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Wagner V, Meese E, Keller A. The intricacies of isomiRs: from classification to clinical relevance. Trends Genet 2024; 40:784-796. [PMID: 38862304 DOI: 10.1016/j.tig.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/13/2024]
Abstract
MicroRNAs (miRNAs) and isoforms of their archetype, called isomiRs, regulate gene expression via complementary base-pair binding to messenger RNAs (mRNAs). The partially evolutionarily conserved isomiR sequence variations are differentially expressed among tissues, populations, and genders, and between healthy and diseased states. Aiming towards the clinical use of isomiRs as diagnostic biomarkers and for therapeutic purposes, several challenges need to be addressed, including (i) clarification of isomiR definition, (ii) improved annotation in databases with new standardization (such as the mirGFF3 format), and (iii) improved methods of isomiR detection, functional verification, and in silico analysis. In this review we discuss the respective challenges, and highlight the opportunities for clinical use of isomiRs, especially in the light of increasing amounts of next-generation sequencing (NGS) data.
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Affiliation(s)
- Viktoria Wagner
- Chair for Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, 66123 Saarbrücken, Germany.
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2
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Orbán TI. One locus, several functional RNAs-emerging roles of the mechanisms responsible for the sequence variability of microRNAs. Biol Futur 2023:10.1007/s42977-023-00154-7. [PMID: 36847925 DOI: 10.1007/s42977-023-00154-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023]
Abstract
With the development of modern molecular genetics, the original "one gene-one enzyme" hypothesis has been outdated. For protein coding genes, the discovery of alternative splicing and RNA editing provided the biochemical background for the RNA repertoire of a single locus, which also serves as an important pillar for the enormous protein variability of the genomes. Non-protein coding RNA genes were also revealed to produce several RNA species with distinct functions. The loci of microRNAs (miRNAs), encoding for small endogenous regulatory RNAs, were also found to produce a population of small RNAs, rather than a single defined product. This review aims to present the mechanisms contributing to the astonishing variability of miRNAs revealed by the new sequencing technologies. One important source is the careful balance of arm selection, producing sequentially different 5p- or 3p-miRNAs from the same pre-miRNA, thereby broadening the number of regulated target RNAs and the phenotypic response. In addition, the formation of 5', 3' and polymorphic isomiRs, with variable end and internal sequences also leads to a higher number of targeted sequences, and increases the regulatory output. These miRNA maturation processes, together with other known mechanisms such as RNA editing, further increase the potential outcome of this small RNA pathway. By discussing the subtle mechanisms behind the sequence diversity of miRNAs, this review intends to reveal this engaging aspect of the inherited "RNA world", how it contributes to the almost infinite molecular variability among living organisms, and how this variability can be exploited to treat human diseases.
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Affiliation(s)
- Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar Tudósok Körútja 2, Budapest, 1117, Hungary.
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3
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Nair MM, Kumar SHK, Jyothsna S, Sundaram KT, Manjunatha C, Sivasamy M, Alagu M. Stem and leaf rust-induced miRNAome in bread wheat near-isogenic lines and their comparative analysis. Appl Microbiol Biotechnol 2022; 106:8211-8232. [PMID: 36385566 DOI: 10.1007/s00253-022-12268-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022]
Abstract
Wheat rusts remain a major threat to global wheat production and food security. The R-gene-mediated resistance has been employed as an efficient approach to develop rust-resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel molecular players, including non-coding RNAs for plant response. This study identified microRNAs associated with Sr36 and Lr45 disease resistance genes in response to stem and leaf rust, respectively. Here, small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem and leaf rust pathotypes. microRNA mining in stem rust-inoculated cultivars revealed a total of distinct 26 known and 7 novel miRNAs, and leaf rust libraries culminated with 22 known and 4 novel miRNAs. The comparative analysis between two disease sets provides a better understanding of altered miRNA profiles associated with respective R-genes and infections. Temporal differential expression pattern of miRNAs pinpoints their role during the progress of infection. Differential expression pattern of miRNAs among various treatments as well as time-course expression of miRNAs revealed stem and leaf rust-responsive miRNAs and their possible role in balancing disease resistance/susceptibility. Disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 from different subgenome origins might serve as a potential link between stem and leaf rust defence mechanisms downstream to respective R-genes. The outcome from the analysis of microRNA dynamics among two rust diseases and further characterization of identified microRNAs can contribute to significant novel insights on wheat-rust interactions and rust management. KEY POINTS: • Identification and comparative analysis of stem and leaf rust-responsive miRNAs. • Chromosomal location and functional prediction of miRNAs. • Time-course expression analysis of pathogen-responsive miRNAs.
