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Avila-Bonilla RG, Salas-Benito JS. Computational Screening to Predict MicroRNA Targets in the Flavivirus 3' UTR Genome: An Approach for Antiviral Development. Int J Mol Sci 2024; 25:10135. [PMID: 39337625 PMCID: PMC11432202 DOI: 10.3390/ijms251810135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 09/16/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
MicroRNAs (miRNAs) are molecules that influence messenger RNA (mRNA) expression levels by binding to the 3' untranslated region (3' UTR) of target genes. Host miRNAs can influence flavivirus replication, either by inducing changes in the host transcriptome or by directly binding to viral genomes. The 3' UTR of the flavivirus genome is a conserved region crucial for viral replication. Cells might exploit this well-preserved region by generating miRNAs that interact with it, ultimately impacting viral replication. Despite significant efforts to identify miRNAs capable of arresting viral replication, the potential of all these miRNAs to interact with the flavivirus 3' UTR is still poorly characterised. In this context, bioinformatic tools have been proposed as a fundamental part of accelerating the discovery of interactions between miRNAs and the 3' UTR of viral genomes. In this study, we performed a computational analysis to reveal potential miRNAs from human and mosquito species that bind to the 3' UTR of flaviviruses. In humans, miR-6842 and miR-661 were found, while in mosquitoes, miR-9-C, miR-2945-5p, miR-11924, miR-282-5p, and miR-79 were identified. These findings open new avenues for studying these miRNAs as antivirals against flavivirus infections.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Laboratorio de Genómica y Biología Molecular de ARNs, Departamento de Genética y Biología Molecular, Cinvestav, Av. IPN 2508, Mexico City 07360, Mexico
| | - Juan Santiago Salas-Benito
- Laboratorio de Biomedicina Molecular 3, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico
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2
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He J, Kang L. Regulation of insect behavior by non-coding RNAs. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1106-1118. [PMID: 38443665 DOI: 10.1007/s11427-023-2482-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/26/2023] [Indexed: 03/07/2024]
Abstract
The adaptation of insects to environments relies on a sophisticated set of behaviors controlled by molecular and physiological processes. Over the past several decades, accumulating studies have unveiled the roles of non-coding RNAs (ncRNAs) in regulating insect behaviors. ncRNAs assume particularly pivotal roles in the behavioral plasticity of insects by rapidly responding to environmental stimuli. ncRNAs also contribute to the maintenance of homeostasis of insects by fine-tuning the expression of target genes. However, a comprehensive review of ncRNAs' roles in regulating insect behaviors has yet to be conducted. Here, we present the recent progress in our understanding of how ncRNAs regulate various insect behaviors, including flight and movement, social behavior, reproduction, learning and memory, and feeding. We refine the intricate mechanisms by which ncRNAs modulate the function of neural, motor, reproductive, and other physiological systems, as well as gene expression in insects like fruit flies, social insects, locusts, and mosquitos. Furthermore, we discuss potential avenues for future studies in ncRNA-mediated insect behaviors.
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Affiliation(s)
- Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, Hebei University, Baoding, 071002, China.
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3
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Huang J, Wang T, Qiu Y, Hassanyar AK, Zhang Z, Sun Q, Ni X, Yu K, Guo Y, Yang C, Lü Y, Nie H, Lin Y, Li Z, Su S. Differential Brain Expression Patterns of microRNAs Related to Olfactory Performance in Honey Bees ( Apis mellifera). Genes (Basel) 2023; 14:genes14051000. [PMID: 37239360 DOI: 10.3390/genes14051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
MicroRNAs (miRNAs) play a vital role in the nerve regulation of honey bees (Apis mellifera). This study aims to investigate the differences in expression of miRNAs in a honey bee's brain for olfactory learning tasks and to explore their potential role in a honey bee's olfactory learning and memory. In this study, 12 day old honey bees with strong and weak olfactory performances were utilized to investigate the influence of miRNAs on olfactory learning behavior. The honey bee brains were dissected, and a small RNA-seq technique was used for high-throughput sequencing. The data analysis of the miRNA sequences revealed that 14 differentially expressed miRNAs (DEmiRNAs) between the two groups, strong (S) and weak (W), for olfactory performance in honey bees were identified, which included seven up-regulated and seven down-regulated. The qPCR verification results of the 14 miRNAs showed that four miRNAs (miR-184-3p, miR-276-3p, miR-87-3p, and miR-124-3p) were significantly associated with olfactory learning and memory. The target genes of these DEmiRNAs were subjected to the GO database annotation and KEGG pathway enrichment analyses. The functional annotation and pathway analysis showed that the neuroactive ligand-receptor interaction pathway, oxidative phosphorylation, biosynthesis of amino acids, pentose phosphate pathway, carbon metabolism, and terpenoid backbone biosynthesis may be a great important pathway related to olfactory learning and memory in honey bees. Our findings together further explained the relationship between olfactory performance and the brain function of honey bees at the molecular level and provides a basis for further study on miRNAs related to olfactory learning and memory in honey bees.
