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Ferre A, Santiago L, Sánchez-Herrero JF, López-Rodrigo O, Sánchez-Curbelo J, Sumoy L, Bassas L, Larriba S. 3'IsomiR Species Composition Affects Reliable Quantification of miRNA/isomiR Variants by Poly(A) RT-qPCR: Impact on Small RNA-Seq Profiling Validation. Int J Mol Sci 2023; 24:15436. [PMID: 37895116 PMCID: PMC10607168 DOI: 10.3390/ijms242015436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Small RNA-sequencing (small RNA-seq) has revealed the presence of small RNA-naturally occurring variants such as microRNA (miRNA) isoforms or isomiRs. Due to their small size and the sequence similarity among miRNA isoforms, their validation by RT-qPCR is challenging. We previously identified two miR-31-5p isomiRs-the canonical and a 3'isomiR variant (3' G addition)-which were differentially expressed between individuals with azoospermia of different origin. Here, we sought to determine the discriminatory capacity between these two closely-related miRNA isoforms of three alternative poly(A) based-RT-qPCR strategies in both synthetic and real biological context. We found that these poly(A) RT-qPCR strategies exhibit a significant cross-reactivity between these miR-31-5p isomiRs which differ by a single nucleotide, compromising the reliable quantification of individual miRNA isoforms. Fortunately, in the biological context, given that the two miRNA variants show changes in the same direction, RT-qPCR results were consistent with the findings of small RNA-seq study. We suggest that miRNA selection for RT-qPCR validation should be performed with care, prioritizing those canonical miRNAs that, in small RNA-seq, show parallel/homogeneous expression behavior with their most prevalent isomiRs, to avoid confounding RT-qPCR-based results. This is suggested as the current best strategy for robust biomarker selection to develop clinically useful tests.
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Affiliation(s)
- Adriana Ferre
- Human Molecular Genetics Group—Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain; (A.F.); (L.S.)
| | - Lucía Santiago
- Human Molecular Genetics Group—Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain; (A.F.); (L.S.)
| | - José Francisco Sánchez-Herrero
- High Content Genomics and Bioinformatics (HCGB), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain; (J.F.S.-H.); (L.S.)
| | - Olga López-Rodrigo
- Laboratory of Andrology and Sperm Bank, Andrology Service-Puigvert Foundation, 08025 Barcelona, Spain; (O.L.-R.); (J.S.-C.); (L.B.)
| | - Josvany Sánchez-Curbelo
- Laboratory of Andrology and Sperm Bank, Andrology Service-Puigvert Foundation, 08025 Barcelona, Spain; (O.L.-R.); (J.S.-C.); (L.B.)
| | - Lauro Sumoy
- High Content Genomics and Bioinformatics (HCGB), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain; (J.F.S.-H.); (L.S.)
| | - Lluís Bassas
- Laboratory of Andrology and Sperm Bank, Andrology Service-Puigvert Foundation, 08025 Barcelona, Spain; (O.L.-R.); (J.S.-C.); (L.B.)
| | - Sara Larriba
- Human Molecular Genetics Group—Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain; (A.F.); (L.S.)
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2
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Erdem M, Cicek M, Erson-Bensan AE. Versatile RNA: overlooked gems of the transcriptome. FEBS J 2023; 290:4843-4851. [PMID: 36719259 DOI: 10.1111/febs.16742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 02/01/2023]
Abstract
The critical role of RNA, its use and targetability concerning different aspects of human health are gaining more attention because our understanding of the versatility of RNA has dramatically evolved over the last decades. We now appreciate that RNA is far more critical than a messenger molecule and possesses many complicated functions. As a multifunctional molecule with its sequence, flexible structures and enzymatic abilities, RNA is genuinely powerful. Mammalian transcriptomes consist of a dynamically regulated plethora of coding and noncoding RNA types. However, some aspects of RNA metabolism remain to be explored. In this Viewpoint, we focus on the transcriptome's unconventional and possibly overlooked aspects to emphasize the importance of RNA in mammalian systems.
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Affiliation(s)
- Murat Erdem
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mustafa Cicek
- Department of Biology, Kamil Ozdag Faculty of Science, Karamanoglu Mehmetbey University, Karaman, Turkey
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3
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Lausten MA, Boman BM. A Review of IsomiRs in Colorectal Cancer. Noncoding RNA 2023; 9:34. [PMID: 37368334 DOI: 10.3390/ncrna9030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
As advancements in sequencing technology rapidly continue to develop, a new classification of microRNAs has occurred with the discovery of isomiRs, which are relatively common microRNAs with sequence variations compared to their established template microRNAs. This review article seeks to compile all known information about isomiRs in colorectal cancer (CRC), which has not, to our knowledge, been gathered previously to any great extent. A brief overview is given of the history of microRNAs, their implications in colon cancer, the canonical pathway of biogenesis and isomiR classification. This is followed by a comprehensive review of the literature that is available on microRNA isoforms in CRC. The information on isomiRs presented herein shows that isomiRs hold great promise for translation into new diagnostics and therapeutics in clinical medicine.
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Affiliation(s)
- Molly A Lausten
- Cawley Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Newark, DE 19713, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19713, USA
| | - Bruce M Boman
- Cawley Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Newark, DE 19713, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19713, USA
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
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4
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Gómez-Martín C, Aparicio-Puerta E, van Eijndhoven MA, Medina JM, Hackenberg M, Pegtel DM. Reassessment of miRNA variant ( isomiRs) composition by small RNA sequencing. Cell Rep Methods 2023; 3:100480. [PMID: 37323569 PMCID: PMC10261927 DOI: 10.1016/j.crmeth.2023.100480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/07/2023] [Accepted: 04/21/2023] [Indexed: 06/17/2023]
Abstract
IsomiRs, sequence variants of mature microRNAs, are usually detected and quantified using high-throughput sequencing. Many examples of their biological relevance have been reported, but sequencing artifacts identified as artificial variants might bias biological inference and therefore need to be ideally avoided. We conducted a comprehensive evaluation of 10 different small RNA sequencing protocols, exploring both a theoretically isomiR-free pool of synthetic miRNAs and HEK293T cells. We calculated that, with the exception of two protocols, less than 5% of miRNA reads can be attributed to library preparation artifacts. Randomized-end adapter protocols showed superior accuracy, with 40% of true biological isomiRs. Nevertheless, we demonstrate concordance across protocols for selected miRNAs in non-templated uridyl additions. Notably, NTA-U calling and isomiR target prediction can be inaccurate when using protocols with poor single-nucleotide resolution. Our results highlight the relevance of protocol choice for biological isomiRs detection and annotation, which has key potential implications for biomedical applications.
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Affiliation(s)
- Cristina Gómez-Martín
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | | | - Monique A.J. van Eijndhoven
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - José M. Medina
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - Michael Hackenberg
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
| | - D. Michiel Pegtel
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
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5
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Aiso T, Ueda M. 5'‑isomiR is the most abundant sequence of miR‑1246, a candidate biomarker of lung cancer, in serum. Mol Med Rep 2023; 27:92. [PMID: 36960865 PMCID: PMC10073804 DOI: 10.3892/mmr.2023.12979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
MicroRNA (miRNA/miR) 5'‑isoforms (5'‑isomiRs) differ from canonical sequences registered in the microRNA database in the length of their 5' ends. The 'seed sequence' of miRNAs that bind to target mRNAs is 2‑8 nucleotides from the 5' end; thus, shifts at the 5' end can cause a 'seed shift'. Accumulating data from miRNA deep sequencing have revealed that, in a substantial number of miRNAs, sequences corresponding to specific isomiRs, not the canonical form, are the most abundant. Studies have so far focused on circulating miRNAs as either markers or intercellular communication factors. miR‑1246 is abundant in the serum and is a candidate diagnostic and prognostic marker for esophageal squamous cell carcinoma, pancreatic cancer, hepatocellular carcinoma, colorectal adenocarcinoma and non‑small cell lung cancer (NSCLC). The present study analyzed the 5'‑end of serum miR‑1246 by fragment analysis and found that a 5'‑isomiR, which is two bases shorter than the canonical sequence, was the most abundant sequence in patients with NSCLC as well as healthy donors. To quantify the 5'‑isomiR, 5'‑isomiR‑specific primers based on primers for allele specific‑PCR were used, primarily because commercially available methods for miRNA Reverse transcription‑quantitative PCR cannot discriminate among sequences, especially those located at the 5' end of miRNA. The total miR‑1246 levels were significantly increased in patients with NSCLC; by contrast, the level of the canonical sequence was significantly decreased. Significant positive correlations were observed between the total miR‑1246 levels and the 5'‑isomiR levels, but not that of the canonical sequence. These results imply that the increase in levels of serum miR‑1246 in patients with NSCLC depends on increase of the 5'‑isomiR.