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Affiliation(s)
- Minu M Nair
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - S Hari Krishna Kumar
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - S Jyothsna
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Krishna T Sundaram
- International Rice Research Institute (IRRI), South Asia Hub, Patancheru, 502324, Telangana, India
| | - C Manjunatha
- ICAR-National Bureau of Agricultural Insect Resources, Bengaluru, 560024, Karnataka, India
| | - M Sivasamy
- ICAR-Indian Agricultural, Research Institute, Regional Station, Wellington, 643231, Tamil Nadu, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671316, Kerala, India.
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Tiwari B, Habermann K, Arif MA, Top O, Frank W. Identification of Small RNAs During High Light Acclimation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:656657. [PMID: 34211484 PMCID: PMC8239388 DOI: 10.3389/fpls.2021.656657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/21/2021] [Indexed: 05/19/2023]
Abstract
The biological significance of non-coding RNAs (ncRNAs) has been firmly established to be important for the regulation of genes involved in stress acclimation. Light plays an important role for the growth of plants providing the energy for photosynthesis; however, excessive light conditions can also cause substantial defects. Small RNAs (sRNAs) are a class of non-coding RNAs that regulate transcript levels of protein-coding genes and mediate epigenetic silencing. Next generation sequencing facilitates the identification of small non-coding RNA classes such as miRNAs (microRNAs) and small-interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), but changes in the ncRNA transcriptome in response to high light are poorly understood. We subjected Arabidopsis plants to high light conditions and performed a temporal in-depth study of the transcriptome data after 3 h, 6 h, and 2 days of high light treatment. We identified a large number of high light responsive miRNAs and sRNAs derived from NAT gene pairs, lncRNAs and TAS transcripts. We performed target predictions for differentially expressed miRNAs and correlated their expression levels through mRNA sequencing data. GO analysis of the targets revealed an overrepresentation of genes involved in transcriptional regulation. In A. thaliana, sRNA-mediated regulation of gene expression in response to high light treatment is mainly carried out by miRNAs and sRNAs derived from NAT gene pairs, and from lncRNAs. This study provides a deeper understanding of sRNA-dependent regulatory networks in high light acclimation.
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Ahmed F. A Network-Based Analysis Reveals the Mechanism Underlying Vitamin D in Suppressing Cytokine Storm and Virus in SARS-CoV-2 Infection. Front Immunol 2020; 11:590459. [PMID: 33362771 PMCID: PMC7756074 DOI: 10.3389/fimmu.2020.590459] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/30/2020] [Indexed: 01/08/2023] Open
Abstract
Background SARS-CoV-2 causes ongoing pandemic coronavirus disease of 2019 (COVID-19), infects the cells of the lower respiratory tract that leads to a cytokine storm in a significant number of patients resulting in severe pneumonia, shortness of breathing, respiratory and organ failure. Extensive studies suggested the role of Vitamin D in suppressing cytokine storm in COVID-19 and reducing viral infection; however, the precise molecular mechanism is not clearly known. In this work, bioinformatics and systems biology approaches were used to understand SARS-CoV-2 induced cytokine pathways and the potential mechanism of Vitamin D in suppressing cytokine storm and enhancing antiviral response. Results This study used transcriptome data and identified 108 differentially expressed host genes (DEHGs) in SARS-CoV-2 infected normal human bronchial epithelial (NHBE) cells compared to control. Then, the DEHGs was integrated with the human protein-protein interaction data to generate a SARS-CoV-2 induced host gene regulatory network (SiHgrn). Analysis of SiHgrn identified a sub-network "Cluster 1" with the highest MCODE score, 31 up-regulated genes, and predominantly associated immune and inflammatory response. Interestingly, the iRegulone tool identified that "Cluster 1" is under the regulation of transcription factors STAT1, STAT2, STAT3, POU2F2, and NFkB1, collectively referred to as "host response signature network". Functional enrichment analysis with NDEx revealed that the "host response signature network" is predominantly associated with critical pathways, including "cytokines and inflammatory response", "non-genomic action of Vitamin D", "the human immune response to tuberculosis", and "lung fibrosis". Finally, in-depth analysis and literature mining revealed that Vitamin D binds with its receptor and could work through two different pathways: (i) it inhibits the expression of pro-inflammatory cytokines through blocking the TNF induced NFkB1 signaling pathway; and (ii) it initiates the expression of interferon-stimulating genes (ISGs) for antiviral defense program through activating the IFN-α induced Jak-STAT signaling pathway. Conclusion This comprehensive study identified the pathways associated with cytokine storm in SARS-CoV-2 infection. The proposed underlying mechanism of Vitamin D could be promising in suppressing the cytokine storm and inducing a robust antiviral response in severe COVID-19 patients. The finding in this study urgently needs further experimental validations for the suitability of Vitamin D in combination with IFN-α to control severe COVID-19.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia.,University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
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6
