biological processes, typically doing so by binding to partially complementary sequences within target RNAs. A plethora of studies has described detailed mechanisms for microRNA biogenesis and function, as well as their temporal and spatial regulation during development. By inducing translational repression and/or degradation of their target RNAs, microRNAs can contribute to achieve highly specific cell- or tissue-specific gene expression, while their aberrant expression can lead to disease. Yet an unresolved aspect of microRNA biology is how such small RNA molecules are themselves cleared from the cell, especially under circumstances where fast microRNA turnover or specific degradation of individual microRNAs is required. In recent years, it was unexpectedly found that binding of specific target RNAs to microRNAs with extensive complementarity can reverse the outcome, triggering degradation of the bound microRNAs. This emerging pathway, named TDMD for Target RNA-Directed MicroRNA Degradation, leads to microRNA 3'-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3' end, and highly specific microRNA loss, providing a new layer of microRNA regulation. Originally described in flies and known to be triggered by viral RNAs, novel endogenous instances of TDMD have been uncovered and are now starting to be understood. Here, we review our current knowledge of this pathway and its potential role in the control and diversification of microRNA expression patterns.
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Affiliation(s)
- Federico Fuchs Wightman
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciana E Giono
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Juan Pablo Fededa
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Manuel de la Mata
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
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Durban J, Sasa M, Calvete JJ. Venom gland transcriptomics and microRNA profiling of juvenile and adult yellow-bellied sea snake, Hydrophis platurus, from Playa del Coco (Guanacaste, Costa Rica). Toxicon 2018; 153:96-105. [DOI: 10.1016/j.toxicon.2018.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/13/2018] [Accepted: 08/29/2018] [Indexed: 02/08/2023]
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Bandi S, Gupta S, Tchaikovskaya T, Gupta S. Differentiation in stem/progenitor cells along fetal or adult hepatic stages requires transcriptional regulators independently of oscillations in microRNA expression. Exp Cell Res 2018; 370:1-12. [PMID: 29883712 DOI: 10.1016/j.yexcr.2018.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/03/2018] [Accepted: 06/04/2018] [Indexed: 01/09/2023]
Abstract
Understanding mechanisms in lineage differentiation is critical for organ development, pathophysiology and oncogenesis. To determine whether microRNAs (miRNA) may serve as drivers or adjuncts in hepatic differentiation, we studied human embryonic stem cell-derived hepatocytes and primary hepatocytes representing fetal or adult stages. Model systems were used for hepatic lineage advancement or regression under culture conditions with molecular assays. Profiles of miRNA in primary fetal and adult hepatocytes shared similarities and distinctions from pluripotent stem cells or stem cell-derived early fetal-like hepatocytes. During phenotypic regression in fetal or adult hepatocytes, miRNA profiles oscillated to regain stemness-associated features that had not been extinguished in stem cell-derived fetal-like hepatocytes. These oscillations in stemness-associated features were not altered in fetal-like hepatocytes by inhibitory mimics for dominantly-expressed miRNA, such as hsa-miR-99b, -100, -214 and -221/222. The stem cell-derived fetal-like hepatocytes were permissive for miRNA characterizing mature hepatocytes, including mimics for hsa-miR-122, -126, -192, -194 and -26b, although transfections of the latter did not advance hepatic differentiation. Examination of genome-wide mRNA expression profiles in stem cell-derived or primary fetal hepatocytes indicated targets of highly abundant miRNA regulated general processes, e.g., cell survival, growth and proliferation, functional maintenance, etc., without directing cell differentiation. Among upstream regulators of gene networks in stem cell-derived hepatocytes included HNF4A, SNAI1, and others, which affect transcriptional circuits directing lineage development or maintenance. Therefore, miRNA expression oscillated in response to microenvironmental conditions, whereas lineage-specific transcriptional regulators, such as HNF4A, were necessary for directing hepatic differentiation. This knowledge will be helpful for understanding the contribution of stem cells in pathophysiological states and oncogenesis, as well as for applications of stem cell-derived hepatocytes.
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Affiliation(s)
- Sriram Bandi
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States; Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, United States.
| | - Sanchit Gupta
- Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, United States.
| | - Tatyana Tchaikovskaya
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States; Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, United States.
| | - Sanjeev Gupta
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States; Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, United States; Diabetes Center, Albert Einstein College of Medicine, Bronx, NY, United States; The Irwin S. and Sylvia Chanin Institute for Cancer Research, Albert Einstein College of Medicine, Bronx, NY, United States; The Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States.
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