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Affiliation(s)
- Toshiko Aiso
- Department of Medical Technology, Faculty of Health Sciences, Kyorin University, Tokyo 181‑8612, Japan
| | - Makiko Ueda
- Department of Medical Technology, Faculty of Health Sciences, Kyorin University, Tokyo 181‑8612, Japan
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Thomas KT, Vermare A, Egleston SO, Wang YD, Mishra A, Lin T, Peng J, Zakharenko SS. MicroRNA 3' ends shorten during adolescent brain maturation. Front Mol Neurosci 2023; 16:1168695. [PMID: 37122627 PMCID: PMC10140418 DOI: 10.3389/fnmol.2023.1168695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
MicroRNA (miRNA) dysregulation is well-documented in psychiatric disease, but miRNA dynamics remain poorly understood during adolescent and early adult brain maturation, when symptoms often first appear. Here, we use RNA sequencing to examine miRNAs and their mRNA targets in cortex and hippocampus from early-, mid-, and late-adolescent and adult mice. Furthermore, we use quantitative proteomics by tandem mass tag mass spectrometry (TMT-MS) to examine protein dynamics in cortex from the same subjects. We found that ~25% of miRNAs' 3' ends shorten with age due to increased 3' trimming and decreased U tailing. Particularly, shorter but functionally competent isoforms (isomiRs) of miR-338-3p increase up to 10-fold during adolescence and only in brain. MiRNAs that undergo 3' shortening exhibit stronger negative correlations with targets that decrease with age and stronger positive correlations with targets that increase with age, than miRNAs with stable 3' ends. Increased 3' shortening with age was also observed in available mouse and human miRNA-seq data sets, and stronger correlations between miRNAs that undergo shortening and their mRNA targets were observed in two of the three available data sets. We conclude that age-associated miRNA 3' shortening is a well-conserved feature of postnatal brain maturation.
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Affiliation(s)
- Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Anaïs Vermare
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Suzannah O. Egleston
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Tong Lin
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, United States
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
- *Correspondence: Stanislav S. Zakharenko,
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7
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Naydenov M, Nikolova M, Apostolov A, Glogovitis I, Salumets A, Baev V, Yahubyan G. The Dynamics of miR-449a/c Expression during Uterine Cycles Are Associated with Endometrial Development. Biology (Basel) 2022; 12:biology12010055. [PMID: 36671747 PMCID: PMC9855972 DOI: 10.3390/biology12010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/30/2022]
Abstract
The human endometrium is a highly dynamic tissue. Increasing evidence has shown that microRNAs (miRs) play essential roles in human endometrium development. Our previous assay, based on small RNA-sequencing (sRNA-seq) indicated the complexity and dynamics of numerous sequence variants of miRs (isomiRs) that can act together to control genes of functional relevance to the receptive endometrium (RE). Here, we used a greater average depth of sRNA-seq to detect poorly expressed small RNAs. The sequencing data confirmed the up-regulation of miR-449c and uncovered other members of the miR-449 family up-regulated in RE-among them miR-449a, as well as several isoforms of both miR-449a and miR-449c, while the third family member, miR-449b, was not identified. Stem-looped RT-qPCR analysis of miR expression at four-time points of the endometrial cycle verified the increased expression of the miR-449a/c family members in RE, among which the 5' isoform of miR-449c-miR-449c.1 was the most strongly up-regulated. Moreover, we found in a case study that the expression of miR-449c.1 and its precursor correlated with the histological assessment of the endometrial phase and patient age. We believe this study will promote the clinical investigation and application of the miR-449 family in the diagnosis and prognosis of human reproductive diseases.
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Affiliation(s)
- Mladen Naydenov
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Maria Nikolova
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
- Center for Women’s Health, 4000 Plovdiv, Bulgaria
| | - Apostol Apostolov
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
- Competence Centre on Health Technologies, 50406 Tartu, Estonia
| | - Ilias Glogovitis
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Andres Salumets
- Competence Centre on Health Technologies, 50406 Tartu, Estonia
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute, Karolinska University Hospital, 14186 Stockholm, Sweden
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
| | - Vesselin Baev
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
| | - Galina Yahubyan
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria
- Correspondence:
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8
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Abstract
MicroRNAs (miRNAs) are key players in gene regulation that target specific mRNAs for degradation or translational repression. Each miRNA is synthesized as a miRNA duplex comprising two strands (5p and 3p). However, only one of the two strands becomes active and is selectively incorporated into the RNA-induced silencing complex in a process known as miRNA strand selection. Recently, significant progress has been made in understanding the factors and processes involved in strand selection. Here, we explore the selection and functionality of the miRNA star strand (either 5p or 3p), which is generally present in the cell at low levels compared to its partner strand and, historically, has been thought to possess no biological activity. We also highlight the concepts of miRNA arm switching and miRNA isomerism. Finally, we offer insights into the impact of aberrant strand selection on immunity and cancer. Leading us through this journey is miR-155, a well-established regulator of immunity and cancer, and the increasing evidence that its 3p strand plays a role in these arenas. Interestingly, the miR-155-5p/-3p ratio appears to vary dependent on the timing of the immune response, and the 3p strand seems to play a regulatory role upon its partner 5p strand.
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Affiliation(s)
- Owen Dawson
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
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9
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Medhi R, Price J, Furlan G, Gorges B, Sapetschnig A, Miska EA. RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type. RNA 2022; 28:353-370. [PMID: 34949722 PMCID: PMC8848932 DOI: 10.1261/rna.078976.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
The human terminal uridyl transferases TUT4 and TUT7 (TUT4/7) catalyze the additions of uridines at the 3' end of RNAs, including the precursors of the tumor suppressor miRNA let-7 upon recruitment by the oncoprotein LIN28A. As a consequence, let-7 family miRNAs are down-regulated. Disruption of this TUT4/7 activity inhibits tumorigenesis. Hence, targeting TUT4/7 could be a potential anticancer therapy. In this study, we investigate TUT4/7-mediated RNA regulation in two cancer cell lines by establishing catalytic knockout models. Upon TUT4/7 mutation, we observe a significant reduction in miRNA uridylation, which results in defects in cancer cell properties such as cell proliferation and migration. With the loss of TUT4/7-mediated miRNA uridylation, the uridylated miRNA variants are replaced by adenylated isomiRs. Changes in miRNA modification profiles are accompanied by deregulation of expression levels in specific cases. Unlike let-7s, most miRNAs do not depend on LIN28A for TUT4/7-mediated regulation. Additionally, we identify TUT4/7-regulated cell-type-specific miRNA clusters and deregulation in their corresponding mRNA targets. Expression levels of miR-200c-3p and miR-141-3p are regulated by TUT4/7 in a cancer cell-type-specific manner. Subsequently, BCL2, which is a well-established target of miR-200c is up-regulated. Therefore, TUT4/7 loss causes deregulation of miRNA-mRNA networks in a cell-type-specific manner. Understanding of the underlying biology of such cell-type-specific deregulation will be an important aspect of targeting TUT4/7 for potential cancer therapies.