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Small RNA profiling reveal regulation of microRNAs in field peanut pod rot pathogen infection. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00485-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ahmed F, Senthil-Kumar M, Dai X, Ramu VS, Lee S, Mysore KS, Zhao PX. pssRNAit: A Web Server for Designing Effective and Specific Plant siRNAs with Genome-Wide Off-Target Assessment. PLANT PHYSIOLOGY 2020; 184:65-81. [PMID: 32651189 PMCID: PMC7479913 DOI: 10.1104/pp.20.00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/30/2020] [Indexed: 05/02/2023]
Abstract
We report an advanced web server, the plant-specific small noncoding RNA interference tool pssRNAit, which can be used to design a pool of small interfering RNAs (siRNAs) for highly effective, specific, and nontoxic gene silencing in plants. In developing this tool, we integrated the transcript dataset of plants, several rules governing gene silencing, and a series of computational models of the biological mechanism of the RNA interference (RNAi) pathway. The designed pool of siRNAs can be used to construct a long double-strand RNA and expressed through virus-induced gene silencing (VIGS) or synthetic transacting siRNA vectors for gene silencing. We demonstrated the performance of pssRNAit by designing and expressing the VIGS constructs to silence Phytoene desaturase (PDS) or a ribosomal protein-encoding gene, RPL10 (QM), in Nicotiana benthamiana We analyzed the expression levels of predicted intended-target and off-target genes using reverse transcription quantitative PCR. We further conducted an RNA-sequencing-based transcriptome analysis to assess genome-wide off-target gene silencing triggered by the fragments that were designed by pssRNAit, targeting different homologous regions of the PDS gene. Our analyses confirmed the high accuracy of siRNA constructs designed using pssRNAit The pssRNAit server, freely available at https://plantgrn.noble.org/pssRNAit/, supports the design of highly effective and specific RNAi, VIGS, or synthetic transacting siRNA constructs for high-throughput functional genomics and trait improvement in >160 plant species.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
- University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah 21589, Saudi Arabia
- Noble Research Institute, Ardmore, Oklahoma 73401
| | - Muthappa Senthil-Kumar
- Noble Research Institute, Ardmore, Oklahoma 73401
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Xinbin Dai
- Noble Research Institute, Ardmore, Oklahoma 73401
| | - Vemanna S Ramu
- Noble Research Institute, Ardmore, Oklahoma 73401
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad Haryana 121001, India
| | - Seonghee Lee
- Noble Research Institute, Ardmore, Oklahoma 73401
- Horticultural Science Department, Institute of Food and Agricultural Science, Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida 33598
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Fard EM, Moradi S, Salekdeh NN, Bakhshi B, Ghaffari MR, Zeinalabedini M, Salekdeh GH. Plant isomiRs: origins, biogenesis, and biological functions. Genomics 2020; 112:3382-3395. [DOI: 10.1016/j.ygeno.2020.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
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Alzahrani FA, Ahmed F, Sharma M, Rehan M, Mahfuz M, Baeshen MN, Hawsawi Y, Almatrafi A, Alsagaby SA, Kamal MA, Warsi MK, Choudhry H, Jamal MS. Investigating the pathogenic SNPs in BLM helicase and their biological consequences by computational approach. Sci Rep 2020; 10:12377. [PMID: 32704157 PMCID: PMC7378827 DOI: 10.1038/s41598-020-69033-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
The BLM helicase protein plays a vital role in DNA replication and the maintenance of genomic integrity. Variation in the BLM helicase gene resulted in defects in the DNA repair mechanism and was reported to be associated with Bloom syndrome (BS) and cancer. Despite extensive investigation of helicase proteins in humans, no attempt has previously been made to comprehensively analyse the single nucleotide polymorphism (SNPs) of the BLM gene. In this study, a comprehensive analysis of SNPs on the BLM gene was performed to identify, characterize and validate the pathogenic SNPs using computational approaches. We obtained SNP data from the dbSNP database version 150 and mapped these data to the genomic coordinates of the "NM_000057.3" transcript expressing BLM helicase (P54132). There were 607 SNPs mapped to missense, 29 SNPs mapped to nonsense, and 19 SNPs mapped to 3'-UTR regions. Initially, we used many consensus tools of SIFT, PROVEAN, Condel, and PolyPhen-2, which together increased the accuracy of prediction and identified 18 highly pathogenic non-synonymous SNPs (nsSNPs) out of 607 SNPs. Subsequently, these 18 high-confidence pathogenic nsSNPs were analysed for BLM protein stability, structure-function relationships and disease associations using various bioinformatics tools. These 18 mutants of the BLM protein along with the native protein were further investigated using molecular dynamics simulations to examine the structural consequences of the mutations, which might reveal their malfunction and contribution to disease. In addition, 28 SNPs were predicted as "stop gained" nonsense SNPs and one SNP was predicted as "start lost". Two SNPs in the 3'UTR were found to abolish miRNA binding and thus may enhance the expression of BLM. Interestingly, we found that BLM mRNA overexpression is associated with different types of cancers. Further investigation showed that the dysregulation of BLM is associated with poor overall survival (OS) for lung and gastric cancer patients and hence led to the conclusion that BLM has the potential to be used as an important prognostic marker for the detection of lung and gastric cancer.
