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Dadhwal G, Samy H, Bouvette J, El-Azzouzi F, Dagenais P, Legault P. Substrate promiscuity of Dicer toward precursors of the let-7 family and their 3'-end modifications. Cell Mol Life Sci 2024; 81:53. [PMID: 38261114 PMCID: PMC10806991 DOI: 10.1007/s00018-023-05090-2] [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: 07/11/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
The human let-7 miRNA family consists of thirteen members that play critical roles in many biological processes, including development timing and tumor suppression, and their levels are disrupted in several diseases. Dicer is the endoribonuclease responsible for processing the precursor miRNA (pre-miRNA) to yield the mature miRNA, and thereby plays a crucial role in controlling the cellular levels of let-7 miRNAs. It is well established that the sequence and structural features of pre-miRNA hairpins such as the 5'-phosphate, the apical loop, and the 2-nt 3'-overhang are important for the processing activity of Dicer. Exceptionally, nine precursors of the let-7 family (pre-let-7) contain a 1-nt 3'-overhang and get mono-uridylated in vivo, presumably to allow efficient processing by Dicer. Pre-let-7 are also oligo-uridylated in vivo to promote their degradation and likely prevent their efficient processing by Dicer. In this study, we systematically investigated the impact of sequence and structural features of all human let-7 pre-miRNAs, including their 3'-end modifications, on Dicer binding and processing. Through the combination of SHAPE structural probing, in vitro binding and kinetic studies using purified human Dicer, we show that despite structural discrepancies among pre-let-7 RNAs, Dicer exhibits remarkable promiscuity in binding and cleaving these substrates. Moreover, the 1- or 2-nt 3'-overhang, 3'-mono-uridylation, and 3'-oligo-uridylation of pre-let-7 substrates appear to have little effect on Dicer binding and cleavage rates. Thus, this study extends current knowledge regarding the broad substrate specificity of Dicer and provides novel insight regarding the effect of 3'-modifications on binding and cleavage by Dicer.
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Affiliation(s)
- Gunjan Dadhwal
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Hebatallah Samy
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Jonathan Bouvette
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
- Molecular Biology Department, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| | - Fatima El-Azzouzi
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
- Biochemistry Department, Wake Forest Biotech Place, 575 Patterson Avenue, Winston-Salem, NC, 27101, USA
| | - Pierre Dagenais
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada
| | - Pascale Legault
- Département de biochimie et médecine moléculaire, Université de Montréal, Downtown Station, Box 6128, Montreal, QC, H3C 3J7, Canada.
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2
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Karpa V, Kalinderi K, Fidani L, Tragiannidis A. Association of microRNA Polymorphisms with Toxicities Induced by Methotrexate in Children with Acute Lymphoblastic Leukemia. Hematol Rep 2023; 15:634-650. [PMID: 37987321 PMCID: PMC10660515 DOI: 10.3390/hematolrep15040065] [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: 09/29/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023] Open
Abstract
Methotrexate (MTX), a structurally related substance to folic acid, is an important chemotherapeutic agent used for decades in the treatment of pediatric acute lymphoblastic leukemia (ALL) and other types of cancer as non-Hodgkin lymphomas and osteosarcomas. Despite the successful outcomes observed, the primary drawback is the variability in the pharmacokinetics and pharmacodynamics between patients. The main adverse events related to its use are nephrotoxicity, mucositis, and myelosuppression, especially when used in high doses. The potential adverse reactions and toxicities associated with MTX are a cause for concern and may lead to dose reduction or treatment interruption. Genetic variants in MTX transport genes have been linked to toxicity. Pharmacogenetic studies conducted in the past focused on single nucleotide polymorphisms (SNPs) in the coding and 5'-regulatory regions of genes. Recent studies have demonstrated a significant role of microRNAs (miRNAs) in the transport and metabolism of drugs and in the regulation of target genes. In the last few years, the number of annotated miRNAs has continually risen, in addition to the studies of miRNA polymorphisms and MTX toxicity. Therefore, the objective of the present study is to investigate the role of miRNA variants related to MTX adverse effects.
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Affiliation(s)
- Vasiliki Karpa
- Laboratory of Medical Biology-Genetics, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (K.K.); (L.F.)
| | - Kallirhoe Kalinderi
- Laboratory of Medical Biology-Genetics, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (K.K.); (L.F.)
| | - Liana Fidani
- Laboratory of Medical Biology-Genetics, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (K.K.); (L.F.)
| | - Athanasios Tragiannidis
- Pediatric & Adolescent Hematology-Oncology Unit, 2nd Pediatric Department, Faculty of Health Sciences, Aristotle University of Thessaloniki, AHEPA Hospital, S. Kiriakidi 1, 54636 Thessaloniki, Greece;
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Wong LL, Fadzil AB, Chen Q, Rademaker MT, Charles CJ, Richards AM, Wang P. Interrogating the Role of miR-125b and Its 3'isomiRs in Protection against Hypoxia. Int J Mol Sci 2023; 24:16015. [PMID: 37958999 PMCID: PMC10650460 DOI: 10.3390/ijms242116015] [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: 10/13/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
MiR-125b has therapeutic potential in the amelioration of myocardial ischemic injury. MicroRNA isomiRs, with either 5' or 3' addition or deletion of nucleotide(s), have been reported from next-generation sequencing data (NGS). However, due to technical challenges, validation and functional studies of isomiRs are few. In this study, we discovered using NGS, four 3'isomiRs of miR-125b, i.e., addition of A (adenosine), along with deletions of A, AG (guanosine) and AGU (uridine) from rat and sheep heart. These findings were validated using RT-qPCR. Comprehensive functional studies were carried out in the H9C2 hypoxia model. After miR-125b, isomiRs of Plus A, Trim A, AG and AGU mimic transfection, the H9C2 cells were subjected to hypoxic challenge. As assessed using cell viability, apoptosis, CCK-8 and LDH release, miR-125b and isomiRs were all protective against hypoxia. However, Plus A and Trim A were more effective than miR-125b, whilst Trim AG and Trim AGU had far weaker effects than miR-125b. Interestingly, both the gene regulation profile and apoptotic gene validation indicated a major overlap among miR-125b, Plus A and Trim A, whilst Trims AG and AGU revealed a different profile compared to miR-125b. Conclusions: miR-125b and its 3' isomiRs are expressed stably in the heart. miR-125b and isomiRs with addition or deletion of A might function concurrently and concordantly under specific physiological and pathophysiological conditions. In-depth understanding of isomiRs' metabolism and function will contribute to better miRNA therapeutic drug design.
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Affiliation(s)
- Lee Lee Wong
- Cardiovascular Research Institute, National University Health System, Singapore 117599, Singapore; (A.B.F.); (Q.C.); (A.M.R.)
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Azizah Binti Fadzil
- Cardiovascular Research Institute, National University Health System, Singapore 117599, Singapore; (A.B.F.); (Q.C.); (A.M.R.)
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Qiying Chen
- Cardiovascular Research Institute, National University Health System, Singapore 117599, Singapore; (A.B.F.); (Q.C.); (A.M.R.)
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Miriam T. Rademaker
- Christchurch Heart Institute, Department of Medicine, University of Otago-Christchurch, Christchurch P.O. Box 4345, New Zealand;
| | - Christopher J. Charles
- Cardiovascular Research Institute, National University Health System, Singapore 117599, Singapore; (A.B.F.); (Q.C.); (A.M.R.)
- Christchurch Heart Institute, Department of Medicine, University of Otago-Christchurch, Christchurch P.O. Box 4345, New Zealand;
| | - Arthur Mark Richards
- Cardiovascular Research Institute, National University Health System, Singapore 117599, Singapore; (A.B.F.); (Q.C.); (A.M.R.)
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Christchurch Heart Institute, Department of Medicine, University of Otago-Christchurch, Christchurch P.O. Box 4345, New Zealand;
| | - Peipei Wang
- Cardiovascular Research Institute, National University Health System, Singapore 117599, Singapore; (A.B.F.); (Q.C.); (A.M.R.)