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Affiliation(s)
- Ragini Medhi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jonathan Price
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Giulia Furlan
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Beronia Gorges
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Alexandra Sapetschnig
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Eric A Miska
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Nikolova M, Naydenov M, Glogovitis I, Apostolov A, Saare M, Boggavarapu N, Salumets A, Baev V, Yahubyan G. Coupling miR/isomiR and mRNA Expression Signatures Unveils New Molecular Layers of Endometrial Receptivity. Life (Basel) 2021; 11:1391. [PMID: 34947922 DOI: 10.3390/life11121391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/27/2022] Open
Abstract
Embryo implantation depends on endometrial receptivity (ER). To achieve ER, the preparation of the uterine lining requires controlled priming by ovarian hormones and the expression of numerous genes in the endometrial tissue. microRNAs (miRs) have emerged as critical genetic regulators of ER in fertility and of the diseases that are associated with infertility. With the rapid development of next-generation sequencing technologies, it has become clear that miR genes can produce canonical miRs and variants—isomiRs. Here, we describe miR/isomiR expression dynamics across the four time points of natural chorionic gonadotropin (hCG)-administered cycles. Sequencing of the small RNAs (sRNA-seq) revealed that the most significant expression changes during the transition from the pre-receptive to the receptive phase occurred in the isomiR families of miR-125a, miR-125b, miR-10a, miR-10b, miR-449c, miR-92a, miR-92b, and miR-99a. Pairing the analysis of the differentially expressed (DE) miRs/isomiRs and their predicted DE mRNA targets uncovered 280 negatively correlating pairs. In the receptive endometrium, the 5′3′-isomiRs of miR-449c, which were among the most highly up-regulated isomiRs, showed a negative correlation with their target, transcription factor (TF) MYCN, which was down-regulated. Joint analysis of the miR/isomiR and TF expression identified several regulatory interactions. Based on these data, a regulatory TF-miR/isomiR gene-target circuit including let7g-5p and miR-345; the isomiR families of miR-10a, miR-10b, miR-92a, and miR-449c; and MYCN and TWIST1 was proposed to play a key role in the establishment of ER. Our work uncovers the complexity and dynamics of the endometrial isomiRs that can act cooperatively with miRs to control the functionally important genes that are critical to ER. Further studies of miR/isomiR expression patterns that are paired with those of their target mRNAs may provide a more in-depth picture of the endometrial pathologies that are associated with implantation failure.
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12
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Glogovitis I, Yahubyan G, Würdinger T, Koppers-Lalic D, Baev V. miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data. Cancers (Basel) 2021; 13:cancers13225663. [PMID: 34830818 PMCID: PMC8616193 DOI: 10.3390/cancers13225663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/25/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary MicroRNAs are essential regulators of gene expression and potential non-invasive biomarker candidates for various human cancers as they can be detected in bodily fluids. Several tools have been developed to analyze small RNA-sequencing data; however, they have limitations and restrictions such as lack of optimal configuration, parameterization, and interoperability with other tools and platforms. miRGalaxy is an open-source, Galaxy-based framework for analyzing NGS data focusing on microRNAs and their sequence variants—isomiRs. Galaxy is a web-based platform for data-intensive biomedical research, allowing user-friendly analysis and accessibility to hundreds of tools. miRGalaxy is designed specifically for identifying and classifying human microRNAs and isomiRs, as well as detecting deregulated microRNAs and isomiRs between two test groups, summarized by output visualization. By examining the differential expression of individual isomiR species across samples, miRGalaxy can help discover novel biomarkers. Abstract Tools for microRNA (miR) sequencing data analyses are broadly used in biomedical research. However, the complexity of computational approaches still remains a challenge for biologists with scarce experience in data analytics and bioinformatics. Here, we present miRGalaxy, a Galaxy-based framework for comprehensive analysis of miRs and their sequence variants—miR isoforms (isomiRs). Though isomiRs are commonly reported in deep-sequencing experiments, their detailed structure complexity and specific differential expression (DE) remain not fully examined by the majority of the available analysis tools. miRGalaxy encompasses biologist-user-friendly tools and workflows dedicated to the analysis of the isomiR-ome and its complex behavior in various biological samples. miRGalaxy is developed as a modular, accessible, redistributable, shareable, and user-friendly framework for scientists working with small RNA (sRNA)-seq data. Due to its modular workflow, advanced users can customize the steps and tools for their needs. In addition, the framework provides an analysis report where the significant output results are summarized in charts and visualizations. miRGalaxy can be accessed via preconfigured Docker image flavor and a Toolshed installation if the user already has a running Galaxy instance. Over the last decade, studies on the expression of miRs and isomiRs in normal and deregulated tissues have led to the discovery of their potential as diagnostic biomarkers. The detection of miRs in biofluids further expanded the exploration of the miR repertoire as a source of liquid biopsy biomarkers. Here we show the miRGalaxy framework application for in-depth analysis of the sRNA-seq data from two different biofluids, milk and plasma, to identify, annotate, and discover specific differentially expressed miRs and isomiRs.
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Affiliation(s)
- Ilias Glogovitis
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (I.G.); (G.Y.)
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (T.W.); (D.K.-L.)
| | - Galina Yahubyan
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (I.G.); (G.Y.)
| | - Thomas Würdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (T.W.); (D.K.-L.)
| | - Danijela Koppers-Lalic
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (T.W.); (D.K.-L.)
| | - Vesselin Baev
- Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (I.G.); (G.Y.)
- Correspondence:
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Zelli V, Compagnoni C, Capelli R, Corrente A, Cornice J, Vecchiotti D, Di Padova M, Zazzeroni F, Alesse E, Tessitore A. Emerging Role of isomiRs in Cancer: State of the Art and Recent Advances. Genes (Basel) 2021; 12:genes12091447. [PMID: 34573429 PMCID: PMC8469436 DOI: 10.3390/genes12091447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
The advent of Next Generation Sequencing technologies brought with it the discovery of several microRNA (miRNA) variants of heterogeneous lengths and/or sequences. Initially ascribed to sequencing errors/artifacts, these isoforms, named isomiRs, are now considered non-canonical variants that originate from physiological processes affecting the canonical miRNA biogenesis. To date, accurate IsomiRs abundance, biological activity, and functions are not completely understood; however, the study of isomiR biology is an area of great interest due to their high frequency in the human miRNome, their putative functions in cooperating with the canonical miRNAs, and potential for exhibiting novel functional roles. The discovery of isomiRs highlighted the complexity of the small RNA transcriptional landscape in several diseases, including cancer. In this field, the study of isomiRs could provide further insights into the miRNA biology and its implication in oncogenesis, possibly providing putative new cancer diagnostic, prognostic, and predictive biomarkers as well. In this review, a comprehensive overview of the state of research on isomiRs in different cancer types, including the most common tumors such as breast cancer, colorectal cancer, melanoma, and prostate cancer, as well as in the less frequent tumors, as for example brain tumors and hematological malignancies, will be summarized and discussed.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Corrente
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Jessica Cornice
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Davide Vecchiotti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Monica Di Padova
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence: ; Tel.: +39-0862433518; Fax: +39-0862433131
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Divisato G, Piscitelli S, Elia M, Cascone E, Parisi S. MicroRNAs and Stem-like Properties: The Complex Regulation Underlying Stemness Maintenance and Cancer Development. Biomolecules 2021; 11:biom11081074. [PMID: 34439740 PMCID: PMC8393604 DOI: 10.3390/biom11081074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
Embryonic stem cells (ESCs) have the extraordinary properties to indefinitely proliferate and self-renew in culture to produce different cell progeny through differentiation. This latter process recapitulates embryonic development and requires rounds of the epithelial-mesenchymal transition (EMT). EMT is characterized by the loss of the epithelial features and the acquisition of the typical phenotype of the mesenchymal cells. In pathological conditions, EMT can confer stemness or stem-like phenotypes, playing a role in the tumorigenic process. Cancer stem cells (CSCs) represent a subpopulation, found in the tumor tissues, with stem-like properties such as uncontrolled proliferation, self-renewal, and ability to differentiate into different cell types. ESCs and CSCs share numerous features (pluripotency, self-renewal, expression of stemness genes, and acquisition of epithelial-mesenchymal features), and most of them are under the control of microRNAs (miRNAs). These small molecules have relevant roles during both embryogenesis and cancer development. The aim of this review was to recapitulate molecular mechanisms shared by ESCs and CSCs, with a special focus on the recently identified classes of microRNAs (noncanonical miRNAs, mirtrons, isomiRs, and competitive endogenous miRNAs) and their complex functions during embryogenesis and cancer development.