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Affiliation(s)
- Faisal A Alzahrani
- Department of Biochemistry, Faculty of Science, Stem Cells Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Aston Medical Research Institute, Aston Medical School, Aston University, Birmingham, B4 7ET, UK
| | - Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia.
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia.
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, India
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Mahfuz
- Department of Computer Science, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Mohammed N Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Yousef Hawsawi
- Department of Genetics, Research Center, King Faisal Specialist Hospital, and Research Center, MBC-03, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Ahmed Almatrafi
- Department of Biology, Faculty of Science, University of Taibah, Medinah, Saudi Arabia
| | - Suliman Abdallah Alsagaby
- Department of Medical Laboratories, Central Biosciences Research Laboratories, College of Science in Al Zulfi, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Mohammad Azhar Kamal
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Mohiuddin Khan Warsi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Sarwar Jamal
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
- Integrative Biosciences Center, Wayne State University, Detroit, MI, 48202, USA.
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Narjala A, Nair A, Tirumalai V, Hari Sundar GV, Shivaprasad PV. A conserved sequence signature is essential for robust plant miRNA biogenesis. Nucleic Acids Res 2020; 48:3103-3118. [PMID: 32025695 PMCID: PMC7102948 DOI: 10.1093/nar/gkaa077] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 12/19/2022] Open
Abstract
Micro (mi)RNAs are 20–22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear. Here, we show that the presence of specific GC-rich sequence signature within miRNA/miRNA* region is required for the precise miRNA biogenesis. The involvement of GC-rich signatures in precise processing and abundance of miRNAs was confirmed through detailed molecular and functional analysis. Consistent with the presence of the miRNA-specific GC signature, target RNAs of miRNAs also possess conserved complementary sequence signatures in their miRNA binding motifs. The selection of these GC signatures was dependent on an RNA binding protein partner of DCL1 named HYL1. Finally, we demonstrate a direct application of this discovery for enhancing the abundance and efficiency of artificial miRNAs that are popular in plant functional genomic studies.
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Affiliation(s)
- Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur 613401, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur 613401, India
| | - Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India.,SASTRA University, Thirumalaisamudram, Thanjavur 613401, India
| | - G Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
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11
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Leclercq J, Wu S, Farinas B, Pointet S, Favreau B, Vignes H, Kuswanhadi K, Ortega-Abboud E, Dufayard JF, Gao S, Droc G, Hu S, Tang C, Montoro P. Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis. PeerJ 2020; 8:e8932. [PMID: 32391199 PMCID: PMC7195832 DOI: 10.7717/peerj.8932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/17/2020] [Indexed: 11/20/2022] Open
Abstract
Background Small RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in Hevea. Methods Genes producing microRNAs (MIR genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different Hevea tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20–22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators. Results Compared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the Argonaute and Dicer-like gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers.
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Affiliation(s)
- Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shuangyang Wu
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Benoît Farinas
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Pointet
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bénédicte Favreau
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Hélène Vignes
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Enrique Ortega-Abboud
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-François Dufayard
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shenghan Gao
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Songnian Hu
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chaorong Tang
- Hainan University, College of Tropical Crops, Haikou, China
| | - Pascal Montoro
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Balyan S, Joseph SV, Jain R, Mutum RD, Raghuvanshi S. Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice. Funct Integr Genomics 2020; 20:509-522. [DOI: 10.1007/s10142-020-00731-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/04/2019] [Accepted: 01/02/2020] [Indexed: 11/28/2022]
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Zhou H, Li C, Qiu X, Lu S. Systematic Analysis of Alkaline/Neutral Invertase Genes Reveals the Involvement of Smi-miR399 in Regulation of SmNINV3 and SmNINV4 in Salvia miltiorrhiza. PLANTS 2019; 8:plants8110490. [PMID: 31717988 PMCID: PMC6918228 DOI: 10.3390/plants8110490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 01/25/2023]
Abstract
Alkaline/neutral invertases (NINVs), which irreversibly catalyze the hydrolysis of sucrose into fructose and glucose, play crucial roles in carbohydrate metabolism and plant development. Comprehensive insights into NINV genes are lacking in Salvia miltiorrhiza, a well-known traditional Chinese medicinal (TCM) plant with significant medicinal and economic value. Through genome-wide prediction, nine putative SmNINV genes, termed SmNINV1-SmNINV9, were identified. Integrated analysis of gene structures, sequence features, conserved domains, conserved motifs and phylogenetic trees revealed the conservation and divergence of SmNINVs. The identified SmNINVs were differentially expressed in roots, stems, leaves, flowers, and different root tissues. They also responded to drought, salicylic acid, yeast extract, and methyl jasmonate treatments. More importantly, computational prediction and experimental validation showed that SmNINV3 and SmNINV4 were targets of Smi-miR399, a conserved miRNA previously shown to affect Pi uptake and translocation through the cleavage of PHOSPHATE2 (PHO2). Consistently, analysis of 43 NINV genes and 26 miR399 sequences from Arabidopsis thaliana, Populus trichocarpa, Manihot esculenta, and Solanum lycopersicum showed that various AtNINV, PtNINV, MeNINV, and SlNINV genes were regulated by miR399. It indicates that the miR399-NINV module exists widely in plants. Furthermore, Smi-miR399 also cleaved SmPHO2 transcripts in S. miltiorrhiza, suggesting the complexity of NINVs, PHO2, and miR399 networks.