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
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Fletcher CE, Taylor MA, Bevan CL. PLK1 Regulates MicroRNA Biogenesis through Drosha Phosphorylation. Int J Mol Sci 2023; 24:14290. [PMID: 37762595 PMCID: PMC10531876 DOI: 10.3390/ijms241814290] [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: 08/21/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Polo-Like Kinase 1 (PLK1), a key mediator of cell-cycle progression, is associated with poor prognosis and is a therapeutic target in a number of malignancies. Putative phosphorylation sites for PLK1 have been identified on Drosha, the main catalytic component of the microprocessor responsible for miR biogenesis. Several kinases, including GSK3β, p70 S6 kinase, ABL, PAK5, p38 MAPK, CSNK1A1 and ANKRD52-PPP6C, have been shown to phosphorylate components of the miR biogenesis machinery, altering their activity and/or localisation, and therefore the biogenesis of distinct miR subsets. We hypothesised that PLK1 regulates miR biogenesis through Drosha phosphorylation. In vitro kinase assays confirmed PLK1 phosphorylation of Drosha at S300 and/or S302. PLK1 inhibition reduced serine-phosphorylated levels of Drosha and its RNA-dependent association with DGCR8. In contrast, a "phospho-mimic" Drosha mutant showed increased association with DGCR8. PLK1 phosphorylation of Drosha alters Drosha Microprocessor complex subcellular localisation, since PLK1 inhibition increased cytosolic protein levels of both DGCR8 and Drosha, whilst nuclear levels were decreased. Importantly, the above effects are independent of PLK1's cell cycle-regulatory role, since altered Drosha:DGCR8 localisation upon PLK1 inhibition occurred prior to significant accumulation of cells in M-phase, and PLK1-regulated miRs were not increased in M-phase-arrested cells. Small RNA sequencing and qPCR validation were used to assess downstream consequences of PLK1 activity on miR biogenesis, identifying a set of ten miRs (miR-1248, miR-1306-5p, miR-2277-5p, miR-29c-5p, miR-93-3p, miR-152-3p, miR-509-3-5p, miR-511-5p, miR-891a-5p and miR-892a) whose expression levels were statistically significantly downregulated by two pharmacological PLK1 kinase domain inhibitors, RO-5203280 and GSK461364. Opposingly, increased levels of these miRs were observed upon transfection of wild-type or constitutively active PLK1. Importantly, pre-miR levels were reduced upon PLK1 inhibition, and pri-miR levels decreased upon PLK1 activation, and hence, PLK1 Drosha phosphorylation regulates MiR biogenesis at the level of pri-miR-to-pre-miR processing. In combination with prior studies, this work identifies Drosha S300 and S302 as major integration points for signalling by several kinases, whose relative activities will determine the relative biogenesis efficiency of different miR subsets. Identified kinase-regulated miRs have potential for use as kinase inhibitor response-predictive biomarkers, in cancer and other diseases.
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Affiliation(s)
- Claire Emily Fletcher
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | | | - Charlotte Lynne Bevan
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
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5
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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.
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Affiliation(s)
- Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, Budapest, 1117, Hungary.
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6
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Vishnevsky O, Vorozheykin P, Titov I. The context signals of mitochondrial miRNAs (mitomiRs) of mammals. Vavilovskii Zhurnal Genet Selektsii 2022; 26:819-825. [PMID: 36694714 PMCID: PMC9834718 DOI: 10.18699/vjgb-22-99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level in the cytoplasm and play an important role in a wide range of biological processes. Recent studies have found that the miRNA sequences are presented not only in the cytoplasm, but also in the mitochondria. These miRNAs (the so-called mitomiRs) may be the sequences of nuclear or mitochondrial origin; some of them are involved in regulation of the mitochondrial gene functions, while the role of others is still unknown. The identification of nucleotide signals, which are unique to mitomiRs, may help to determine this role. We formed a dataset that combined the experimentally discovered mitomiRs in human, rat and mouse. To isolate signals that may be responsible for the mitomiRs' functions or for their translocation from or into mitochondria a context analysis was carried out for the sequences. For three species in the group mitomiRs/non-mitomiRs and the group of all miRNAs from the miRBase database statistically overrepresented 8-letter motifs were identified (p-value < 0.01 with Bonferroni correction for multiple comparisons), for these motifs the patterns of the localization in functionally important regions for different types of miRNAs were found. Also, for the group mitomiRs/non-mitomiRs we found the statistically significant features of the miRNA nucleotide context near the Dicer and Drosha cleavage sites (Pearson's χ2 test of independence for the first three positions of the miRNA, p-value < 0.05). The observed nucleotide frequencies may indicate a more homogeneous pri-miRNA cleavage by the Drosha complex during the formation of the 5' end of mitomiRs. The obtained results can help to determine the role of the nucleotide signals in the origin, processing, and functions of the mitomiRs.
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Affiliation(s)
- O.V. Vishnevsky
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - I.I. Titov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
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7
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Carro MDLM, Grimson A, Cohen PE. Small RNAs and their protein partners in animal meiosis. Curr Top Dev Biol 2022; 151:245-279. [PMID: 36681472 DOI: 10.1016/bs.ctdb.2022.06.001] [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] [Indexed: 01/25/2023]
Abstract
Meiosis is characterized by highly regulated transitions in gene expression that require diverse mechanisms of gene regulation. For example, in male mammals, transcription undergoes a global shut-down in early prophase I of meiosis, followed by increasing transcriptional activity into pachynema. Later, as spermiogenesis proceeds, the histones bound to DNA are replaced with transition proteins, which are themselves replaced with protamines, resulting in a highly condensed nucleus with repressed transcriptional activity. In addition, two specialized gene silencing events take place during prophase I: meiotic silencing of unsynapsed chromatin (MSUC), and the sex chromatin specific mechanism, meiotic sex chromosome inactivation (MSCI). Notably, conserved roles for the RNA binding protein (RBP) machinery that functions with small non-coding RNAs have been described as participating in these meiosis-specific mechanisms, suggesting that RNA-mediated gene regulation is critical for fertility in many species. Here, we review roles of small RNAs and their associated RBPs in meiosis-related processes such as centromere function, silencing of unpaired chromatin and meiotic recombination. We will discuss the emerging evidence of non-canonical functions of these components in meiosis.
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Affiliation(s)
- María de Las Mercedes Carro
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States; Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States
| | - Andrew Grimson
- Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States; Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, United States.
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States; Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States.
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8
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Bell J, Hendrix DA. Predicting Drosha and Dicer Cleavage Sites with DeepMirCut. Front Mol Biosci 2022; 8:799056. [PMID: 35141278 PMCID: PMC8819831 DOI: 10.3389/fmolb.2021.799056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs are a class of small RNAs involved in post-transcriptional gene silencing with roles in disease and development. Many computational tools have been developed to identify novel microRNAs. However, there have been no attempts to predict cleavage sites for Drosha from primary sequence, or to identify cleavage sites using deep neural networks. Here, we present DeepMirCut, a recurrent neural network-based software that predicts both Dicer and Drosha cleavage sites. We built a microRNA primary sequence database including flanking genomic sequences for 34,713 microRNA annotations. We compare models trained on sequence data, sequence and secondary structure data, as well as input data with annotated structures. Our best model is able to predict cuts within closer average proximity than results reported for other methods. We show that a guanine nucleotide before and a uracil nucleotide after Dicer cleavage sites on the 3′ arm of the microRNA precursor had a positive effect on predictions while the opposite order (U before, G after) had a negative effect. Our analysis was also able to predict several positions where bulges had either positive or negative effects on the score. We expect that our approach and the data we have curated will enable several future studies.