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Morsiani C, Terlecki‐Zaniewicz L, Skalicky S, Bacalini MG, Collura S, Conte M, Sevini F, Garagnani P, Salvioli S, Hackl M, Grillari J, Franceschi C, Capri M. Circulating miR-19a-3p and miR-19b-3p characterize the human aging process and their isomiRs associate with healthy status at extreme ages. Aging Cell 2021; 20:e13409. [PMID: 34160893 PMCID: PMC8282272 DOI: 10.1111/acel.13409] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/14/2021] [Accepted: 05/08/2021] [Indexed: 12/15/2022] Open
Abstract
Blood circulating microRNAs (c-miRs) are potential biomarkers to trace aging and longevity trajectories to identify molecular targets for anti-aging therapies. Based on a cross-sectional study, a discovery phase was performed on 12 donors divided into four groups: young, old, healthy, and unhealthy centenarians. The identification of healthy and unhealthy phenotype was based on cognitive performance and capabilities to perform daily activities. Small RNA sequencing identified 79 differentially expressed c-miRs when comparing young, old, healthy centenarians, and unhealthy centenarians. Two miRs, that is, miR-19a-3p and miR-19b-3p, were found increased at old age but decreased at extreme age, as confirmed by RT-qPCR in 49 donors of validation phase. The significant decrease of those miR levels in healthy compared to unhealthy centenarians appears to be due to the presence of isomiRs, not detectable with RT-qPCR, but only with a high-resolution technique such as deep sequencing. Bioinformatically, three main common targets of miR-19a/b-3p were identified, that is, SMAD4, PTEN, and BCL2L11, converging into the FoxO signaling pathway, known to have a significant role in aging mechanisms. For the first time, this study shows the age-related increase of plasma miR-19a/b-3p in old subjects but a decrease in centenarians. This decrease is more pronounced in healthy centenarians and was confirmed by the modified pattern of isomiRs comparing healthy and unhealthy centenarians. Thus, our study paves the way for functional studies using c-miRs and isomiRs as additional parameter to track the onset of aging and age-related diseases using new potential biomarkers.
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Affiliation(s)
- Cristina Morsiani
- DIMES‐Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Lucia Terlecki‐Zaniewicz
- Christian Doppler Laboratory for Biotechnology of Skin Aging Vienna Austria
- Department of Biotechnology Institute of Molecular Biotechnology BOKU – University of Natural Resources and Life Sciences Vienna Austria
| | | | | | - Salvatore Collura
- DIMES‐Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Maria Conte
- DIMES‐Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
- Interdepartmental Center "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)" University of Bologna Bologna Italy
| | - Federica Sevini
- DIMES‐Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Paolo Garagnani
- DIMES‐Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
- Applied Biomedical Research Center (CRBA) S. Orsola‐Malpighi Polyclinic Bologna Italy
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli‐Sforza" – Unit of Bologna Bologna Italy
- Department of Laboratory Medicine Clinical Chemistry Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | - Stefano Salvioli
- DIMES‐Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
- Interdepartmental Center "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)" University of Bologna Bologna Italy
| | | | - Johannes Grillari
- Christian Doppler Laboratory for Biotechnology of Skin Aging Vienna Austria
- Department of Biotechnology Institute of Molecular Biotechnology BOKU – University of Natural Resources and Life Sciences Vienna Austria
- Austrian Cluster for Tissue Regeneration Vienna Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology Vienna Austria
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics Lobachevsky University Nizhny Novgorod Russia
| | - Miriam Capri
- DIMES‐Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
- Interdepartmental Center "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)" University of Bologna Bologna Italy
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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: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Pifková L, Veselá P, Slabý O. The development and significance of microRNA sequence variants in carcinogenesis. Klin Onkol 2021; 34:20-25. [PMID: 33657815 DOI: 10.48095/ccko202120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND MicroRNA (miRNA) are a class of short non-coding RNAs that regulate gene expression at the posttranscriptional level. They are involved in key cellular processes and development as well as progression of many diseases. Their levels reflect the physiological state of organisms; therefore, the expression profiles of these molecules are analyzed in bio-marker studies. Due to their properties, miRNA appear to be promising dia-gnostic, prognostic and predictive bio-markers of cancer. Recent studies indicate the existence of sequence variants in miRNA, so-called isomiRs, which differ from the annotated miRNAs by altered sequences due to posttranscriptional modifications. These isomiRs may have a higher abundance than canonical miRNA. The characterization of isomiRs reveals their regulated distribution and different bio-logical properties and thus suggest the possible bio-logical significance of the modifications. The presence of isomiRs can also significantly affect the results of bio-marker studies. Currently, the research is focused on their possible clinical significance. PURPOSE The aim of this review is to provide an overview of current knowledge about sequence variants in miRNA. The review summarizes the mechanisms of isomiRs bio-genesis and describes the effects of sequence heterogeneity on miRNA stability, function and analysis. Subsequently, the role of isomiRs in bio-marker studies is discussed.
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Glogovitis I, Yahubyan G, Würdinger T, Koppers-Lalic D, Baev V. isomiRs-Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them? Biomolecules 2020; 11:41. [PMID: 33396892 DOI: 10.3390/biom11010041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/22/2020] [Accepted: 12/26/2020] [Indexed: 02/06/2023] Open
Abstract
Numerous studies on microRNAs (miRNA) in cancer and other diseases have been accompanied by diverse computational approaches and experimental methods to predict and validate miRNA biological and clinical significance as easily accessible disease biomarkers. In recent years, the application of the next-generation deep sequencing for the analysis and discovery of novel RNA biomarkers has clearly shown an expanding repertoire of diverse sequence variants of mature miRNAs, or isomiRs, resulting from alternative post-transcriptional processing events, and affected by (patho)physiological changes, population origin, individual's gender, and age. Here, we provide an in-depth overview of currently available bioinformatics approaches for the detection and visualization of both mature miRNA and cognate isomiR sequences. An attempt has been made to present in a systematic way the advantages and downsides of in silico approaches in terms of their sensitivity and accuracy performance, as well as used methods, workflows, and processing steps, and end output dataset overlapping issues. The focus is given to the challenges and pitfalls of isomiR expression analysis. Specifically, we address the availability of tools enabling research without extensive bioinformatics background to explore this fascinating corner of the small RNAome universe that may facilitate the discovery of new and more reliable disease biomarkers.
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Nersisyan SA, Shkurnikov MY, Knyazev EN. Factors Involved in miRNA Processing Change Its Expression Level during Imitation of Hypoxia in BeWo b30 Cells. DOKL BIOCHEM BIOPHYS 2020; 493:205-207. [PMID: 32894466 DOI: 10.1134/s1607672920040110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 11/23/2022]
Abstract
One of the main complications of pregnancy and causes of maternal and perinatal mortality is preeclampsia. The pathophysiology of preeclampsia is associated with the development of placenta and fetal hypoxia and secretion of a number of effective molecules. The human choriocarcinoma cell line BeWo b30 is often used as a model of the placental barrier. It was shown that oxyquinoline derivatives can mimic hypoxia by suppressing HIF-prolyl hydroxylases and the accumulation of HIF-1α. This effect also leads to a change in the expression of microRNAs and their target genes. However, with hypoxia in cells, not only the level of individual miRNAs but also the ratio of miRNA isoforms (isomiRs) can change, presumably due to inaccuracies in the work of the Drosha and Dicer enzymes. In this work, we showed a change in the expression of the factors involved in the maturation of miRNAs when simulating hypoxia in BeWo b30 cells with an oxyquinoline derivative, which may be one of the causes for the change in the ratio of miRNA isoforms.
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Affiliation(s)
- S A Nersisyan
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia.,Faculty of Mechanics and Mathematics, Moscow State University, Moscow, Russia
| | - M Yu Shkurnikov
- Hertsen Moscow Oncology Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - E N Knyazev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia. .,Translational Technology Center, Moscow, Russia.
