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Zhang J, Shi J, Yuan C, Liu X, Du G, Fan R, Zhang B. MicroRNA Expression Profile Analysis of Chlamydomonas reinhardtii during Lipid Accumulation Process under Nitrogen Deprivation Stresses. Bioengineering (Basel) 2021; 9:bioengineering9010006. [PMID: 35049715 PMCID: PMC8773410 DOI: 10.3390/bioengineering9010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
Lipid accumulation in various microalgae has been found induced by nitrogen deprivation, and it controls many different genes expression. Yet, the underlying molecular mechanisms still remain largely unknown. MicroRNA (miRNAs) play a critical role in post-transcriptional gene regulation. In this study, miRNAs were hypothesized involved in lipid accumulation by nitrogen deprivation. A deep-sequencing platform was used to explore miRNAs-mediated responses induced by nitrogen deprivation in Chlamydomonas reinhardtii. The eukaryotic orthologous groups of proteins (KOG) function in the predicted target genes of miRNA with response to nitrogen deprivation were mainly involved in signal transduction mechanisms, including transcription, lipid transport, and metabolism. A total of 109 miRNA were predicted, including 79 known miRNA and 30 novel miRNA. A total of 29 miRNAs showed significantly differential expressions after nitrogen deprivation, and most of them were upregulated. A total of 10 miRNAs and their targeting genes might involve in lipid transport and metabolism biological process. This study first investigates nitrogen deprivation-regulated miRNAs in microalgae and broadens perspectives on miRNAs importance in microalgae lipid accumulation via nitrogen deprivation. This study provides theoretical guidance for the application of microalgae in bio-oil engineering production.
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Affiliation(s)
- Jingxian Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chenyang Yuan
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiangcen Liu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guilin Du
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ruimei Fan
- Sino-UK Joint Laboratory for Brain Function and Injury and Department of Physiology and Neurobiology, Xinxiang Medical University, Xinxiang 453003, China
- Correspondence: (R.F.); (B.Z.)
| | - Baoguo Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai 201210, China; (J.Z.); (J.S.); (C.Y.); (X.L.); (G.D.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (R.F.); (B.Z.)
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Li F, Mei L, Zhan C, Mao Q, Yao M, Wang S, Tang L, Chen F. Liquid Hybridization and Solid Phase Detection: A Highly Sensitive and Accurate Strategy for MicroRNA Detection in Plants and Animals. Int J Mol Sci 2016; 17:E1457. [PMID: 27598139 PMCID: PMC5037736 DOI: 10.3390/ijms17091457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/31/2016] [Accepted: 08/22/2016] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in nearly every aspect of biology, including physiological, biochemical, developmental and pathological processes. Therefore, a highly sensitive and accurate method of detection of miRNAs has great potential in research on theory and application, such as the clinical approach to medicine, animal and plant production, as well as stress response. Here, we report a strategic method to detect miRNAs from multicellular organisms, which mainly includes liquid hybridization and solid phase detection (LHSPD); it has been verified in various species and is much more sensitive than traditional biotin-labeled Northern blots. By using this strategy and chemiluminescent detection with digoxigenin (DIG)-labeled or biotin-labeled oligonucleotide probes, as low as 0.01-0.25 fmol [for DIG-CDP Star (disodium2-chloro-5-(4-methoxyspiro{1,2-dioxetane-3,2'-(5'-chloro)tricyclo[3.3.1.13,7]decan}-4-yl)phenyl phosphate) system], 0.005-0.1 fmol (for biotin-CDP Star system), or 0.05-0.5 fmol (for biotin-luminol system) of miRNA can be detected and one-base difference can be distinguished between miRNA sequences. Moreover, LHSPD performed very well in the quantitative analysis of miRNAs, and the whole process can be completed within about 9 h. The strategy of LHSPD provides an effective solution for rapid, accurate, and sensitive detection and quantitative analysis of miRNAs in plants and animals.
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Affiliation(s)
- Fosheng Li
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Lanju Mei
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Cheng Zhan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Qiang Mao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
- Chengdu Botanical Garden, Chengdu 610083, Sichuan, China.
| | - Min Yao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Shenghua Wang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Lin Tang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
| | - Fang Chen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610000, Sichuan, China.