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Affiliation(s)
- Jimmy Bell
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, United States
| | - David A. Hendrix
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, United States
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
- *Correspondence: David A. Hendrix,
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Panzade G, Li L, Hebbar S, Veksler-Lublinsky I, Zinovyeva A. Global profiling and annotation of templated isomiRs dynamics across Caenorhabditis elegans development. RNA Biol 2022; 19:928-942. [PMID: 35848953 PMCID: PMC9298154 DOI: 10.1080/15476286.2022.2099646] [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: 11/11/2022] Open
Abstract
microRNAs (miRNAs) are small non-coding RNAs that regulate gene expression through translational repression and mRNA destabilization. During canonical miRNA biogenesis, several miRNA isoforms, or isomiRs, are produced from a single precursor miRNA. Templated isomiRs are generated through Drosha or Dicer cleavage at alternate positions on either the primary or the precursor miRNAs, generating truncated or extended 5’ and/or 3’ miRNA ends. As changes to the mature miRNA sequence can alter miRNA gene target repertoire, we investigated the extent of templated isomiR prevalence, providing a profiling map for templated isomiRs across stages of C. elegans development. While most miRNA loci did not produce abundant templated isomiRs, a substantial number of miRNA loci produced isomiRs were just as, or more, abundant than their annotated canonical mature miRNAs. 3’ end miRNA alterations were more frequent than the seed-altering 5’ end extensions or truncations. However, we identified several miRNA loci that produced a considerable amount of isomiRs with 5’ end alterations, predicted to target new, distinct sets of genes. Overall, the presented annotation of templated isomiR dynamics across C. elegans developmental stages provides a basis for further studies into miRNA biogenesis and the intriguing potential of functional miRNA diversification through isomiR production.
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Affiliation(s)
- Ganesh Panzade
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Li Li
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-sheva, Israel
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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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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Tomasello L, Distefano R, Nigita G, Croce CM. The MicroRNA Family Gets Wider: The IsomiRs Classification and Role. Front Cell Dev Biol 2021; 9:668648. [PMID: 34178993 PMCID: PMC8220208 DOI: 10.3389/fcell.2021.668648] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are the most characterized class of non-coding RNAs and are engaged in many cellular processes, including cell differentiation, development, and homeostasis. MicroRNA dysregulation was observed in several diseases, cancer included. Epitranscriptomics is a branch of epigenomics that embraces all RNA modifications occurring after DNA transcription and RNA synthesis and involving coding and non-coding RNAs. The development of new high-throughput technologies, especially deep RNA sequencing, has facilitated the discovery of miRNA isoforms (named isomiRs) resulting from RNA modifications mediated by enzymes, such as deaminases and exonucleases, and differing from the canonical ones in length, sequence, or both. In this review, we summarize the distinct classes of isomiRs, their regulation and biogenesis, and the active role of these newly discovered molecules in cancer and other diseases.
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Affiliation(s)
- Luisa Tomasello
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
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12
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Moraghebi M, Maleki R, Ahmadi M, Negahi AA, Abbasi H, Mousavi P. In silico Analysis of Polymorphisms in microRNAs Deregulated in Alzheimer Disease. Front Neurosci 2021; 15:631852. [PMID: 33841080 PMCID: PMC8024493 DOI: 10.3389/fnins.2021.631852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a degenerative condition characterized by progressive cognitive impairment and dementia. Findings have revolutionized current knowledge of miRNA in the neurological conditions. Two regulatory mechanisms determine the level of mature miRNA expression; one is miRNA precursor processing, and the other is gene expression regulation by transcription factors. This study is allocated to the in-silico investigation of miRNA's SNPs and their effect on other cell mechanisms. METHODS We used databases which annotate the functional effect of SNPs on mRNA-miRNA and miRNA-RBP interaction. Also, we investigated SNPs which are located on the promoter or UTR region. RESULTS miRNA SNP3.0 database indicated several SNPs in miR-339 and miR-34a in the upstream and downstream of pre-miRNA and mature miRNAs. While, for some miRNAs miR-124, and miR-125, no polymorphism was observed, and also miR-101 with ΔG -3.1 and mir-328 with ΔG 5.8 had the highest and lowest potencies to produce mature microRNA. SNP2TFBS web-server presented several SNPs which altered the Transcription Factor Binding Sites (TFBS) or generated novel TFBS in the promoter regions of related miRNA. At last, RBP-Var database provided a list of SNPs which alter miRNA-RBP interaction pattern and can also influence other miRNAs' expression. DISCUSSION The results indicated that SNPs microRNA affects both miRNA function and miRNA expression. Our study expands molecular insight into how SNPs in different parts of miRNA, including the regulatory (promoter), the precursor (pre-miRNA), functional regions (seed region of mature miRNA), and RBP-binding motifs, which theoretically may be correlated to the Alzheimer's disease.
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Affiliation(s)
- Mahta Moraghebi
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Reza Maleki
- Student Research Committee, Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Ahmadi
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ahmad Agha Negahi
- Department of Internal Medicine, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hossein Abbasi
- Student Research Committee, Faculty of Para-Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Pegah Mousavi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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13
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Galka-Marciniak P, Urbanek-Trzeciak MO, Nawrocka PM, Kozlowski P. A pan-cancer atlas of somatic mutations in miRNA biogenesis genes. Nucleic Acids Res 2021; 49:601-620. [PMID: 33406242 PMCID: PMC7826265 DOI: 10.1093/nar/gkaa1223] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/28/2020] [Accepted: 12/04/2020] [Indexed: 02/07/2023] Open
Abstract
It is a well-known and intensively studied phenomenon that the levels of many miRNAs are differentiated in cancer. miRNA biogenesis and functional expression are complex processes orchestrated by many proteins cumulatively called miRNA biogenesis proteins. To characterize cancer somatic mutations in the miRNA biogenesis genes and investigate their potential impact on the levels of miRNAs, we analyzed whole-exome sequencing datasets of over 10 000 cancer/normal sample pairs deposited within the TCGA repository. We identified and characterized over 3600 somatic mutations in 29 miRNA biogenesis genes and showed that some of the genes are overmutated in specific cancers and/or have recurrent hotspot mutations (e.g. SMAD4 in PAAD, COAD and READ; DICER1 in UCEC; PRKRA in OV and LIN28B in SKCM). We identified a list of miRNAs whose level is affected by particular types of mutations in either SMAD4, SMAD2 or DICER1 and showed that hotspot mutations in the RNase domains in DICER1 not only decrease the level of 5p-miRNAs but also increase the level of 3p-miRNAs, including many well-known cancer-related miRNAs. We also showed an association of the mutations with patient survival. Eventually, we created an atlas/compendium of miRNA biogenesis alterations providing a useful resource for different aspects of biomedical research.
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Affiliation(s)
| | | | | | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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14
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Huang S, Yoshitake K, Asaduzzaman M, Kinoshita S, Watabe S, Asakawa S. Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach. RNA Biol 2021; 18:1702-1715. [PMID: 33356816 DOI: 10.1080/15476286.2020.1867798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of these small non-coding RNAs, microRNAs (miRNAs) guide post-translational gene regulation in cellular development, proliferation, apoptosis, oncogenesis, and differentiation. Here, we performed a genome-wide computational prediction of miRNAs to improve the understanding of miRNA observation and function in molluscs. As an initial step, hundreds of conserved miRNAs were predicted in 35 species of molluscs through genome scanning. Afterwards, the miRNAs' population, isoforms, organization, and function were characterized in detail. Furthermore, the key miRNA biogenesis factors, including AGO2, DGCR8, DICER, DROSHA, TRABP2, RAN, and XPO5, were elucidated based on homologue sequence searching. We also summarized the miRNAs' function in biomineralization, immune and stress response, as well as growth and development in molluscs. Because miRNAs play a vital role in various lifeforms, this study will provide insight into miRNA biogenesis and function in molluscs, as well as other invertebrates.