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Cherlin T, Magee R, Jing Y, Pliatsika V, Loher P, Rigoutsos I. Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner. BMC Biol 2020; 18:38. [PMID: 32279660 PMCID: PMC7153239 DOI: 10.1186/s12915-020-0763-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/03/2020] [Indexed: 01/02/2023] Open
Abstract
Background The advent of next generation sequencing (NGS) has allowed the discovery of short and long non-coding RNAs (ncRNAs) in an unbiased manner using reverse genetics approaches, enabling the discovery of multiple categories of ncRNAs and characterization of the way their expression is regulated. We previously showed that the identities and abundances of microRNA isoforms (isomiRs) and transfer RNA-derived fragments (tRFs) are tightly regulated, and that they depend on a person’s sex and population origin, as well as on tissue type, tissue state, and disease type. Here, we characterize the regulation and distribution of fragments derived from ribosomal RNAs (rRNAs). rRNAs form a group that includes four (5S, 5.8S, 18S, 28S) rRNAs encoded by the human nuclear genome and two (12S, 16S) by the mitochondrial genome. rRNAs constitute the most abundant RNA type in eukaryotic cells. Results We analyzed rRNA-derived fragments (rRFs) across 434 transcriptomic datasets obtained from lymphoblastoid cell lines (LCLs) derived from healthy participants of the 1000 Genomes Project. The 434 datasets represent five human populations and both sexes. We examined each of the six rRNAs and their respective rRFs, and did so separately for each population and sex. Our analysis shows that all six rRNAs produce rRFs with unique identities, normalized abundances, and lengths. The rRFs arise from the 5′-end (5′-rRFs), the interior (i-rRFs), and the 3′-end (3′-rRFs) or straddle the 5′ or 3′ terminus of the parental rRNA (x-rRFs). Notably, a large number of rRFs are produced in a population-specific or sex-specific manner. Preliminary evidence suggests that rRF production is also tissue-dependent. Of note, we find that rRF production is not affected by the identity of the processing laboratory or the library preparation kit. Conclusions Our findings suggest that rRFs are produced in a regimented manner by currently unknown processes that are influenced by both ubiquitous as well as population-specific and sex-specific factors. The properties of rRFs mirror the previously reported properties of isomiRs and tRFs and have implications for the study of homeostasis and disease.
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Affiliation(s)
- Tess Cherlin
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Rogan Magee
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Yi Jing
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Venetia Pliatsika
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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Gaffo E, Bortolomeazzi M, Bisognin A, Di Battista P, Lovisa F, Mussolin L, Bortoluzzi S. MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data. Int J Mol Sci 2020; 21:ijms21051754. [PMID: 32143373 PMCID: PMC7084216 DOI: 10.3390/ijms21051754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/26/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function.
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Affiliation(s)
- Enrico Gaffo
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (M.B.); (A.B.)
- Correspondence: (E.G.); (S.B.); Tel.: +39-049-827-6502 (S.B.)
| | - Michele Bortolomeazzi
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (M.B.); (A.B.)
| | - Andrea Bisognin
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (M.B.); (A.B.)
| | - Piero Di Battista
- Division of Pediatric Hematology, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (P.D.B.); (F.L.); (L.M.)
- Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Federica Lovisa
- Division of Pediatric Hematology, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (P.D.B.); (F.L.); (L.M.)
- Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Lara Mussolin
- Division of Pediatric Hematology, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (P.D.B.); (F.L.); (L.M.)
- Istituto di Ricerca Pediatrica Città della Speranza, 35127 Padova, Italy
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (M.B.); (A.B.)
- Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, 35131 Padova, Italy
- Correspondence: (E.G.); (S.B.); Tel.: +39-049-827-6502 (S.B.)
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22
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van der Kwast RV, Quax PH, Nossent AY. An Emerging Role for isomiRs and the microRNA Epitranscriptome in Neovascularization. Cells 2019; 9:cells9010061. [PMID: 31881725 PMCID: PMC7017316 DOI: 10.3390/cells9010061] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Therapeutic neovascularization can facilitate blood flow recovery in patients with ischemic cardiovascular disease, the leading cause of death worldwide. Neovascularization encompasses both angiogenesis, the sprouting of new capillaries from existing vessels, and arteriogenesis, the maturation of preexisting collateral arterioles into fully functional arteries. Both angiogenesis and arteriogenesis are highly multifactorial processes that require a multifactorial regulator to be stimulated simultaneously. MicroRNAs can regulate both angiogenesis and arteriogenesis due to their ability to modulate expression of many genes simultaneously. Recent studies have revealed that many microRNAs have variants with altered terminal sequences, known as isomiRs. Additionally, endogenous microRNAs have been identified that carry biochemically modified nucleotides, revealing a dynamic microRNA epitranscriptome. Both types of microRNA alterations were shown to be dynamically regulated in response to ischemia and are able to influence neovascularization by affecting the microRNA’s biogenesis, or even its silencing activity. Therefore, these novel regulatory layers influence microRNA functioning and could provide new opportunities to stimulate neovascularization. In this review we will highlight the formation and function of isomiRs and various forms of microRNA modifications, and discuss recent findings that demonstrate that both isomiRs and microRNA modifications directly affect neovascularization and vascular remodeling.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul H.A. Quax
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Laboratory Medicine and Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
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23
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Wright C, Rajpurohit A, Burke EE, Williams C, Collado-Torres L, Kimos M, Brandon NJ, Cross AJ, Jaffe AE, Weinberger DR, Shin JH. Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. BMC Genomics 2019; 20:513. [PMID: 31226924 PMCID: PMC6588940 DOI: 10.1186/s12864-019-5870-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias. Furthermore, evaluations of the quantification of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited. No study had yet evaluated the quantification of isomiRs of altered length or compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases. RESULTS All methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency. CONCLUSIONS Our data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.
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Affiliation(s)
- Carrie Wright
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,AstraZeneca Postdoc Program, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Anandita Rajpurohit
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Emily E Burke
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Courtney Williams
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Martha Kimos
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Nicholas J Brandon
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Alan J Cross
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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24
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Yang A, Bofill-De Ros X, Shao TJ, Jiang M, Li K, Villanueva P, Dai L, Gu S. 3' Uridylation Confers miRNAs with Non-canonical Target Repertoires. Mol Cell 2019; 75:511-522.e4. [PMID: 31178353 DOI: 10.1016/j.molcel.2019.05.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/14/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022]
Abstract
Many microRNAs (miRNAs) exist alongside abundant miRNA isoforms (isomiRs), most of which arise from post-maturation sequence modifications such as 3' uridylation. However, the ways in which these sequence modifications affect miRNA function remain poorly understood. Here, using human miR-27a in cell lines as a model, we discovered that a nonfunctional target site unable to base-pair extensively with the miRNA seed sequence can regain function when an upstream adenosine is able to base-pair with a post-transcriptionally added uridine in the miR-27a tail. This tail-U-mediated repression (TUMR) is abolished in cells lacking the uridylation enzymes TUT4 and TUT7, indicating that uridylation alters miRNA function by modulating target recognition. We identified a set of non-canonical targets in human cells that are specifically regulated by uridylated miR-27a. We provide evidence that TUMR expands the targets of other endogenous miRNAs. Our study reveals a function of uridylated isomiRs in regulating non-canonical miRNA targets.
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Affiliation(s)
- Acong Yang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Xavier Bofill-De Ros
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Tie-Juan Shao
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Minjie Jiang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Katherine Li
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Patricia Villanueva
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisheng Dai
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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25
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Thibord F, Perret C, Roux M, Suchon P, Germain M, Deleuze JF, Morange PE, Trégouët DA. OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis. RNA 2019; 25:657-668. [PMID: 30819774 PMCID: PMC6521604 DOI: 10.1261/rna.069708.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Next-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs' detection and quantification still remain a challenge as they can undergo different posttranscriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy. OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers. OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).
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Affiliation(s)
- Florian Thibord
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
- INSERM UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, 33076 Bordeaux, France
| | - Claire Perret
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - Maguelonne Roux
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
| | - Pierre Suchon
- Laboratory of Haematology, La Timone Hospital, 13885 Marseille, France
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1062, Nutrition Obesity and Risk of Thrombosis, Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, 13885 Marseille, France
| | - Marine Germain
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
- INSERM UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, 33076 Bordeaux, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Direction de la Recherche Fondamentale, CEA, 91057 Evry, France
- CEPH, Fondation Jean Dausset, 75011 Paris, France
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, 13885 Marseille, France
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1062, Nutrition Obesity and Risk of Thrombosis, Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, 13885 Marseille, France
| | - David-Alexandre Trégouët
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics and Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
- Institute for Cardiometabolism and Nutrition (ICAN), 75013 Paris, France
- INSERM UMR_S 1219, Bordeaux Population Health Research Center, University of Bordeaux, 33076 Bordeaux, France
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26
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Bofill-De Ros X, Kasprzak WK, Bhandari Y, Fan L, Cavanaugh Q, Jiang M, Dai L, Yang A, Shao TJ, Shapiro BA, Wang YX, Gu S. Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires. Cell Rep 2019; 26:447-459.e4. [PMID: 30625327 PMCID: PMC6369706 DOI: 10.1016/j.celrep.2018.12.054] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/11/2018] [Accepted: 12/11/2018] [Indexed: 12/16/2022] Open
Abstract
MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low-grade glioma patient samples indicate that the alternative-miR-9 has a potential role in tumor progression. Furthermore, we provide evidence that distortion of pri-miRNA stems induced by asymmetric internal loops correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing.