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Affiliation(s)
- Jingnan Huang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianbao Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanmei Qiu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Aqai Kalan Hassanyar
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhaonan Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Laboratory of Evolution and Diversity Biology, UMR5174, University Toulouse III Paul Sabatier, CNRS, 31062 Toulouse, France
| | - Qiaoling Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Xiaomin Ni
- Faculty of Science, University of Queensland, Brisbane, QLD 4072, Australia
| | - Kejun Yu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongkang Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Changsheng Yang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yang Lü
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang 157041, China
| | - Hongyi Nie
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yan Lin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhiguo Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Songkun Su
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Academy of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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4
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Vasiliev GV, Ovchinnikov VY, Lisachev PD, Bondar NP, Grinkevich LN. The Expression of miRNAs Involved in Long-Term Memory Formation in the CNS of the Mollusk Helix lucorum. Int J Mol Sci 2022; 24:ijms24010301. [PMID: 36613744 PMCID: PMC9820140 DOI: 10.3390/ijms24010301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Mollusks are unique animals with a relatively simple central nervous system (CNS) containing giant neurons with identified functions. With such simple CNS, mollusks yet display sufficiently complex behavior, thus ideal for various studies of behavioral processes, including long-term memory (LTM) formation. For our research, we use the formation of the fear avoidance reflex in the terrestrial mollusk Helix lucorum as a learning model. We have shown previously that LTM formation in Helix requires epigenetic modifications of histones leading to both activation and inactivation of the specific genes. It is known that microRNAs (miRNAs) negatively regulate the expression of genes; however, the role of miRNAs in behavioral regulation has been poorly investigated. Currently, there is no miRNAs sequencing data being published on Helix lucorum, which makes it impossible to investigate the role of miRNAs in the memory formation of this mollusk. In this study, we have performed sequencing and comparative bioinformatics analysis of the miRNAs from the CNS of Helix lucorum. We have identified 95 different microRNAs, including microRNAs belonging to the MIR-9, MIR-10, MIR-22, MIR-124, MIR-137, and MIR-153 families, known to be involved in various CNS processes of vertebrates and other species, particularly, in the fear behavior and LTM. We have shown that in the CNS of Helix lucorum MIR-10 family (26 miRNAs) is the most representative one, including Hlu-Mir-10-S5-5p and Hlu-Mir-10-S9-5p as top hits. Moreover, we have shown the involvement of the MIR-10 family in LTM formation in Helix. The expression of 17 representatives of MIR-10 differentially changes during different periods of LTM consolidation in the CNS of Helix. In addition, using comparative analysis of microRNA expression upon learning in normal snails and snails with deficient learning abilities with dysfunction of the serotonergic system, we identified a number of microRNAs from several families, including MIR-10, which expression changes only in normal animals. The obtained data can be used for further fundamental and applied behavioral research.
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Affiliation(s)
- Gennady V. Vasiliev
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Vladimir Y. Ovchinnikov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Pavel D. Lisachev
- Federal Research Center for Information and Computational Technologies, 6 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Natalia P. Bondar
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Larisa N. Grinkevich
- The Federal State Budget Scientific Institution Pavlov Institute of Physiology, Russian Academy of Sciences, 6 nab. Makarova, St. Petersburg 199034, Russia
- Correspondence:
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Noyes NC, Phan A, Davis RL. Memory suppressor genes: Modulating acquisition, consolidation, and forgetting. Neuron 2021; 109:3211-3227. [PMID: 34450024 PMCID: PMC8542634 DOI: 10.1016/j.neuron.2021.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/15/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023]
Abstract
The brain has a remarkable but underappreciated capacity to limit memory formation and expression. The term "memory suppressor gene" was coined in 1998 as an attempt to explain emerging reports that some genes appeared to limit memory. At that time, only a handful of memory suppressor genes were known, and they were understood to work by limiting cAMP-dependent consolidation. In the intervening decades, almost 100 memory suppressor genes with diverse functions have been discovered that affect not only consolidation but also acquisition and forgetting. Here we highlight the surprising extent to which biological limits are placed on memory formation through reviewing the literature on memory suppressor genes. In this review, we present memory suppressors within the framework of their actions on different memory operations: acquisition, consolidation, and forgetting. This is followed by a discussion of the reasons why there may be a biological need to limit memory formation.