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Affiliation(s)
- Songqian Huang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Md Asaduzzaman
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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15
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Fittipaldi S, Visconti VV, Tarantino U, Novelli G, Botta A. Genetic variability in noncoding RNAs: involvement of miRNAs and long noncoding RNAs in osteoporosis pathogenesis. Epigenomics 2020; 12:2035-2049. [PMID: 33264054 DOI: 10.2217/epi-2020-0233] [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] [Indexed: 12/21/2022] Open
Abstract
The pathogenesis of osteoporosis is multifactorial and is the consequence of genetic, hormonal and lifestyle factors. Epigenetics, including noncoding RNA (ncRNA) deregulation, represents a link between susceptibility to develop the disease and environmental influences. The majority of studies investigated the expression of ncRNAs in osteoporosis patients; however, very little information is available on their genetic variability. In this review, we focus on two classes of ncRNAs: miRNAs and long noncoding RNAs (lncRNAs). We summarize recent findings on how polymorphisms in miRNAs and lncRNAs can perturb the lncRNA/miRNA/mRNA axis and may be involved in osteoporosis clinical outcome. We also provide a general overview on databases and bioinformatic tools useful for associating miRNAs and lncRNAs variability with complex genetic diseases.
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Affiliation(s)
- Simona Fittipaldi
- Department of Biomedicine & Prevention, Medical Genetics Section, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy
| | - Virginia Veronica Visconti
- Department of Biomedicine & Prevention, Medical Genetics Section, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy.,Department of Orthopedics & Traumatology, PTV Foundation, 00133 Rome, Italy
| | - Umberto Tarantino
- Department of Orthopedics & Traumatology, PTV Foundation, 00133 Rome, Italy.,Department of Clinical Sciences & Translational Medicine, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine & Prevention, Medical Genetics Section, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy.,IRCCS Neuromed, Pozzilli, IS, Italy
| | - Annalisa Botta
- Department of Biomedicine & Prevention, Medical Genetics Section, University of Rome 'Tor Vergata', Via Montpellier 1, 00133 Rome, Italy
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16
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Vorozheykin PS, Titov II. Erratum to: How Animal miRNAs Structure Influences Their Biogenesis. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420220019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Kirchner B, Buschmann D, Paul V, Pfaffl MW. Postprandial transfer of colostral extracellular vesicles and their protein and miRNA cargo in neonatal calves. PLoS One 2020; 15:e0229606. [PMID: 32109241 PMCID: PMC7048281 DOI: 10.1371/journal.pone.0229606] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/10/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) such as exosomes are key regulators of intercellular communication that can be found in almost all bio fluids. Although studies in the last decade have made great headway in discerning the role of EVs in many physiological and pathophysiological processes, the bioavailability and impact of dietary EVs and their cargo still remain to be elucidated. Due to its widespread consumption and high content of EV-associated microRNAs and proteins, a major focus in this field has been set on EVs in bovine milk and colostrum. Despite promising in vitro studies in recent years that show high resiliency of milk EVs to degradation and uptake of milk EV cargo in a variety of intestinal and blood cell types, in vivo experiments continue to be inconclusive and sometimes outright contradictive. To resolve this discrepancy, we assessed the potential postprandial transfer of colostral EVs to the circulation of newborn calves by analysing colostrum-specific protein and miRNAs, including specific isoforms (isomiRs) in cells, EV isolations and unfractionated samples from blood and colostrum. Our findings reveal distinct populations of EVs in colostrum and blood from cows that can be clearly separated by density, particle concentration and protein content (BTN1A1, MFGE8). Postprandial blood samples of calves show a time-dependent increase in EVs that share morphological and protein characteristics of colostral EVs. Analysis of miRNA expression profiles by Next-Generation Sequencing gave a different picture however. Although significant postprandial expression changes could only be detected for calf EV samples, expression profiles show very limited overlap with highly expressed miRNAs in colostral EVs or colostrum in general. Taken together our results indicate a selective uptake of membrane-associated protein cargo but not luminal miRNAs from colostral EVs into the circulation of neonatal calves.
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Affiliation(s)
- Benedikt Kirchner
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- * E-mail:
| | - Dominik Buschmann
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
| | - Vijay Paul
- National Research Centre on Yak, ICAR, Dirang, India
| | - Michael W. Pfaffl
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
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18
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19
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Xiong P, Schneider RF, Hulsey CD, Meyer A, Franchini P. Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes. Sci Rep 2019; 9:13848. [PMID: 31554838 PMCID: PMC6761260 DOI: 10.1038/s41598-019-50124-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/05/2019] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in the post-transcriptional control of messenger RNA (mRNA). These miRNA-mRNA regulatory networks are present in nearly all organisms and contribute to development, phenotypic divergence, and speciation. To examine the miRNA landscape of cichlid fishes, one of the most species-rich families of vertebrates, we profiled the expression of both miRNA and mRNA in a diverse set of cichlid lineages. Among these, we found that conserved miRNAs differ from recently arisen miRNAs (i.e. lineage specific) in average expression levels, number of target sites, sequence variability, and physical clustering patterns in the genome. Furthermore, conserved miRNA target sites tend to be enriched at the 5' end of protein-coding gene 3' UTRs. Consistent with the presumed regulatory role of miRNAs, we detected more negative correlations between the expression of miRNA-mRNA functional pairs than in random pairings. Finally, we provide evidence that novel miRNA targets sites are enriched in genes involved in protein synthesis pathways. Our results show how conserved and evolutionarily novel miRNAs differ in their contribution to the genomic landscape and highlight their particular evolutionary roles in the adaptive diversification of cichlids.
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Affiliation(s)
- Peiwen Xiong
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Ralf F Schneider
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Marine Ecology, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR), 24105 Kiel, Germany
| | - C Darrin Hulsey
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Paolo Franchini
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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20
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Somatic Mutations in miRNA Genes in Lung Cancer-Potential Functional Consequences of Non-Coding Sequence Variants. Cancers (Basel) 2019; 11:cancers11060793. [PMID: 31181801 PMCID: PMC6627760 DOI: 10.3390/cancers11060793] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023] Open
Abstract
A growing body of evidence indicates that miRNAs may either drive or suppress oncogenesis. However, little is known about somatic mutations in miRNA genes. To determine the frequency and potential consequences of miRNA gene mutations, we analyzed whole exome sequencing datasets of 569 lung adenocarcinoma (LUAD) and 597 lung squamous cell carcinoma (LUSC) samples generated in The Cancer Genome Atlas (TCGA) project. Altogether, we identified 1091 somatic sequence variants affecting 522 different miRNA genes and showed that half of all cancers had at least one such somatic variant/mutation. These sequence variants occurred in most crucial parts of miRNA precursors, including mature miRNA and seed sequences. Due to our findings, we hypothesize that seed mutations may affect miRNA:target interactions, drastically changing the pool of predicted targets. Mutations may also affect miRNA biogenesis by changing the structure of miRNA precursors, DROSHA and DICER cleavage sites, and regulatory sequence/structure motifs. We identified 10 significantly overmutated hotspot miRNA genes, including the miR-379 gene in LUAD enriched in mutations in the mature miRNA and regulatory sequences. The occurrence of mutations in the hotspot miRNA genes was also shown experimentally. We present a comprehensive analysis of somatic variants in miRNA genes and show that some of these genes are mutational hotspots, suggesting their potential role in cancer.
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21
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Guan R, Hu S, Li H, Shi Z, Miao X. The in vivo dsRNA Cleavage Has Sequence Preference in Insects. Front Physiol 2018; 9:1768. [PMID: 30618790 PMCID: PMC6295558 DOI: 10.3389/fphys.2018.01768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/23/2018] [Indexed: 12/21/2022] Open
Abstract
Exogenous dsRNA enters the insect body and can induce the RNAi effect only when it is cleaved into siRNA. However, what kinds of base composition are easier to cut and what kinds of siRNA will be produced in vivo is largely unknown. In this study, we found that dsRNA processing into siRNA has sequence preference and regularity in insects. We injected 0.04 mg/g dsRNA into Asian corn borers or cotton bollworms according to their body weight, and then the siRNAs produced in vivo were analyzed by RNA-Seq. We discovered that a large number of siRNAs were produced with GGU nucleotide residues at the 5′- and 3′-ends and produced a siRNA peak on the sequence. Once the GGU site is mutated, the number of siRNAs will decrease significantly and the siRNA peak will also lost. However, in the red flour beetle, a member of Coleoptera, dsRNA was cut at more diverse sites, such as AAG, GUG, and GUU; more importantly, these enzyme restriction sites have a high conservation base of A/U. Our discovery regarding dsRNA in vivo cleavage preference and regularity will help us understand the RNAi mechanism and its application.