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Affiliation(s)
| | | | | | - Shanfa Lu
- Correspondence: ; Tel./Fax: +86-10-57833366
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14
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Ahmed F. Integrated Network Analysis Reveals FOXM1 and MYBL2 as Key Regulators of Cell Proliferation in Non-small Cell Lung Cancer. Front Oncol 2019; 9:1011. [PMID: 31681566 PMCID: PMC6804573 DOI: 10.3389/fonc.2019.01011] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Loss of control on cell division is an important factor for the development of non-small cell lung cancer (NSCLC), however, its molecular mechanism and gene regulatory network are not clearly understood. This study utilized the systems bioinformatics approach to reveal the “driver-network” involve in tumorigenic processes in NSCLC. Methods: A meta-analysis of gene expression data of NSCLC was integrated with protein-protein interaction (PPI) data to construct an NSCLC network. MCODE and iRegulone were used to identify the local clusters and its upstream transcription regulators involve in NSCLC. Pair-wise gene expression correlation was performed using GEPIA. The survival analysis was performed by the Kaplan-Meier plot. Results: This study identified a local “driver-network” with highest MCODE score having 26 up-regulated genes involved in the process of cell proliferation in NSCLC. Interestingly, the “driver-network” is under the regulation of TFs FOXM1 and MYBL2 as well as miRNAs. Furthermore, the overexpression of member genes in “driver-network” and the TFs are associated with poor overall survival (OS) in NSCLC patients. Conclusion: This study identified a local “driver-network” and its upstream regulators responsible for the cell proliferation in NSCLC, which could be promising biomarkers and therapeutic targets for NSCLC treatment.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, University of Jeddah, Jeddah, Saudi Arabia.,University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
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15
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Yang M, Lu H, Xue F, Ma L. Identifying High Confidence microRNAs in the Developing Seeds of Jatropha curcas. Sci Rep 2019; 9:4510. [PMID: 30872797 PMCID: PMC6418140 DOI: 10.1038/s41598-019-41189-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/01/2019] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenously short noncoding regulatory RNAs implicated in plant development and physiology. Nine small RNA (sRNA) libraries from three typical seed developmental stages (young, intermediate, and mature) were generated by deep sequencing to identify the miRNAs of J. curcas, a potential oilseed crop for the production of renewable oil. Strict criteria were adopted to identify 93 high confidence miRNAs including 48 conserved miRNAs and 45 novel miRNAs. Target genes of these miRNAs were involved in a broad range of physiological functions, including gene expression regulation, primary & secondary metabolism, growth & development, signal transduction, and stress response. About one third (29 out of 93) miRNAs showed significant changes in expression levels during the seed developmental process, indicating that the miRNAs might regulate its targets by their changes of transcription levels in seed development. However, most miRNAs were found differentially expressed in the late stage of seed development, suggesting that miRNAs play more important roles in the stage when seed accumulating organic matters and suffering dehydration stress. This study presents the first large scale identification of high confidence miRNAs in the developing seeds of J. curcas.
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Affiliation(s)
- Mingfeng Yang
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Heshu Lu
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Feiyan Xue
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China
| | - Lanqing Ma
- Key Laboratory of Urban Agriculture (North China) Ministry of Agriculture, Beijing University of Agriculture, Beijing, 102206, China.
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16
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Dhanoa JK, Verma R, Sethi RS, Arora JS, Mukhopadhyay CS. Biogenesis and biological implications of isomiRs in mammals- a review. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41544-018-0003-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Yang K, Wen X, Mudunuri S, Varma GPS, Sablok G. Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants. Sci Rep 2019; 9:1406. [PMID: 30723229 PMCID: PMC6363768 DOI: 10.1038/s41598-019-38932-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/11/2022] Open
Abstract
Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.