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Affiliation(s)
- Nathaniel C Noyes
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Anna Phan
- Department of Biological Sciences, University of Alberta, 11355 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Ronald L Davis
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, FL 33458, USA.
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6
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Medvedeva AV, Tokmatcheva EV, Kaminskaya AN, Vasileva SA, Nikitina EA, Zhuravlev SA, Zakharov GA, Zatsepina OG, Savvateeva-Popova EV. Parent-of-origin effects on nuclear chromatin organization and behavior in a Drosophila model for Williams-Beuren Syndrome. Vavilovskii Zhurnal Genet Selektsii 2021; 25:472-485. [PMID: 34595370 PMCID: PMC8460428 DOI: 10.18699/vj21.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Prognosis of neuropsychiatric disorders in progeny requires consideration of individual (1) parent-of-origin effects (POEs) relying on (2) the nerve cell nuclear 3D chromatin architecture and (3) impact of parent-specific miRNAs. Additionally, the shaping of cognitive phenotypes in parents depends on both learning acquisition and forgetting, or memory erasure. These processes are independent and controlled by different signal cascades: the first is cAMPdependent, the second relies on actin remodeling by small GTPase Rac1 - LIMK1 (LIM-kinase 1). Simple experimental model systems such as Drosophila help probe the causes and consequences leading to human neurocognitive pathologies. Recently, we have developed a Drosophila model for Williams-Beuren Syndrome (WBS): a mutant agnts3 of the agnostic locus (X:11AB) harboring the dlimk1 gene. The agnts3 mutation drastically increases the frequency of ectopic contacts (FEC) in specific regions of intercalary heterochromatin, suppresses learning/memory and affects locomotion. As is shown in this study, the polytene X chromosome bands in reciprocal hybrids between agnts3 and the wild type strain Berlin are heterogeneous in modes of FEC regulation depending either on maternal or paternal gene origin. Bioinformatic analysis reveals that FEC between X:11AB and the other X chromosome bands correlates with the occurrence of short (~30 bp) identical DNA fragments partly homologous to Drosophila 372-bp satellite DNA repeat. Although learning acquisition in a conditioned courtship suppression paradigm is similar in hybrids, the middle-term memory formation shows patroclinic inheritance. Seemingly, this depends on changes in miR-974 expression. Several parameters of locomotion demonstrate heterosis. Our data indicate that the agnts3 locus is capable of trans-regulating gene activity via POEs on the chromatin nuclear organization, thereby affecting behavior.
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Affiliation(s)
- A V Medvedeva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - E V Tokmatcheva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A N Kaminskaya
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - S A Vasileva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - E A Nikitina
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia Herzen State Pedagogical University of Russia, St. Petersburg, Russia
| | - S A Zhuravlev
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - G A Zakharov
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - O G Zatsepina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - E V Savvateeva-Popova
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
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7
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Juvale IIA, Che Has AT. The Potential Role of miRNAs as Predictive Biomarkers in Neurodevelopmental Disorders. J Mol Neurosci 2021; 71:1338-1355. [PMID: 33774758 DOI: 10.1007/s12031-021-01825-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/02/2021] [Indexed: 12/22/2022]
Abstract
Neurodevelopmental disorders are defined as a set of abnormal brain developmental conditions marked by the early childhood onset of cognitive, behavioral, and functional deficits leading to memory and learning problems, emotional instability, and impulsivity. Autism spectrum disorder, attention-deficit/hyperactivity disorder, Tourette syndrome, fragile X syndrome, and Down's syndrome are a few known examples of neurodevelopmental disorders. Although they are relatively common in both developed and developing countries, very little is currently known about their underlying molecular mechanisms. Both genetic and environmental factors are known to increase the risk of neurodevelopmental disorders. Current diagnostic and screening tests for neurodevelopmental disorders are not reliable; hence, individuals with neurodevelopmental disorders are often diagnosed in the later stages. This negatively affects their prognosis and quality of life, prompting the need for a better diagnostic biomarker. Recent studies on microRNAs and their altered regulation in diseases have shed some light on the possible role they could play in the development of the central nervous system. This review attempts to elucidate our current understanding of the role that microRNAs play in neurodevelopmental disorders with the hope of utilizing them as potential biomarkers in the future.
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Affiliation(s)
- Iman Imtiyaz Ahmed Juvale
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Ahmad Tarmizi Che Has
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.