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Affiliation(s)
- Ruobing Guan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,State key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shaoru Hu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Haichao Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xuexia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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22
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Evolutionary Divergence of Brain-specific Precursor miRNAs Drives Efficient Processing and Production of Mature miRNAs in Human. Neuroscience 2018; 392:141-159. [PMID: 30273624 DOI: 10.1016/j.neuroscience.2018.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022]
Abstract
The hallmark of human evolution encompasses the dramatic increase in brain size and complexity. The intricate interplays of micro-RNAs (miRNAs) and their target genes are indispensable in brain development. Sequence divergence in distinct structural regions of Brain-specific precursor miRNAs (pre-miRNAs) and its consequence in the production of corresponding mature miRNAs in human are unknown. To address these questions, first we classified miRNAs into three categories based on tissue expression: Brain-specific (expressed exclusively in brain), Non-brain (expressed in Non-brain tissues) and Common (expressed in all tissues) and compared the sequence divergence of different structural regions (basal segment, lower and upper stem, internal and terminal loop) of categorized pre-miRNAs across human, non-human primates and rodents. Our analysis revealed that unpaired regions of Brain-specific pre-miRNAs in human bear traces of relatively high rate of evolutionary divergence compared to those in other species. Cross-tissue expression analysis unveiled the higher expression of the Brain-specific miRNAs in human compared to other species. Intriguingly, in human brain, expression levels of these miRNAs superseded the levels of the ubiquitously expressed "Common-miRNAs". Further analysis revealed that presence of certain motif and nucleotide preference in the Brain-specific pre-miRNAs may favor DROSHA and DICER to ameliorate miRNA processing. The higher processing efficiency of human Brain-specific miRNAs was reflected as an elevated production of corresponding mature miRNAs in the human brain. Finally, re-construction of gene-regulatory network uncovers different pathways driven by Brain-specific miRNAs that may contribute to the development of brain in human.
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23
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Bick JT, Flöter VL, Robinson MD, Bauersachs S, Ulbrich SE. Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression. BMC Genomics 2018; 19:590. [PMID: 30081835 PMCID: PMC6090871 DOI: 10.1186/s12864-018-4954-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/23/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The expression of microRNAs (miRNAs) is essential for the proper development of the mammalian embryo. A maternal exposure to endocrine disrupting chemicals during preimplantation bears the potential for transgenerational inheritance of disease through the epigenetic perturbation of the developing embryo. A comprehensive assembly of embryo-specific miRNAs and respective isoforms (isomiR) is lacking to date. We aimed at revealing the sex-specific miRNA expression profile of single porcine blastocysts developing in gilts orally exposed to exogenous estradiol-17 (E2). Therefore we analyzed the miRNA profile specifically focusing on isomiRs and potentially embryo-specific miRNAs. RESULTS Deep sequencing of small RNA (small RNA-seq) result in the detection of miRNA sequences mapping to known and predicted porcine miRNAs as well as novel miRNAs highly conserved in human and cattle. A set of highly abundant miRNAs and a large number of rarely expressed miRNAs were identified by using a small RNA analysis pipeline, which was integrated into a novel Galaxy workflow specifically benefits incompletely annotated species. In particular, orthologue species information increased the total number of annotated miRNAs, while mapping to other non-coding RNAs avoided falsely annotated miRNAs. Neither the low nor the high dose of E2 treatment (10 and 1000 µ E2/kg body weight daily, respectively) affected the miRNA profile in blastocysts despite the distinct differential mRNA expression and DNA methylation found in previous studies. The high number of generated sequence reads enabled a comprehensive analysis of the isomiR repertoire showing various templated and non-templated modifications. Furthermore, potentially blastocyst-specific miRNAs were identified. CONCLUSIONS In pre-implantation embryos, numerous distinct isomiRs were discovered indicating a high complexity of miRNA expression. Neither the sex of the embryo nor a maternal E2 exposure affected the miRNA expression profile of developing porcine blastocysts. The adaptation to the continuous duration of the E2 treatment might explain the lack of an effect.
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Affiliation(s)
- Jochen T. Bick
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Veronika L. Flöter
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
- Physiology Weihenstephan, Technische Universität München, Freising, Germany
| | - Mark D. Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Stefan Bauersachs
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
- University of Zurich, Genetics and Functional Genomics, Clinic for Animal Reproduction Medicine, Zurich, Switzerland
| | - Susanne E. Ulbrich
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
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24
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Menezes MR, Balzeau J, Hagan JP. 3' RNA Uridylation in Epitranscriptomics, Gene Regulation, and Disease. Front Mol Biosci 2018; 5:61. [PMID: 30057901 PMCID: PMC6053540 DOI: 10.3389/fmolb.2018.00061] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 06/14/2018] [Indexed: 12/31/2022] Open
Abstract
Emerging evidence implicates a wide range of post-transcriptional RNA modifications that play crucial roles in fundamental biological processes including regulating gene expression. Collectively, they are known as epitranscriptomics. Recent studies implicate 3' RNA uridylation, the non-templated addition of uridine(s) to the terminal end of RNA, as a key player in epitranscriptomics. In this review, we describe the functional roles and significance of 3' terminal RNA uridylation that has diverse functions in regulating both mRNAs and non-coding RNAs. In mammals, three Terminal Uridylyl Transferases (TUTases) are primarily responsible for 3' RNA uridylation. These enzymes are also referred to as polyU polymerases. TUTase 1 (TUT1) is implicated in U6 snRNA maturation via uridylation. The TUTases TUT4 and/or TUT7 are the predominant mediators of all other cellular uridylation. Terminal uridylation promotes turnover for many polyadenylated mRNAs, replication-dependent histone mRNAs that lack polyA-tails, and aberrant structured noncoding RNAs. In addition, uridylation regulates biogenesis of a subset of microRNAs and generates isomiRs, sequent variant microRNAs that have altered function in specific cases. For example, the RNA binding protein and proto-oncogene LIN28A and TUT4 work together to polyuridylate pre-let-7, thereby blocking biogenesis and function of the tumor suppressor let-7 microRNA family. In contrast, monouridylation of Group II pre-miRNAs creates an optimal 3' overhang that promotes recognition and subsequent cleavage by the Dicer-TRBP complex that then yields the mature microRNA. Also, uridylation may play a role in non-canonical microRNA biogenesis. The overall significance of 3' RNA uridylation is discussed with an emphasis on mammalian development, gene regulation, and disease, including cancer and Perlman syndrome. We also introduce recent changes to the HUGO-approved gene names for multiple terminal nucleotidyl transferases that affects in part TUTase nomenclature (TUT1/TENT1, TENT2/PAPD4/GLD2, TUT4/ZCCHC11/TENT3A, TUT7/ZCCHC6/TENT3B, TENT4A/PAPD7, TENT4B/PAPD5, TENT5A/FAM46A, TENT5B/FAM46B, TENT5C/FAM46C, TENT5D/FAM46D, MTPAP/TENT6/PAPD1).
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Affiliation(s)
- Miriam R Menezes
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Julien Balzeau
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - John P Hagan
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
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Abstract
miRNA regulome is whole set of regulatory elements that regulate miRNA expression or are under control of miRNAs. Its understanding is vital for comprehension of miRNA functions. Classification of miRNA-related genetic variability is challenging because miRNA interact with different genomic elements and are studied at different omics levels. In the present study, miRNA-associated genetic variability is presented at three levels: miRNA genes and their upstream regulation, miRNA silencing machinery and miRNA targets. Several types of miRNA-associated genetic variations are known, including short and structural polymorphisms and epimutations. Differential expression can also affect miRNA regulome function. Classification of miRNA-associated genetic variability presents a baseline for complementing sequence variant nomenclature, planning of experiments, protocols for multi-omics data integration and development of biomarkers.