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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, 550025, Guizhou Province, P. R. 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, 550025, Guizhou Province, P. R. China.
| | - Suresh Mudunuri
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - G P Saradhi Varma
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - Gaurav Sablok
- Finnish Museum of Natural History, Helsinki, Finland. .,Organismal and Evolutionary Biology (OEB) Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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18
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Tripathi AM, Singh A, Singh R, Verma AK, Roy S. Modulation of miRNA expression in natural populations of A. thaliana along a wide altitudinal gradient of Indian Himalayas. Sci Rep 2019; 9:441. [PMID: 30679759 PMCID: PMC6345966 DOI: 10.1038/s41598-018-37465-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/26/2018] [Indexed: 01/07/2023] Open
Abstract
Plant populations growing along an altitudinal gradient are exposed to different environmental conditions. They are excellent resources to study regulatory mechanisms adopted by plants to respond to different environmental stresses. Regulation by miRNA is one of such strategies. Here, we report how different miRNAs are preferentially expressed in the three natural populations of A. thaliana originating from a wide altitudinal range. The expression level of miRNAs was mostly governed by temperature and radiation. Majority of the identified miRNAs expressed commonly in the three populations. However, 30 miRNAs expressed significantly at different level between the low and the high altitude populations. Most of these miRNAs regulate the genes associated with different developmental processes, abiotic stresses including UV, cold, secondary metabolites, etc. Further, the expression of miR397 and miR858 involved in lignin biosynthesis and regulation of secondary metabolites respectively, may be regulated by light intensity. A few miRNAs expressed at increasing level with the increase in the altitude of the site indicating environment driven tight regulation of these miRNAs. Further, several novel miRNAs and isomiR diversity specific to the Himalayas are reported which might have an adaptive advantage. To the best of our knowledge, this is the first report on miRNA expression from natural plant populations.
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Affiliation(s)
- Abhinandan Mani Tripathi
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, India
| | - Akanksha Singh
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, India
| | - Rajneesh Singh
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh, India
| | - Ashwani Kumar Verma
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh, India
| | - Sribash Roy
- Division of Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh, India. .,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, India.
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19
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Abstract
microRNA molecules have been shown to play various significant roles in many physiological and pathophysiological processes in living organisms. The tremendous interest in these molecules has led to the significant development and constant release of a number of computational tools useful for basic as well as advanced miRNA-related analyses. These approaches have various constantly evolving utilities, such as detection, target prediction, functional annotation, and many others. In this chapter, we provide an overview of several computational tools useful for broadly defined plant miRNA analysis.
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Affiliation(s)
- Anna Lukasik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
- Department of Plant Molecular Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Warsaw, Poland.
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20
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Pinhal D, Bovolenta LA, Moxon S, Oliveira AC, Nachtigall PG, Acencio ML, Patton JG, Hilsdorf AWS, Lemke N, Martins C. Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development. Sci Rep 2018; 8:8248. [PMID: 29844338 PMCID: PMC5974277 DOI: 10.1038/s41598-018-26607-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs.
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Affiliation(s)
- Danillo Pinhal
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Luiz A Bovolenta
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, United Kingdom
| | - Arthur C Oliveira
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Pedro G Nachtigall
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcio L Acencio
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - James G Patton
- Stevenson Center, Vanderbilt University, Nashville, TN, USA
| | | | - Ney Lemke
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
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21
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Identification of the miRNAome of early mesoderm progenitor cells and cardiomyocytes derived from human pluripotent stem cells. Sci Rep 2018; 8:8072. [PMID: 29795287 PMCID: PMC5966391 DOI: 10.1038/s41598-018-26156-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/01/2018] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are small non-coding RNAs involved in post-transcriptional regulation of gene expression related to many cellular functions. We performed a small-RNAseq analysis of cardiac differentiation from pluripotent stem cells. Our analyses identified some new aspects about microRNA expression in this differentiation process. First, we described a dynamic expression profile of microRNAs where some of them are clustered according to their expression level. Second, we described the extensive network of isomiRs and ADAR modifications. Third, we identified the microRNAs families and clusters involved in the establishment of cardiac lineage and define the mirRNAome based on these groups. Finally, we were able to determine a more accurate miRNAome associated with cardiomyocytes by comparing the expressed microRNAs with other mature cells. MicroRNAs exert their effect in a complex and interconnected way, making necessary a global analysis to better understand their role. Our data expands the knowledge of microRNAs and their implications in cardiomyogenesis.