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Affiliation(s)
- Xavier Bofill-De Ros
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wojciech K Kasprzak
- Basic Science Program, RNA Biology Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Yuba Bhandari
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Lixin Fan
- Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Quinn Cavanaugh
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Minjie Jiang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisheng Dai
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Acong Yang
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Tie-Juan Shao
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Bruce A Shapiro
- RNA Structure and Design Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Shuo Gu
- RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Koter MD, Święcicka M, Matuszkiewicz M, Pacak A, Derebecka N, Filipecki M. The miRNAome dynamics during developmental and metabolic reprogramming of tomato root infected with potato cyst nematode. Plant Sci 2018; 268:18-29. [PMID: 29362080 DOI: 10.1016/j.plantsci.2017.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/05/2017] [Accepted: 12/09/2017] [Indexed: 05/20/2023]
Abstract
Cyst-forming plant-parasitic nematodes are pests threatening many crops. By means of their secretions cyst nematodes induce the developmental and metabolic reprogramming of host cells that lead to the formation of a syncytium, which is the sole food source for growing nematodes. The in depth micro RNA (miRNA) dynamics in the syncytia induced by Globodera rostochiensis in tomato roots was studied. The miRNAomes were obtained from syncytia covering the early and intermediate developmental stages, and were the subject of differential expression analysis. The expression of 1235 miRNAs was monitored. The fold change (log2FC) ranged from -7.36 to 8.38, indicating that this transcriptome fraction was very variable. Moreover, we showed that the DE (differentially expressed) miRNAs do not fully overlap between the selected time points, suggesting infection stage specific regulation by miRNA. The correctness of RNA-seq expression profiling was confirmed by qRT-PCR (quantitative Real Time Polymerase Chain Reaction) for seven miRNA species. Down- and up-regulated miRNA species, including their isomiRs, were further used to identify their potential targets. Among them there are a large number of transcription factors linked to different aspects of plant development belonging to gene families, such as APETALA2 (AP2), SQUAMOSA (MADS-box), MYB, GRAS, and AUXIN RESPONSE FACTOR (ARF). The substantial portion of potential target genes belong to the NB-LRR and RLK (RECEPTOR-LIKE KINASE) families, indicating the involvement of miRNA mediated regulation in defense responses. We also collected the evidence for target cleavage in the case of 29 miRNAs using one of three alternative methods: 5' RACE (5' Rapid Amplification of cDNA Ends), a search of tasiRNA within our datasets, and the meta-analysis of tomato degradomes in the GEO (Gene Expression Omnibus) database. Eight target transcripts showed a negative correlation with their respective miRNAs at two or three time points. These results indicate a large regulatory potential for miRNAs in tuning the development and defense responses.
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Affiliation(s)
- Marek D Koter
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Magdalena Święcicka
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Mateusz Matuszkiewicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Marcin Filipecki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland.
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29
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Tripathi A, Chacon O, Singla-Pareek SL, Sopory SK, Sanan-Mishra N. Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice. Curr Genomics 2018; 19:21-35. [PMID: 29491730 PMCID: PMC5817874 DOI: 10.2174/1389202918666170228134530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 12/01/2022] Open
Abstract
In the recent years, glyoxalase pathway has been an active area of research in both human and plants. This pathway is reported to confer stress tolerance in plants, by modulating the glutathione homeostasis to achieve detoxification of a potent cytotoxic and mutagenic compound, methylglyoxal. The microRNAs (miRNAs) are also reported to play significant role in stress tolerance for plants. However, the cross-talk of miRNAs with the metabolism regulated by glyoxalase in the salinity-tolerance is unexplored. We therefore investigated whether expression profiles of miRNAs are altered in response to glyoxalase overexpression, and if any of these are also responsible for modulating the stress responses of plants. In this study, the Next Generation Sequencing (NGS) was employed to profile miRNA expression levels from glyoxalase overexpressing transgenic lines. The associated targets of differentially expressed miRNAs were predicted and their functional annotation was carried out using Gene Ontology (GO) and KEGG Orthology (KO), which showed their involvement in several crucial biological pathways. The analysis of NGS datasets also identified other isoforms or isomiRs of selected miRNAs, which may have an active role in developing tolerance against salt stress. Different aspects of miRNA modifications were also studied in glyoxalase overexpressing lines.
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Affiliation(s)
- Anita Tripathi
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Osmani Chacon
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sneh Lata Singla-Pareek
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sudhir K. Sopory
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Neeti Sanan-Mishra
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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30
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Yang K, Wen X, Mudunuri SB, Sablok G. Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants. Front Plant Sci 2018; 9:1881. [PMID: 30723486 PMCID: PMC6349829 DOI: 10.3389/fpls.2018.01881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/05/2018] [Indexed: 05/15/2023]
Abstract
microRNAs (miRNAs) play an important role as key regulators controlling the post-transcriptional events in plants across development, abiotic and biotic stress, tissue polarity and also in defining the evolutionary basis of the origin of the post-transcriptional machinery. Identifying patterns of regulated and co-regulated small RNAs, in particular miRNAs and their sequence variants with the availability of next generation sequencing approaches has widely demonstrated the role of miRNAs and their temporal regulation in maintaining plant development and their response to stress conditions. Although the role of canonical miRNAs has been widely explored and functional diversity is revealed, those works for isomiRs are still limited and urgent to be carried out across plants. This relative lack of information with respect to isomiRs might be attributed to the non-availability of large-scale detection of isomiRs across wide plant species. In the present research, we addressed this by developing Plant isomiR Atlas, which provides large-scale detection of isomiRs across 23 plant species utilizing 677 smallRNAs datasets and reveals a total of 98,374 templated and non-templated isomiRs from 6,167 precursors. Plant isomiR Atlas provides several visualization features such as species specific isomiRs, isomiRs and canonical miRNAs overlap, terminal modification classifications, target identification using psRNATarget and TargetFinder and also canonical miRNAs:target interactions. Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate to understand the functional role of isomiRs. Plant isomiR Atlas is available at www.mcr.org.in/isomir. One Sentence Summary Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate the understanding and diversity of functional targets of plants isomiRs.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang, China
- *Correspondence: Xiaopeng Wen
| | - Suresh B. Mudunuri
- Centre for Bioinformatics Research, SRKR Engineering College, Bhimavaram, India
| | - Gaurav Sablok
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology (OEB) Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Gaurav Sablok
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Koppers-Lalic D, Hackenberg M, de Menezes R, Misovic B, Wachalska M, Geldof A, Zini N, de Reijke T, Wurdinger T, Vis A, van Moorselaar J, Pegtel M, Bijnsdorp I. Non‑invasive prostate cancer detection by measuring miRNA variants ( isomiRs) in urine extracellular vesicles. Oncotarget 2016; 7:22566-78. [PMID: 26992225 DOI: 10.18632/oncotarget.8124] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/24/2016] [Indexed: 12/26/2022] Open
Abstract
In many cancer types, the expression and function of ~22 nucleotide-long microRNAs (miRNA) is deregulated. Mature miRNAs can be stably detected in extracellular vesicles (EVs) in biofluids, therefore they are considered to have great potential as biomarkers. In the present study, we investigated whether miRNAs have a distinct expression pattern in urine-EVs of prostate cancer (PCa) patients compared to control males. By next generation sequencing, we determined the miRNA expression in a discovery cohort of 4 control men and 9 PCa patients. miRNAs were validated by using a stemloop RT-PCR in an independent cohort of 74 patients (26 control and 48 PCa-patients). Whereas standard mapping protocols identified > 10 PCa associated miRNAs in urinary EVs, miR-21, miR-375 and miR-204 failed to robustly discriminate for disease in a validation study with RT-PCR-detection of mature miRNA sequences. In contrast, we observed that miRNA isoforms (isomiRs) with 3' end modifications were highly discriminatory between samples from control men and PCa patients. Highly differentially expressed isomiRs of miR-21, miR-204 and miR-375 were subsequently validated in an independent group of 74 patients. Receiver-operating characteristic analysis was performed to evaluate the diagnostic performance of three isomiRs, resulting in a 72.9% sensitivity with a high (88%) specificity and an area under the curve (AUC) of 0.866. In comparison, prostate specific antigen had an AUC of 0.707 and measuring the mature form of these miRNAs yielded a lower 70.8% sensitivity and 72% specificity (AUC 0.766). We propose that isomiRs may carry discriminatory information which is useful to generate stronger biomarkers.