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Affiliation(s)
- Karin Hrovatin
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
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Abstract
BACKGROUND MicroRNAs proceeds through the different canonical and non-canonical pathways; the most frequent of the non-canonical ones is the splicing-dependent biogenesis of mirtrons. We compare the mirtrons and non-mirtrons of human and mouse to explore how their maturation appears in the precursor structure around the miRNA. RESULTS We found the coherence of the overhang lengths what indicates the dependence between the cleavage sites. To explain this dependence we suggest the 2-lever model of the Dicer structure that couples the imprecisions in Drosha and Dicer. Considering the secondary structure of all animal pre-miRNAs we confirmed that single-stranded nucleotides tend to be located near the miRNA boundaries and in its center and are characterized by a higher mutation rate. The 5' end of the canonical 5' miRNA approaches the nearest single-stranded nucleotides what suggests the extension of the loop-counting rule from the Dicer to the Drosha cleavage site. A typical structure of the annotated mirtron pre-miRNAs differs from the canonical pre-miRNA structure and possesses the 1- and 2 nt hanging ends at the hairpin base. Together with the excessive variability of the mirtron Dicer cleavage site (that could be partially explained by guanine at its ends inherited from splicing) this is one more evidence for the 2-lever model. In contrast with the canonical miRNAs the mirtrons have higher snp densities and their pre-miRNAs are inversely associated with diseases. Therefore we supported the view that mirtrons are under positive selection while canonical miRNAs are under negative one and we suggested that mirtrons are an intrinsic source of silencing variability which produces the disease-promoting variants. Finally, we considered the interference of the pre-miRNA structure and the U2snRNA:pre-mRNA basepairing. We analyzed the location of the branchpoints and found that mirtron structure tends to expose the branchpoint site what suggests that the mirtrons can readily evolve from occasional hairpins in the immediate neighbourhood of the 3' splice site. CONCLUSION The miRNA biogenesis manifests itself in the footprints of the secondary structure. Close inspection of these structural properties can help to uncover new pathways of miRNA biogenesis and to refine the known miRNA data, in particular, new non-canonical miRNAs may be predicted or the known miRNAs can be re-classified.
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Affiliation(s)
- Igor I Titov
- Federal State Budget Scientific Institution "The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences", Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
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27
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Olejniczak M, Kotowska-Zimmer A, Krzyzosiak W. Stress-induced changes in miRNA biogenesis and functioning. Cell Mol Life Sci 2018; 75:177-191. [PMID: 28717872 PMCID: PMC5756259 DOI: 10.1007/s00018-017-2591-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/30/2017] [Accepted: 07/11/2017] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that play key roles in the regulation of cellular homeostasis in eukaryotic organisms. There is emerging evidence that some of these processes are influenced by various forms of cellular stresses, including DNA damage, pathogen invasion or chronic stress associated with diseases. Many reports over the last decade demonstrate examples of stress-induced miRNA deregulation at the level of transcription, processing, subcellular localization and functioning. Moreover, core miRNA biogenesis proteins and their interactions with partners can be selectively regulated in response to stress signaling. However, little is known about the role of isomiRs and the interactions of miRNA with non-canonical targets in the context of the stress response. In this review, we summarize the current knowledge on miRNA functions under various stresses, including chronic stress and miRNA deregulation in the pathogenesis of age-associated neurodegenerative disorders.
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Affiliation(s)
- Marta Olejniczak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Anna Kotowska-Zimmer
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Wlodzimierz Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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28
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Yu F, Pillman KA, Neilsen CT, Toubia J, Lawrence DM, Tsykin A, Gantier MP, Callen DF, Goodall GJ, Bracken CP. Naturally existing isoforms of miR-222 have distinct functions. Nucleic Acids Res 2017; 45:11371-11385. [PMID: 28981911 PMCID: PMC5737821 DOI: 10.1093/nar/gkx788] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/31/2017] [Indexed: 12/14/2022] Open
Abstract
Deep-sequencing reveals extensive variation in the sequence of endogenously expressed microRNAs (termed ‘isomiRs’) in human cell lines and tissues, especially in relation to the 3′ end. From the immunoprecipitation of the microRNA-binding protein Argonaute and the sequencing of associated small RNAs, we observe extensive 3′-isomiR variation, including for miR-222 where the majority of endogenously expressed miR-222 is extended by 1–5 nt compared to the canonical sequence. We demonstrate this 3′ heterogeneity has dramatic implications for the phenotype of miR-222 transfected cells, with longer isoforms promoting apoptosis in a size (but not 3′ sequence)-dependent manner. The transfection of longer miR-222 isomiRs did not induce an interferon response, but did downregulate the expression of many components of the pro-survival PI3K-AKT pathway including PIK3R3, a regulatory subunit whose knockdown phenocopied the expression of longer 222 isoforms in terms of apoptosis and the inhibition of other PI3K-AKT genes. As this work demonstrates the capacity for 3′ isomiRs to mediate differential functions, we contend more attention needs to be given to 3′ variance given the prevalence of this class of isomiR.
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Affiliation(s)
- Feng Yu
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - Corine T Neilsen
- School of Health, Medical and Applied Sciences, Central Queensland University, Queensland 4000, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - David M Lawrence
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - Anna Tsykin
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - David F Callen
- School of Medicine, Discipline of Medicine, University of Adelaide, SA 5000, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA 5000, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA 5000, Australia
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29
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Burke JM, Kincaid RP, Aloisio F, Welch N, Sullivan CS. Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes. Nucleic Acids Res 2017; 45:e154. [PMID: 28973449 PMCID: PMC5622367 DOI: 10.1093/nar/gkx653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/19/2017] [Indexed: 12/03/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are effective in generating stable repression of gene expression. RNA polymerase III (RNAP III) type III promoters (U6 or H1) are typically used to drive shRNA expression. While useful for some knockdown applications, the robust expression of U6/H1-driven shRNAs can induce toxicity and generate heterogeneous small RNAs with undesirable off-target effects. Additionally, typical U6/H1 promoters encompass the majority of the ∼270 base pairs (bp) of vector space required for shRNA expression. This can limit the efficacy and/or number of delivery vector options, particularly when delivery of multiple gene/shRNA combinations is required. Here, we develop a compact shRNA (cshRNA) expression system based on retroviral microRNA (miRNA) gene architecture that uses RNAP III type II promoters. We demonstrate that cshRNAs coded from as little as 100 bps of total coding space can precisely generate small interfering RNAs (siRNAs) that are active in the RNA-induced silencing complex (RISC). We provide an algorithm with a user-friendly interface to design cshRNAs for desired target genes. This cshRNA expression system reduces the coding space required for shRNA expression by >2-fold as compared to the typical U6/H1 promoters, which may facilitate therapeutic RNAi applications where delivery vector space is limiting.
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Affiliation(s)
- James M Burke
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Rodney P Kincaid
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Francesca Aloisio
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Nicole Welch
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Christopher S Sullivan
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
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Comprehensive miRNA expression profiling in human T-cell acute lymphoblastic leukemia by small RNA-sequencing. Sci Rep 2017; 7:7901. [PMID: 28801656 PMCID: PMC5554241 DOI: 10.1038/s41598-017-08148-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/05/2017] [Indexed: 12/21/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease that can be classified into different molecular genetic subtypes according to their mRNA gene expression profile. In this study, we applied RNA sequencing to investigate the full spectrum of miRNA expression in primary T-ALL patient samples, T-ALL leukemia cell lines and healthy donor thymocytes. Notably, this analysis revealed that genetic subtypes of human T-ALL also display unique miRNA expression signatures, which are largely conserved in human T-ALL cell lines with corresponding genetic background. Furthermore, small RNA-sequencing also unraveled the variety of isoforms that are expressed for each miRNA in T-ALL and showed that a significant number of miRNAs are actually represented by an alternative isomiR. Finally, comparison of CD34+ and CD4+CD8+ healthy donor thymocytes and T-ALL miRNA profiles allowed identifying several novel miRNAs with putative oncogenic or tumor suppressor functions in T-ALL. Altogether, this study provides a comprehensive overview of miRNA expression in normal and malignant T-cells and sets the stage for functional evaluation of novel miRNAs in T-ALL disease biology.