- National and Local Joint Engineering Laboratory for Energy Plant Bio-Oil Production and Application, Chengdu 610000, Sichuan, China.
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Abstract
Large numbers of diverse small non-coding RNAs have been discovered and characterized in eukaryotic RNA interference pathways. These small RNAs have distinctive characteristics and are associated with Argonaute family proteins to regulate gene expression and genomes at various levels. These small RNAs include the Dicer-dependent group such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the Dicer-independent group such as Piwi-interacting RNAs (piRNAs). This review summarizes the various classes of eukaryotic small RNAs and the general knowledge of their characteristics, biogenesis, and functions, with emphasis on some of the recently identified small RNAs.
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Affiliation(s)
- Liande Li
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Wang X, Tong Y, Wang S. Rapid and accurate detection of plant miRNAs by liquid northern hybridization. Int J Mol Sci 2010; 11:3138-48. [PMID: 20957084 PMCID: PMC2956085 DOI: 10.3390/ijms11093138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 08/30/2010] [Accepted: 08/30/2010] [Indexed: 01/01/2023] Open
Abstract
Northern blot analysis is a powerful research tool for discovery, validation and expression of genes, and is currently widely used to detect microRNA (miRNA) accumulation. However, the traditional Northern blot procedure, which is based on a support membrane, is overly elaborate and time-consuming, although it is unsurpassed in accuracy for determining the sizes and amounts of multiple small RNAs sharing high sequence identity. Here we present an alternative method derived from plant miRNAs, liquid Northern hybridization, using fluorescently labeled oligonucleotide probes and characterized by simple and specific miRNA determination and quantitation. The entire detection process is completed within a few hours, and multiple miRNAs can be simultaneously detected in a single experiment.
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Affiliation(s)
- Xiaosu Wang
- Lab of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China; E-Mails: (X.W.); (Y.T.)
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Xie ZH. [Natural antisense transcript and its mechanism of gene regulation]. YI CHUAN = HEREDITAS 2010; 32:122-128. [PMID: 20176555 DOI: 10.3724/sp.j.1005.2010.00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level through a variety of biological mechanisms, such as transcription interference, RNA masking, dsRNA-dependent mechanisms, and chromatin remodelling (modification). We speculated that both of sense and antisense transcripts may be sliced to form small RNAs, which is also an important mechanism for NATs to regulate gene expression, such as rasiRNAs in "ping-pong". Experimental and computational analyses have demonstrated the wide-spread occurrence of NATs in a wide range of species. Here, we reviewed the current understanding of NATs function and its mechanistic basis. We hypothesized that the regulation of antisense transcription and small RNAs were derived from NATs.
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Affiliation(s)
- Zhao-Hui Xie
- Department of Biology, Dezhou University, Dezhou 253023, China.
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Lelandais-Brière C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M. Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. THE PLANT CELL 2009; 21:2780-96. [PMID: 19767456 PMCID: PMC2768930 DOI: 10.1105/tpc.109.068130] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 07/09/2009] [Accepted: 07/26/2009] [Indexed: 05/18/2023]
Abstract
Posttranscriptional regulation of a variety of mRNAs by small 21- to 24-nucleotide RNAs, notably the microRNAs (miRNAs), is emerging as a novel developmental mechanism. In legumes like the model Medicago truncatula, roots are able to develop a de novo meristem through the symbiotic interaction with nitrogen-fixing rhizobia. We used deep sequencing of small RNAs from root apexes and nodules of M. truncatula to identify 100 novel candidate miRNAs encoded by 265 hairpin precursors. New atypical precursor classes producing only specific 21- and 24-nucleotide small RNAs were found. Statistical analysis on sequencing reads abundance revealed specific miRNA isoforms in a same family showing contrasting expression patterns between nodules and root apexes. The differentially expressed conserved and nonconserved miRNAs may target a large variety of mRNAs. In root nodules, which show diverse cell types ranging from a persistent meristem to a fully differentiated central region, we discovered miRNAs spatially enriched in nodule meristematic tissues, vascular bundles, and bacterial infection zones using in situ hybridization. Spatial regulation of miRNAs may determine specialization of regulatory RNA networks in plant differentiation processes, such as root nodule formation.