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Muiwo P, Pandey P, Ahmad HM, Ramachandran SS, Bhattacharya A. IsomiR processing during differentiation of myelogenous leukemic cell line K562 by phorbol ester PMA. Gene 2017; 641:172-179. [PMID: 29051025 DOI: 10.1016/j.gene.2017.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/18/2017] [Accepted: 10/10/2017] [Indexed: 01/28/2023]
Abstract
Chronic myelocytic leukemia cell line K562 undergoes differentiation by phorbol esters to megakaryocytes and we have used this system to understand miRNA processing leading to isomiR generation. PMA treatment significantly altered the production of miRNA in K562 cells. Expression of 24.4% of miRNAs were found to be stimulated whereas expression of 10% miRNAs were inhibited by PMA treatment. Our results suggest that miRNA precursors are processed into isomiRs in a deterministic manner. The relative levels of different isomiRs of a miRNA remained mainly unchanged even after PMA treatment irrespective of overall changes in expression (either up-regulation or down-regulation). However, not all miRNAs behave in the same way, about 7% showed a variation of isomiR profiles after PMA treatment. Most of the later class of miRNAs were found to be oncogenic miRNAs. Further, it was also found that number of isomiRs was independent of abundance of a miRNA. Functional importance of different isomiRs was demonstrated using three different isomiRs of miR-22. Our results showed that different isomiRs could inhibit expression of targets genes with different efficiencies. Our study suggests that the heterogeneity of a miRNA population generated during processing is in general regulated and that variation in the generation of an isomiR can be a functionally important regulatory feature.
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Affiliation(s)
- Pamchui Muiwo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Priyatama Pandey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Hafiz M Ahmad
- Department of Molecular Cell and Cancer Biology, Umass Medical School, Worcester, MA, USA.
| | | | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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33
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Goswami K, Tripathi A, Sanan-Mishra N. Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice. J Integr Bioinform 2017; 14:/j/jib.2017.14.issue-1/jib-2017-0002/jib-2017-0002.xml. [PMID: 28637931 PMCID: PMC6042804 DOI: 10.1515/jib-2017-0002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/16/2017] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage. They also play an important role in regulating plant's response to salt-stress. In this work we adopted the approach of comparative and integrated data-mining to understand the miRNA-mediated regulation of salt-stress in rice. We profiled and compared the miRNA regulations using natural varieties and transgenic lines with contrasting behaviors in response to salt-stress. The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRNAs, their targets and the associated metabolic pathways. The analysis revealed the modulation of many biological pathways, which are involved in salt-tolerance and play an important role in plant phenotype and physiology. The end modifications of the miRNAs were also studied in our analysis and isomiRs having a dynamic role in salt-tolerance mechanism were identified.
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Affiliation(s)
- Kavita Goswami
- Plant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Anita Tripathi
- Plant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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34
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Gutiérrez-Vázquez C, Enright AJ, Rodríguez-Galán A, Pérez-García A, Collier P, Jones MR, Benes V, Mizgerd JP, Mittelbrunn M, Ramiro AR, Sánchez-Madrid F. 3' Uridylation controls mature microRNA turnover during CD4 T-cell activation. RNA 2017; 23:882-891. [PMID: 28351886 PMCID: PMC5435861 DOI: 10.1261/rna.060095.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/23/2017] [Indexed: 05/23/2023]
Abstract
Activation of T lymphocytes requires a tight regulation of microRNA (miRNA) expression. Terminal uridyltransferases (TUTases) catalyze 3' nontemplated nucleotide addition (3'NTA) to miRNAs, which may influence miRNA stability and function. Here, we investigated 3'NTA to mature miRNA in CD4 T lymphocytes by deep sequencing. Upon T-cell activation, miRNA sequences bearing terminal uridines are specifically decreased, concomitantly with down-regulation of TUT4 and TUT7 enzymes. Analyzing TUT4-deficient T lymphocytes, we proved that this terminal uridyltransferase is essential for the maintenance of miRNA uridylation in the steady state of T lymphocytes. Analysis of synthetic uridylated miRNAs shows that 3' addition of uridine promotes degradation of these uridylated miRNAs after T-cell activation. Our data underline post-transcriptional uridylation as a mechanism to fine-tune miRNA levels during T-cell activation.
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Affiliation(s)
- Cristina Gutiérrez-Vázquez
- Instituto de Investigación Sanitaria Princesa, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid 28006, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Anton J Enright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ana Rodríguez-Galán
- Instituto de Investigación Sanitaria Princesa, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid 28006, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Arantxa Pérez-García
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Paul Collier
- European Molecular Biology Laboratory (EMBL), Core Facilities and Services, Heidelberg 69117, Germany
| | - Matthew R Jones
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Core Facilities and Services, Heidelberg 69117, Germany
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - María Mittelbrunn
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Almudena R Ramiro
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Francisco Sánchez-Madrid
- Instituto de Investigación Sanitaria Princesa, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid 28006, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
- CIBER: Centro Investigación en Red Cardiovascular, Madrid 28029, Spain
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35
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Yang K, Sablok G, Qiao G, Nie Q, Wen X. isomiR2Function: An Integrated Workflow for Identifying MicroRNA Variants in Plants. Front Plant Sci 2017; 8:322. [PMID: 28377776 PMCID: PMC5359237 DOI: 10.3389/fpls.2017.00322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 02/22/2017] [Indexed: 05/28/2023]
Abstract
In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking. In the present research, we present isomiR2Function, a standalone easily deployable tool that allows for the robust and high-throughput discovery of templated and non-templated isomiRs. Additionally, isomiR2Function allows for identification of differentially expressed isomiRs and in parallel target prediction based on both transcripts or PARE-Seq either using Targetfinder or Cleaveland. isomiR2Function allows for the functional enrichment of the detected targets using TopGO package. Benchmarking of isomiR2Function revealed highly accurate prediction and classification of isomiRs as compared to the previously developed isomiR prediction tools. Additionally, the downstream implementation of additional features allows isomiR2Function to be classified as a single standalone tool for isomiR profiling from discovery to functional roles. All in all, isomiR2Function allows the streamline processing of the miRNA-seq for the identification and characterization of isomiRs with minimal efforts. isomiR2Function can be accessed through: https://github.com/347033139/isomiR2Function.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Gaurav Sablok
- Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
| | - Guang Qiao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Qiong Nie
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
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36
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Rhodes LV, Martin EC, Segar HC, Miller DFB, Buechlein A, Rusch DB, Nephew KP, Burow ME, Collins-Burow BM. Dual regulation by microRNA-200b-3p and microRNA-200b-5p in the inhibition of epithelial-to-mesenchymal transition in triple-negative breast cancer. Oncotarget 2016; 6:16638-52. [PMID: 26062653 PMCID: PMC4599295 DOI: 10.18632/oncotarget.3184] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/23/2015] [Indexed: 12/31/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) involves loss of an epithelial phenotype and activation of a mesenchymal one. Enhanced expression of genes associated with a mesenchymal transition includes ZEB1/2, TWIST, and FOXC1. miRNAs are known regulators of gene expression and altered miRNA expression is known to enhance EMT in breast cancer. Here we demonstrate that the tumor suppressive miRNA family, miR-200, is not expressed in triple negative breast cancer (TNBC) cell lines and that miR-200b-3p over-expression represses EMT, which is evident through decreased migration and increased CDH1 expression. Despite the loss of migratory capacity following re-expression of miR-200b-3p, no subsequent loss of the conventional miR-200 family targets and EMT markers ZEB1/2 was observed. Next generation RNA-sequencing analysis showed that enhanced expression of pri-miR-200b lead to ectopic expression of both miR-200b-3p and miR-200b-5p with multiple isomiRs expressed for each of these miRNAs. Furthermore, miR-200b-5p was expressed in the receptor positive, epithelial breast cancer cell lines but not in the TNBC (mesenchymal) cell lines. In addition, a compensatory mechanism for miR-200b-3p/200b-5p targeting, where both miRNAs target the RHOGDI pathway leading to non-canonical repression of EMT, was demonstrated. Collectively, these data are the first to demonstrate dual targeting by miR-200b-3p and miR-200b-5p and a previously undescribed role for microRNA processing and strand expression in EMT and TNBC, the most aggressive breast cancer subtype.