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31
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Telonis AG, Magee R, Loher P, Chervoneva I, Londin E, Rigoutsos I. Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types. Nucleic Acids Res 2017; 45:2973-2985. [PMID: 28206648 PMCID: PMC5389567 DOI: 10.1093/nar/gkx082] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/07/2017] [Indexed: 12/21/2022] Open
Abstract
Isoforms of human miRNAs (isomiRs) are constitutively expressed with tissue- and disease-subtype-dependencies. We studied 10 271 tumor datasets from The Cancer Genome Atlas (TCGA) to evaluate whether isomiRs can distinguish amongst 32 TCGA cancers. Unlike previous approaches, we built a classifier that relied solely on ‘binarized’ isomiR profiles: each isomiR is simply labeled as ‘present’ or ‘absent’. The resulting classifier successfully labeled tumor datasets with an average sensitivity of 90% and a false discovery rate (FDR) of 3%, surpassing the performance of expression-based classification. The classifier maintained its power even after a 15× reduction in the number of isomiRs that were used for training. Notably, the classifier could correctly predict the cancer type in non-TCGA datasets from diverse platforms. Our analysis revealed that the most discriminatory isomiRs happen to also be differentially expressed between normal tissue and cancer. Even so, we find that these highly discriminating isomiRs have not been attracting the most research attention in the literature. Given their ability to successfully classify datasets from 32 cancers, isomiRs and our resulting ‘Pan-cancer Atlas’ of isomiR expression could serve as a suitable framework to explore novel cancer biomarkers.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
| | - Rogan Magee
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
| | - Inna Chervoneva
- Division of Biostatistics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA
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32
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Brandão BB, Guerra BA, Mori MA. Shortcuts to a functional adipose tissue: The role of small non-coding RNAs. Redox Biol 2017; 12:82-102. [PMID: 28214707 PMCID: PMC5312655 DOI: 10.1016/j.redox.2017.01.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 01/30/2017] [Indexed: 12/20/2022] Open
Abstract
Metabolic diseases such as type 2 diabetes are a major public health issue worldwide. These diseases are often linked to a dysfunctional adipose tissue. Fat is a large, heterogenic, pleiotropic and rather complex tissue. It is found in virtually all cavities of the human body, shows unique plasticity among tissues, and harbors many cell types in addition to its main functional unit - the adipocyte. Adipose tissue function varies depending on the localization of the fat depot, the cell composition of the tissue and the energy status of the organism. While the white adipose tissue (WAT) serves as the main site for triglyceride storage and acts as an important endocrine organ, the brown adipose tissue (BAT) is responsible for thermogenesis. Beige adipocytes can also appear in WAT depots to sustain heat production upon certain conditions, and it is becoming clear that adipose tissue depots can switch phenotypes depending on cell autonomous and non-autonomous stimuli. To maintain such degree of plasticity and respond adequately to changes in the energy balance, three basic processes need to be properly functioning in the adipose tissue: i) adipogenesis and adipocyte turnover, ii) metabolism, and iii) signaling. Here we review the fundamental role of small non-coding RNAs (sncRNAs) in these processes, with focus on microRNAs, and demonstrate their importance in adipose tissue function and whole body metabolic control in mammals.
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Affiliation(s)
- Bruna B Brandão
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Beatriz A Guerra
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Marcelo A Mori
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, Brazil.
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33
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Yang CM, Chen CC, Tseng YK, Huang SJ, Liou HH, Lee YC, Lee JH, Wang JS, Chen HC, Chi CC, Kang BH, Lin YC, Tsai KW, Ger LP. The variant of pri-mir-26a-1 polymorphism is associated with decreased risk of betel quid-related oral premalignant lesions and oral squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2017; 124:378-389.e1. [PMID: 28743663 DOI: 10.1016/j.oooo.2017.05.515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 01/05/2023]
Abstract
OBJECTIVES This case-control study evaluated the association of the single nucleotide polymorphism rs7372209 (T>C) in pri-mir-26a-1 with the risk and progression of betel quid (BQ)-related oral premalignant lesions (OPLs) and oral squamous cell carcinoma (OSCC). STUDY DESIGN In total, 597 BQ chewers were recruited: 196 healthy controls, 241 patients with OPLs, and 160 patients with OSCC. Genotypes were determined using the TaqMan real-time assay. RESULTS The C/T + T/T genotypes and T allele in pri-mir-26a-1 were correlated with a decreased risk of BQ-related OPLs (P = .038 and .005, respectively), oral leukoplakia (P = .01 and .001, respectively), and advanced-stage OSCC (P = .021 and .004, respectively). The effects of the C/T + T/T genotypes and T allele on the decreased risk of OPLs were potent in the older age group (both Pinteraction < .001), heavy smokers (Pinteraction ≤ .003 and .006, respectively) and alcohol drinkers (Pinteraction ≤ .004 and .001, respectively). Furthermore, among patients with OSCC, the C/T + T/T genotypes and T allele were associated with a decreased risk of advanced pathologic stage (P = .032) and lymph node involvement (P = .017). CONCLUSIONS BQ chewers carrying the T allele or C/T + T/T genotypes in pri-mir-26a-1 may have a decreased risk of oral leukoplakia, OPLs, and advanced-stage OSCC.
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Affiliation(s)
- Cheng-Mei Yang
- Director, Division of Endodontics, Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; Assistant Professor, Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Chien-Chou Chen
- Director, Department of Family Medicine, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan
| | - Yu-Kai Tseng
- Resident Doctor, Department of Orthopedics, Show Chwan Memorial Hospital, Changhua, Taiwan; Resident Doctor, Department of Orthopedics, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Sin-Jhih Huang
- Research Assistant, Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Huei-Han Liou
- Research Assistant, Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yi-Cheng Lee
- Research Assistant, Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; Registered Nurse, Department of Nursing, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Jang-Hwa Lee
- Director, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Jyh-Seng Wang
- Attending Doctor, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hung-Chih Chen
- Assistant Professor, Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan; Director, Division of Oral & Maxillary surgery, Department of Stomatology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chao-Chuan Chi
- Director, Division of Laryngology, Department of Otorhinolaryngology-Head & Neck Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Bor-Hwang Kang
- Director, Division of Rhinology, Department of Otorhinolaryngology-Head & Neck Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yun-Chung Lin
- Resident Doctor, Department of Pathology, China Medical University Hospital, Taichung, Taiwan
| | - Kuo-Wang Tsai
- Investigator, Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; Assistant Professor, Department of Chemical Biology, National Pingtung University of Education, Pingtung, Taiwan.
| | - Luo-Ping Ger
- Investigator, Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; Professor, Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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Ciesiolka A, Jazurek M, Drazkowska K, Krzyzosiak WJ. Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions. Front Cell Neurosci 2017; 11:97. [PMID: 28442996 PMCID: PMC5387085 DOI: 10.3389/fncel.2017.00097] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions. A growing body of recent evidence revealed that the RNA structures formed by these mutant RNA repeat tracts exhibit toxic effects on cells. Therefore, in this review article, we present existing knowledge on the structural aspects of different RNA repeat tracts as revealed mainly using well-established biochemical and biophysical methods. Furthermore, in several cases, it was shown that these expanded RNA structures are potent traps for a variety of RNA-binding proteins and that the sequestration of these proteins from their normal intracellular environment causes alternative splicing aberration, inhibition of nuclear transport and export, or alteration of a microRNA biogenesis pathway. Therefore, in this review article, we also present the most studied examples of abnormal interactions that occur between mutant RNAs and their associated proteins.