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22
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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 SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 268:18-29. [PMID: 29362080 DOI: 10.1016/j.plantsci.2017.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [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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23
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High-throughput sequencing analysis revealed the regulation patterns of small RNAs on the development of A. comosus var. bracteatus leaves. Sci Rep 2018; 8:1947. [PMID: 29386560 PMCID: PMC5792487 DOI: 10.1038/s41598-018-20261-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 01/16/2018] [Indexed: 12/15/2022] Open
Abstract
Studies of the molecular mechanisms involved in the formation of the albino leaf cells are important for understanding the development of chimera leaves in Ananas comosus var. bracteatus. In this study, we identified a total of 163 novel miRNAs involved in the development of complete white (CWh) and complete green (CGr) leaves using high-throughput sequencing method. The potential miRNA target genes were predicted and annotated using the NR, Swiss-Prot, GO, COG, KEGG, KOG and Pfam databases. The main biological processes regulated by miRNAs were revealed. The miRNAs which potentially play important roles in the development of the leaves and the albino of the CWh leaf cells were selected and their expression patterns were analyzed. The expression levels of nine miRNAs and their potential target genes were studied using qRT-PCR. These results will help to elucidate the functional and regulatory roles of miRNAs in the formation of the albino cells and the development of the leaves of A. comosus var. bracteatus. These data may also be helpful as a resource for studies of small RNA in other leaf color chimeric plant species.
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24
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Lang PLM, Christie MD, Dogan ES, Schwab R, Hagmann J, van de Weyer AL, Scacchi E, Weigel D. A Role for the F-Box Protein HAWAIIAN SKIRT in Plant microRNA Function. PLANT PHYSIOLOGY 2018; 176:730-741. [PMID: 29114080 PMCID: PMC5761791 DOI: 10.1104/pp.17.01313] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/06/2017] [Indexed: 05/02/2023]
Abstract
As regulators of gene expression in multicellular organisms, microRNAs (miRNAs) are crucial for growth and development. Although a plethora of factors involved in their biogenesis and action in Arabidopsis (Arabidopsis thaliana) has been described, these processes and their fine-tuning are not fully understood. Here, we used plants expressing an artificial miRNA target mimic (MIM) to screen for negative regulators of miR156. We identified a new mutant allele of the F-box gene HAWAIIAN SKIRT (HWS; At3G61590), hws-5, as a suppressor of the MIM156-induced developmental and molecular phenotypes. In hws plants, levels of some endogenous miRNAs are increased and their mRNA targets decreased. Plants constitutively expressing full-length HWS-but not a truncated version lacking the F-box domain-display morphological and molecular phenotypes resembling those of mutants defective in miRNA biogenesis and activity. In combination with such mutants, hws loses its delayed floral organ abscission ("skirt") phenotype, suggesting epistasis. Also, the hws transcriptome profile partially resembles those of well-known miRNA mutants hyl1-2, se-3, and ago1-27, pointing to a role in a common pathway. We thus propose HWS as a novel, F-box dependent factor involved in miRNA function.
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Affiliation(s)
| | | | - Ezgi S Dogan
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Rebecca Schwab
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jörg Hagmann
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Emanuele Scacchi
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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25
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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. FRONTIERS IN PLANT SCIENCE 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] [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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26
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Yu F, Pillman KA, Neilsen CT, Toubia J, Lawrence DM, Tsykin A, Gantier MP, Callen DF, Goodall GJ, Bracken CP. Naturally existing isoforms of miR-222 have distinct functions. Nucleic Acids Res 2017; 45:11371-11385. [PMID: 28981911 PMCID: PMC5737821 DOI: 10.1093/nar/gkx788] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/31/2017] [Indexed: 12/14/2022] Open
Abstract
Deep-sequencing reveals extensive variation in the sequence of endogenously expressed microRNAs (termed ‘isomiRs’) in human cell lines and tissues, especially in relation to the 3′ end. From the immunoprecipitation of the microRNA-binding protein Argonaute and the sequencing of associated small RNAs, we observe extensive 3′-isomiR variation, including for miR-222 where the majority of endogenously expressed miR-222 is extended by 1–5 nt compared to the canonical sequence. We demonstrate this 3′ heterogeneity has dramatic implications for the phenotype of miR-222 transfected cells, with longer isoforms promoting apoptosis in a size (but not 3′ sequence)-dependent manner. The transfection of longer miR-222 isomiRs did not induce an interferon response, but did downregulate the expression of many components of the pro-survival PI3K-AKT pathway including PIK3R3, a regulatory subunit whose knockdown phenocopied the expression of longer 222 isoforms in terms of apoptosis and the inhibition of other PI3K-AKT genes. As this work demonstrates the capacity for 3′ isomiRs to mediate differential functions, we contend more attention needs to be given to 3′ variance given the prevalence of this class of isomiR.