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Affiliation(s)
- Christine Lelandais-Brière
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Loreto Naya
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
| | - Erika Sallet
- Laboratoire des Interactions Plantes Micro-organismes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique–Institut National de la Recherche Agronomique 2594/441, F- 31320 Castanet Tolosan, France
- Plateforme Bioinformatique du Génopole Toulouse Midi-Pyrénées, Groupement d'Intérêt Scientifique Toulouse Genopole, F-31320 Castanet Tolosan, France
| | - Fanny Calenge
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Florian Frugier
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
| | - Caroline Hartmann
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Jérome Gouzy
- Laboratoire des Interactions Plantes Micro-organismes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique–Institut National de la Recherche Agronomique 2594/441, F- 31320 Castanet Tolosan, France
| | - Martin Crespi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
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Nandi A, Vaz C, Bhattacharya A, Ramaswamy R. miRNA-regulated dynamics in circadian oscillator models. BMC SYSTEMS BIOLOGY 2009; 3:45. [PMID: 19413912 PMCID: PMC2685780 DOI: 10.1186/1752-0509-3-45] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 05/05/2009] [Indexed: 11/12/2022]
Abstract
Background We have studied the dynamics of miRNA regulation in two models of circadian oscillators. miRNAs are a class of small RNA molecules (18–24 nucleotides) that are known to regulate gene expression at the post-transcriptional level by reducing the amount of proteins produced by translation. This is done either by blocking translation or by degradation of mRNAs, the latter being mainly due to the initiation of a set of processes induced by formation of the miRNA:mRNA complex. Although miRNAs are known to regulate a large number of fundamental biological processes such as growth and development, their role in the dynamics of regulation is not completely understood. In exceptional cases, in particular, they can also up-regulate gene expression. Results We have studied simple biological systems wherein oscillations originate from negative auto regulation of gene expression. The regulation of gene expression by miRNAs is introduced into these models and the dynamics is studied via standard stochastic simulation techniques. We find that in addition to a reduction in the amplitude of the oscillation, inclusion of miRNAs in the models has the effect of altering the frequency of oscillation and thereby regulating the dynamics of protein production. Conclusion miRNAs can have a profound effect on the dynamics of regulatory modules, both by control of amplitude, namely by affecting the level of gene expression, as well as by control or alteration of frequency, namely by interference with the temporal sequence of gene production or delivery. We believe that our results are valid for a variety of regulatory systems, beyond the exemplars discussed here.
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Affiliation(s)
- Amitabha Nandi
- Center for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Delhi 110067, India.
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Siomi H. Transposable elements, RNA silencing, and their impacts on the genome throughout evolution. Uirusu 2008; 58:55-60. [PMID: 19122389 DOI: 10.2222/jsv.58.55] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
It is remarkable to consider that more than 40% of the human genome is comprised of transposable elements (TEs) and their relics. TEs were long thought of as either 'selfish' or 'parasitic' DNA elements that were there not for the sake of the host organism, but for their own sake in an evolutionary sense; thus they were considered to be either neutral or deleterious to their hosts. However, it is becoming increasingly clear that there are more complex interactions between TEs and their hosts than strict parasitism; these elements produce changes that have a broad range of fitness values at an organismal level. Recent evidence indicates that these elements confer a fitness benefit to the host more frequently than previously recognized. RNA silencing is thought to have evolved as a form of nucleic-acid-based, and thus sequence-directed, immunity to block the action of viruses and TEs. Host-parasite interactions are typically associated with rapid evolution because of a permanent antagonistic relationship resembling an "arms race" in which parasite adaptations are countered by host adaptations. Complex interactions between TEs and RNA silencing machineries have been co-opted to regulate cellular genes.
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Affiliation(s)
- Haruhiko Siomi
- Department of Molecular Biology Keio University School of Medicine, Tokyo, Japan.