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Affiliation(s)
- Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Karolina Drazkowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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Zhao S, Gordon W, Du S, Zhang C, He W, Xi L, Mathur S, Agostino M, Paradis T, von Schack D, Vincent M, Zhang B. QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing. BMC Bioinformatics 2017; 18:180. [PMID: 28320324 PMCID: PMC5359966 DOI: 10.1186/s12859-017-1601-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/14/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate miRNA quantification from large-scale miRNA-seq dataset. We implemented a pipeline called QuickMIRSeq for accurate quantification of known miRNAs and miRNA isoforms (isomiRs) from multiple samples simultaneously. RESULTS QuickMIRSeq considers the unique nature of miRNAs and combines many important features into its implementation. First, it takes advantage of high redundancy of miRNA reads and introduces joint mapping of multiple samples to reduce computational time. Second, it incorporates the strand information in the alignment step for more accurate quantification. Third, reads potentially arising from background noise are filtered out to improve the reliability of miRNA detection. Fourth, sequences aligned to miRNAs with mismatches are remapped to a reference genome to further reduce false positives. Finally, QuickMIRSeq generates a rich set of QC metrics and publication-ready plots. CONCLUSIONS The rich visualization features implemented allow end users to interactively explore the results and gain more insights into miRNA-seq data analyses. The high degree of automation and interactivity in QuickMIRSeq leads to a substantial reduction in the time and effort required for miRNA-seq data analysis.
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Affiliation(s)
- Shanrong Zhao
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
| | - William Gordon
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Sarah Du
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Chi Zhang
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Wen He
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Li Xi
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Sachin Mathur
- Business Technology, Pfizer Worldwide Research and Development, Andover, MA, 01810, USA
| | - Michael Agostino
- Business Technology, Pfizer Worldwide Research and Development, Andover, MA, 01810, USA
| | - Theresa Paradis
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - David von Schack
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Michael Vincent
- I&I Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Baohong Zhang
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
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Galka-Marciniak P, Olejniczak M, Starega-Roslan J, Szczesniak MW, Makalowska I, Krzyzosiak WJ. siRNA release from pri-miRNA scaffolds is controlled by the sequence and structure of RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:639-49. [DOI: 10.1016/j.bbagrm.2016.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/17/2023]
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37
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Urgese G, Paciello G, Acquaviva A, Ficarra E. isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation. BMC Bioinformatics 2016; 17:148. [PMID: 27036505 PMCID: PMC4815201 DOI: 10.1186/s12859-016-0958-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/19/2016] [Indexed: 01/01/2023] Open
Abstract
Background Massive parallel sequencing of transcriptomes, revealed the presence of many miRNAs and miRNAs variants named isomiRs with a potential role in several cellular processes through their interaction with a target mRNA. Many methods and tools have been recently devised to detect and quantify miRNAs from sequencing data. However, all of them are implemented on top of general purpose alignment methods, thus providing poorly accurate results and no information concerning isomiRs and conserved miRNA-mRNA interaction sites. Results To overcome these limitations we present a novel algorithm named isomiR-SEA, that is able to provide users with very accurate miRNAs expression levels and both isomiRs and miRNA-mRNA interaction sites precise classifications. Tags are mapped on the known miRNAs sequences thanks to a specialized alignment algorithm developed on top of biological evidence concerning miRNAs structure. Specifically, isomiR-SEA checks for miRNA seed presence in the input tags and evaluates, during all the alignment phases, the positions of the encountered mismatches, thus allowing to distinguish among the different isomiRs and conserved miRNA-mRNA interaction sites. Conclusions isomiR-SEA performances have been assessed on two public RNA-Seq datasets proving that the implemented algorithm is able to account for more reliable and accurate miRNAs expression levels with respect to those provided by two compared state of the art tools. Moreover, differently from the few methods currently available to perform isomiRs detection, the proposed algorithm implements the evaluation of isomiRs and conserved miRNA-mRNA interaction sites already in the first alignment phases, thus avoiding any additional filtering stages potentially responsible for the loss of useful information. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0958-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gianvito Urgese
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino,, C.so Duca degli Abruzzi 24, Turin, 10129, IT, Italy.
| | - Giulia Paciello
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino,, C.so Duca degli Abruzzi 24, Turin, 10129, IT, Italy
| | - Andrea Acquaviva
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino,, C.so Duca degli Abruzzi 24, Turin, 10129, IT, Italy
| | - Elisa Ficarra
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino,, C.so Duca degli Abruzzi 24, Turin, 10129, IT, Italy
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Starega-Roslan J, Galka-Marciniak P, Krzyzosiak WJ. Nucleotide sequence of miRNA precursor contributes to cleavage site selection by Dicer. Nucleic Acids Res 2015; 43:10939-51. [PMID: 26424848 PMCID: PMC4678860 DOI: 10.1093/nar/gkv968] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/15/2015] [Indexed: 12/21/2022] Open
Abstract
The ribonuclease Dicer excises mature miRNAs from a diverse group of precursors (pre-miRNAs), most of which contain various secondary structure motifs in their hairpin stem. In this study, we analyzed Dicer cleavage in hairpin substrates deprived of such motifs. We searched for the factors other than the secondary structure, which may influence the length diversity and heterogeneity of miRNAs. We found that the nucleotide sequence at the Dicer cleavage site influences both of these miRNA characteristics. With regard to cleavage mechanism, we demonstrate that the Dicer RNase IIIA domain that cleaves within the 3′ arm of the pre-miRNA is more sensitive to the nucleotide sequence of its substrate than is the RNase IIIB domain. The RNase IIIA domain avoids releasing miRNAs with G nucleotide and prefers to generate miRNAs with a U nucleotide at the 5′ end. We also propose that the sequence restrictions at the Dicer cleavage site might be the factor that contributes to the generation of miRNA duplexes with 3′ overhangs of atypical lengths. This finding implies that the two RNase III domains forming the single processing center of Dicer may exhibit some degree of flexibility, which allows for the formation of these non-standard 3′ overhangs.
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Affiliation(s)
- Julia Starega-Roslan
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
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Viral Small-RNA Analysis of Bombyx mori Larval Midgut during Persistent and Pathogenic Cytoplasmic Polyhedrosis Virus Infection. J Virol 2015; 89:11473-86. [PMID: 26339065 DOI: 10.1128/jvi.01695-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/28/2015] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED The lepidopteran innate immune response against RNA viruses remains poorly understood, while in other insects several studies have highlighted an essential role for the exo-RNAi pathway in combating viral infection. Here, by using deep-sequencing technology for viral small-RNA (vsRNA) assessment, we provide evidence that exo-RNAi is operative in the silkworm Bombyx mori against both persistent and pathogenic infection of B. mori cytoplasmic polyhedrosis virus (BmCPV) which is characterized by a segmented double-stranded RNA (dsRNA) genome. Further, we show that Dicer-2 predominantly targets viral dsRNA and produces 20-nucleotide (nt) vsRNAs, whereas an additional pathway is responsive to viral mRNA derived from segment 10. Importantly, vsRNA distributions, which define specific hot and cold spot profiles for each viral segment, to a considerable degree overlap between Dicer-2-related (19 to 21 nt) and Dicer-2-unrelated vsRNAs, suggesting a common origin for these profiles. We found a degenerate motif significantly enriched at the cut sites of vsRNAs of various lengths which link an unknown RNase to the origins of vsRNAs biogenesis and distribution. Accordingly, the indicated RNase activity may be an important early factor for the host's antiviral defense in Lepidoptera. IMPORTANCE This work contributes to the elucidation of the lepidopteran antiviral response against infection of segmented double-stranded RNA (dsRNA) virus (CPV; Reoviridae) and highlights the importance of viral small-RNA (vsRNA) analysis for getting insights into host-pathogen interactions. Three vsRNA pathways are implicated in antiviral defense. For dsRNA, two pathways are proposed, either based on Dicer-2 cleavage to generate 20-nucleotide vsRNAs or based on the activity of an uncharacterized endo-RNase that cleaves the viral RNA substrate at a degenerate motif. The analysis also indicates the existence of a degradation pathway that targets the positive strand of segment 10.
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