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Affiliation(s)
- Feng Yu
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - Corine T Neilsen
- School of Health, Medical and Applied Sciences, Central Queensland University, Queensland 4000, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - David M Lawrence
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - Anna Tsykin
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - David F Callen
- School of Medicine, Discipline of Medicine, University of Adelaide, SA 5000, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA 5000, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA 5000, Australia
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27
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Androvic P, Valihrach L, Elling J, Sjoback R, Kubista M. Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification. Nucleic Acids Res 2017; 45:e144. [PMID: 28911110 PMCID: PMC5587787 DOI: 10.1093/nar/gkx588] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/28/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on two-step RT-qPCR with SYBR-green detection chemistry called Two-tailed RT-qPCR. It takes advantage of novel, target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of seven logs and a sensitivity sufficient to detect down to ten target miRNA molecules. It is capable to capture the full isomiR repertoire, leading to accurate representation of the complete miRNA content in a sample. The reverse transcription step can be multiplexed and the miRNA profiles measured with Two-tailed RT-qPCR show excellent correlation with the industry standard TaqMan miRNA assays (r2 = 0.985). Moreover, Two-tailed RT-qPCR allows for rapid testing with a total analysis time of less than 2.5 hours.
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Affiliation(s)
- Peter Androvic
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic.,Laboratory of Growth Regulators, Faculty of Science, Palacky University, Olomouc 783 71, Czech Republic
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic
| | | | | | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, Biocev, Vestec 252 50, Czech Republic.,TATAA Biocenter AB, Gothenburg 411 03, Sweden
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28
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Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver. Sci Rep 2017; 7:6396. [PMID: 28743867 PMCID: PMC5527063 DOI: 10.1038/s41598-017-06634-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 06/14/2017] [Indexed: 12/22/2022] Open
Abstract
RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform. As a result, we identified 665 genes, 57 miRNAs and 33 lncRNAs that displayed differential expression patterns across periods. Subsequently, a total of 41ceRNA pairs (lncRNA-mRNA) sharing 11 miRNAs were constructed including 30 differentially expressed genes. Importantly, 12 among them were presented in our large metabolic networks, and predicted to influence the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, thus, these genes were considered as the most promising candidates for milk fat formation. To our knowledge, this is first investigation to profile the ceRNA regulatory networks of liver transcriptome that could affect milk fat synthesis in bovine, providing a new view of the regulatory mechanism of RNAs.
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29
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Li J, Xu C, Liang H, Cong W, Wang Y, Luan K, Liu Y. RGRNA: prediction of RNA secondary structure based on replacement and growth of stems. Comput Methods Biomech Biomed Engin 2017; 20:1261-1272. [DOI: 10.1080/10255842.2017.1340460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jin Li
- College of Automation, Harbin Engineering University, Harbin, China
| | - Chengzhen Xu
- College of Automation, Harbin Engineering University, Harbin, China
| | - Hong Liang
- College of Automation, Harbin Engineering University, Harbin, China
| | - Wang Cong
- College of Automation, Harbin Engineering University, Harbin, China
| | - Ying Wang
- College of Automation, Harbin Engineering University, Harbin, China
| | - Kuan Luan
- College of Automation, Harbin Engineering University, Harbin, China
| | - Yunlong Liu
- College of Automation, Harbin Engineering University, Harbin, China
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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30
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Su Y, Zhang Y, Huang N, Liu F, Su W, Xu L, Ahmad W, Wu Q, Guo J, Que Y. Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection. BMC Genomics 2017; 18:325. [PMID: 28438123 PMCID: PMC5404671 DOI: 10.1186/s12864-017-3716-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 04/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing. RESULTS The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common. Expression of differential miRNAs under S. scitamineum challenge was mostly downregulated, with similar trends in the two varieties. Gene ontology (GO) analysis showed that the target gene classification of known miRNAs was similar to that of the newly identified miRNAs. These were mainly associated with cellular processes and metabolic processes in the biological process category, as well as combination and catalytic activity in the molecular function category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these predicted target genes involved in a series of physiological and biochemical pathways or disease resistance-related physiological metabolism and signal transduction pathways, suggesting that the molecular interaction mechanism between sugarcane and S. scitamineum was a complex network system. These findings also showed certain predicted target genes of miR5671, miR5054, miR5783, miR5221, and miR6478 play roles in the mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, and plant-pathogen interaction. Quantitative real-time PCR (qRT-PCR) analysis showed that majority of the known miRNAs and its predicted target genes followed a negatively regulated mode. Seven out of eight predicted target genes showed identical expression after 12 h treatment and reached the highest degree of matching at 48 h, indicating that the regulatory role of miRNAs on the target genes in sugarcane was maximized at 48 h after S. scitamineum challenge. CONCLUSIONS Taken together, our findings serve as evidence for the association of miRNA expression with the molecular mechanism underlying the pathogenesis of sugarcane smut, particularly on the significance of miRNA levels in relation to the cultivation of smut-resistant sugarcane varieties.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuye Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Waqar Ahmad
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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31
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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. FRONTIERS IN PLANT SCIENCE 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] [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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