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Murphy D, Dancis B, Brown JR. The evolution of core proteins involved in microRNA biogenesis. BMC Evol Biol 2008; 8:92. [PMID: 18366743 PMCID: PMC2287173 DOI: 10.1186/1471-2148-8-92] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 03/25/2008] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are a recently discovered class of non-coding RNAs (ncRNAs) which play important roles in eukaryotic gene regulation. miRNA biogenesis and activation is a complex process involving multiple protein catalysts and involves the large macromolecular RNAi Silencing Complex or RISC. While phylogenetic analyses of miRNA genes have been previously published, the evolution of miRNA biogenesis itself has been little studied. In order to better understand the origin of miRNA processing in animals and plants, we determined the phyletic occurrences and evolutionary relationships of four major miRNA pathway protein components; Dicer, Argonaute, RISC RNA-binding proteins, and Exportin-5. RESULTS Phylogenetic analyses show that all four miRNA pathway proteins were derived from large multiple protein families. As an example, vertebrate and invertebrate Argonaute (Ago) proteins diverged from a larger family of PIWI/Argonaute proteins found throughout eukaryotes. Further gene duplications among vertebrates after the evolution of chordates from urochordates but prior to the emergence of fishes lead to the evolution of four Ago paralogues. Invertebrate RISC RNA-binding proteins R2D2 and Loquacious are related to other RNA-binding protein families such as Staufens as well as vertebrate-specific TAR (HIV trans-activator RNA) RNA-binding protein (TRBP) and protein kinase R-activating protein (PACT). Export of small RNAs from the nucleus, including miRNA, is facilitated by three closely related karyopherin-related nuclear transporters, Exportin-5, Exportin-1 and Exportin-T. While all three exportins have direct orthologues in deutrostomes, missing exportins in arthropods (Exportin-T) and nematodes (Exportin-5) are likely compensated by dual specificities of one of the other exportin paralogues. CONCLUSION Co-opting particular isoforms from large, diverse protein families seems to be a common theme in the evolution of miRNA biogenesis. Human miRNA biogenesis proteins have direct, orthologues in cold-blooded fishes and, in some cases, urochordates and deutrostomes. However, lineage specific expansions of Dicer in plants and invertebrates as well as Argonaute and RNA-binding proteins in vertebrates suggests that novel ncRNA regulatory mechanisms can evolve in relatively short evolutionary timeframes. The occurrence of multiple homologues to RNA-binding and Argonaute/PIWI proteins also suggests the possible existence of further pathways for additional types of ncRNAs.
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Affiliation(s)
- Dennis Murphy
- Bioinformatics, Molecular Discovery Research, GlaxoSmithKline, 1250 South Collegeville Road, UP1345, Collegeville, Pennsylvania 19426, USA.
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Abstract
While the hereditary information encoded in the Watson-Crick base pairing of genomes is largely static within a given individual, access to this information is controlled by dynamic mechanisms. The human genome is pervasively transcribed, but the roles played by the majority of the non-protein-coding genome sequences are still largely unknown. In this review we focus on insights to gene transcriptional regulation by placing special emphasis on genome-wide approaches, and on how non-coding RNAs, which derive from global transcription of the genome, in turn control gene expression. We review recent progress in the field with highlights on the immune system.
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Affiliation(s)
- Matthew E Pipkin
- Immune Disease Institute and Harvard Medical School, Boston, MA, USA
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Chapter 16. How to define targets for small guide RNAs in RNA silencing: a biochemical approach. Methods Enzymol 2008; 449:345-55. [PMID: 19215766 DOI: 10.1016/s0076-6879(08)02416-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
RNA silencing involves various forms of sequence-specific gene silencing triggered by small RNAs. In RNA silencing, Argonautes are crucial protein components that are directed to the target messenger RNAs (mRNAs) through their association with small RNAs by base pairing. Argonautes repress the expression of the target genes at posttranscriptional levels. Full complementarity between a small RNA and its target mRNA results in Argonaute-mediated cleavage ("slicing") of the target mRNA. The D-D-H (asparagine-asparagine-histidine) triad that exists in the PIWI domain of Argonautes is the catalytic center for rendering their target cleavage ("slicer") activity. This chapter describes in vitro target RNA cleavage assays using Aubergine in a complex form with PIWI-interacting RNAs. Aubergine is one of the Argonautes expressed primarily in fly germ lines and is immunopurified from fly testes using the specific antibody against it. The method discussed is useful for defining targets for the small RNAs that function in RNA silencing.
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