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Affiliation(s)
- Lyndsay V Rhodes
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Elizabeth C Martin
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, USA
| | - H Chris Segar
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, USA
| | - David F B Miller
- Medical Sciences and Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Bloomington, IN, USA
| | - Aaron Buechlein
- Indiana University Center for Genomics and Bioinformatics, Bloomington, IN, USA
| | - Douglas B Rusch
- Indiana University Center for Genomics and Bioinformatics, Bloomington, IN, USA
| | - Kenneth P Nephew
- Medical Sciences and Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Bloomington, IN, USA
| | - Matthew E Burow
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, USA.,Department of Pharmacology, Tulane University, New Orleans, LA, USA
| | - Bridgette M Collins-Burow
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, USA
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37
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Ahmed F, Senthil-Kumar M, Lee S, Dai X, Mysore KS, Zhao PX. Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in Arabidopsis thaliana. RNA Biol 2015; 11:1414-29. [PMID: 25629686 PMCID: PMC4615835 DOI: 10.1080/15476286.2014.996474] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from Arabidopsis to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in Arabidopsis. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
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Affiliation(s)
- Firoz Ahmed
- a Plant Biology Division; Samuel Roberts Noble Foundation ; Ardmore , OK USA
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38
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Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. Plant Sci 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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39
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Sablok G, Srivastva AK, Suprasanna P, Baev V, Ralph PJ. isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology. Front Plant Sci 2015; 6:949. [PMID: 26617614 PMCID: PMC4639611 DOI: 10.3389/fpls.2015.00949] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/17/2015] [Indexed: 05/11/2023]
Affiliation(s)
- Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
- *Correspondence: Gaurav Sablok
| | - Ashish K. Srivastva
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreMumbai, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreMumbai, India
| | - Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Peter J. Ralph
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
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40
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Muller H, Marzi MJ, Nicassio F. IsomiRage: From Functional Classification to Differential Expression of miRNA Isoforms. Front Bioeng Biotechnol 2014; 2:38. [PMID: 25325056 PMCID: PMC4179619 DOI: 10.3389/fbioe.2014.00038] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 09/12/2014] [Indexed: 01/29/2023] Open
Abstract
As more small RNA sequencing libraries are becoming available, it clearly emerges that microRNAs (miRNAs) are highly heterogeneous both in length and sequence. In comparison to canonical miRNAs, miRNA isoforms (termed as “isomiRs”) might exhibit different biological properties, such as a different target repertoire, or enhanced/reduced stability. Nonetheless, this layer of information has remained largely unexplored due to the scarcity of small RNA NGS-datasets and the absence of proper analytical tools. Here, we present a workflow for the characterization and analysis of miRNAs and their variants in next-generation sequencing datasets. IsomiRs can originate from an alternative dicing event (“templated” forms) or from the addition of nucleotides through an enzymatic activity or target-dependent mechanisms (“non-templated” forms). Our pipeline allows distinguishing canonical miRNAs from templated and non-templated isomiRs by alignment to a custom database, which comprises all possible 3′-, 5′-, and trimmed variants. Functionally equivalent isomiRs can be grouped together according to the type of modification (e.g., uridylation, adenylation, trimming …) to assess which miRNAs are more intensively modified in a given biological context. When applied to the analysis of primary epithelial breast cancer cells, our methodology provided a 40% increase in the number of detected miRNA species and allowed to easily identify and classify more than 1000 variants. Most modifications were compatible with templated IsomiRs, as a consequence of imprecise Drosha or Dicer cleavage. However, some non-templated variants were consistently found either in the normal or in the cancer cells, with the 3′-end adenylation and uridylation as the most frequent events, suggesting that miRNA post-transcriptional modification frequently occurs. In conclusion, our analytical tool permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms.
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Affiliation(s)
- Heiko Muller
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
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41
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Sablok G, Milev I, Minkov G, Minkov I, Varotto C, Yahubyan G, Baev V. isomiRex: web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets. FEBS Lett 2013; 587:2629-34. [PMID: 23831580 DOI: 10.1016/j.febslet.2013.06.047] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/22/2013] [Accepted: 06/25/2013] [Indexed: 01/04/2023]
Abstract
We present an open-access web platform isomiRex, to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. The open-access web-platform is not restricted only to NGS sequence dataset from animals and potentially analyzes a wider dataset for plants, animals and viral NGS dataset supporting miRBase (version 19 supporting 193 species). The platform can handle the bloated amount of the read counts and reports the annotated microRNAs from plant, animal and viral NGS datasets. isomiRex also provides an estimation of the the isomiRs, of miRNAs with higher copy number relative to their mature reference sequences indexed in miRBase (version 19 supporting 193 species). Visually enhanced graphs potentially display differentially expressed isomiRs, which will help the user to demonstrate and correlate the abundance of the isomiR as a signature event to the specific condition. An additional module for estimating the differential expression has been implemented allowing the users to postulate the differential expression across the user input samples. The developed web-platform can be accessed at http://bioinfo1.uni-plovdiv.bg/isomiRex/.
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Affiliation(s)
- Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E Mach 1, 38010S Michele all'Adige, TN, Italy.
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Colaiacovo M, Bernardo L, Centomani I, Crosatti C, Giusti L, Orrù L, Tacconi G, Lamontanara A, Cattivelli L, Faccioli P. A Survey of MicroRNA Length Variants Contributing to miRNome Complexity in Peach (Prunus Persica L.). Front Plant Sci 2012; 3:165. [PMID: 22855688 PMCID: PMC3405489 DOI: 10.3389/fpls.2012.00165] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 07/04/2012] [Indexed: 05/13/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNA molecules produced from hairpin structures and involved in gene expression regulation with major roles in plant development and stress response. Although each annotated miRNA in miRBase (www.mirbase.org) is a single defined sequence with no further details on possible variable sequence length, isomiRs - namely the population of variants of miRNAs coming from the same precursors - have been identified in several species and could represent a way of broadening the regulatory network of the cell. Next-gen-based sequencing makes it possible to comprehensively and accurately assess the entire miRNA repertoire including isomiRs. The aim of this work was to survey the complexity of the peach miRNome by carrying out Illumina high-throughput sequencing of miRNAs in three replicates of five biological samples arising from a set of different peach organs and/or phenological stages. Three hundred-ninety-two isomiRs (miRNA and miRNA*-related) corresponding to 26 putative miRNA coding loci, have been highlighted by mirDeep-P and analyzed. The presence of the same isomiRs in different biological replicates of a sample and in different tissues demonstrates that the generation of most of the detected isomiRs is not random. The degree of mature sequence heterogeneity is very different for each individual locus. Results obtained in the present work can thus contribute to a deeper view of the miRNome complexity and to better explore the mechanism of action of these tiny regulators.
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Affiliation(s)
| | | | | | | | | | - Luigi Orrù
- CRA Genomics Research Centre, Fiorenzuola d’ArdaItaly
| | | | | | | | - Primetta Faccioli
- CRA Genomics Research Centre, Fiorenzuola d’ArdaItaly
- *Correspondence: Primetta Faccioli, CRA Genomics Research Centre, via S.Protaso 302, I-29017 Fiorenzuola d’Arda (Pc), Italy. e-mail:
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