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8
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A neural m 6A/Ythdf pathway is required for learning and memory in Drosophila. Nat Commun 2021; 12:1458. [PMID: 33674589 PMCID: PMC7935873 DOI: 10.1038/s41467-021-21537-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023] Open
Abstract
Epitranscriptomic modifications can impact behavior. Here, we used Drosophila melanogaster to study N6-methyladenosine (m6A), the most abundant modification of mRNA. Proteomic and functional analyses confirm its nuclear (Ythdc1) and cytoplasmic (Ythdf) YTH domain proteins as major m6A binders. Assays of short term memory in m6A mutants reveal neural-autonomous requirements of m6A writers working via Ythdf, but not Ythdc1. Furthermore, m6A/Ythdf operate specifically via the mushroom body, the center for associative learning. We map m6A from wild-type and Mettl3 mutant heads, allowing robust discrimination of Mettl3-dependent m6A sites that are highly enriched in 5' UTRs. Genomic analyses indicate that Drosophila m6A is preferentially deposited on genes with low translational efficiency and that m6A does not affect RNA stability. Nevertheless, functional tests indicate a role for m6A/Ythdf in translational activation. Altogether, our molecular genetic analyses and tissue-specific m6A maps reveal selective behavioral and regulatory defects for the Drosophila Mettl3/Ythdf pathway.
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9
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Liu J, Zeng X, Han K, Jia X, Zhou M, Zhang Z, Wang Y. The expression regulation of Cyclins and CDKs in ovary via miR-9c and miR-263a of Scylla paramamosain. Comp Biochem Physiol B Biochem Mol Biol 2021; 254:110567. [PMID: 33548504 DOI: 10.1016/j.cbpb.2021.110567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 12/14/2022]
Abstract
Scylla paramamosain is an economically important cultured crab species in China. Cyclins and cyclin-dependent kinases (CDKs) play important roles in regulations of cell cycle and ovarian development. MiRNAs can negatively regulate gene expression at the post-transcriptional level through base-complementary pairing with the 3'-untranslated region (3-UTR) of the target gene. In this study, bioinformatics prediction showed that miR-9c and miR-263a identified from our group's gonad miRNAome of S. paramamosain may bind to the 3' UTR region of cyclin A, cyclin B, cyclin E, cyclin H, CDK1, and CDK2. Furthermore, the results of double luciferase reporter gene assay showed that the luciferase activities of HEK293T cells co-transfected with miR-9c mimics/miR-9c inhibitor and the 3'-UTR plasmid vectors of the five genes (cyclin A, cyclin B, cyclin H, CDK1, and CDK2) were significantly decreased/increased compared with those in the NC (negative control) and BC (blank control) groups. The results in miR-263a were similar to miR-9c, but all of the six genes could be regulated by miR-263a. In in vivo experiments, agomiR-9c (miR-9c enhancer) injection resulted in decreases of cyclin A and CDK1 expression level, and reverse effects were observed by injecting antagomiR-9c. AgomiR-263a decreased the expression of cyclin A, cyclin B, cyclin H, CDK1, and CDK2, but antagomiR-263a increased their expression. Both the in vitro and in vivo experiments confirmed functions of miR-9c and miR-263a in cell cycle progress of ovarian development by expression regulation of cyclin A, cyclin B, cyclin E, cyclin H, CDK1, and CDK2. The findings provide new insights into the reproductive regulation mechanism in mud crab and further enrich the knowledge of cell cycle and ovarian development regulation in invertebrates.
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Affiliation(s)
- Jianan Liu
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Xianyuan Zeng
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China; School of Life Sciences, Ningde Normal University, Ningde 352100, China
| | - Kunhuang Han
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China; School of Life Sciences, Ningde Normal University, Ningde 352100, China
| | - Xiwei Jia
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China
| | - Mingcan Zhou
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziping Zhang
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yilei Wang
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Fisheries College, Jimei University, Xiamen 361021, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, China.
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10
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miR-92a Suppresses Mushroom Body-Dependent Memory Consolidation in Drosophila. eNeuro 2020; 7:ENEURO.0224-20.2020. [PMID: 32737186 PMCID: PMC7642123 DOI: 10.1523/eneuro.0224-20.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) fine tune gene expression to regulate many aspects of nervous system physiology. Here, we show that miR-92a suppresses memory consolidation that occurs in the αβ and γ mushroom body neurons (MBns) of Drosophila, making miR-92a a memory suppressor miRNA. Bioinformatics analyses suggested that mRNAs encoding kinesin heavy chain 73 (KHC73), a protein that belongs to Kinesin-3 family of anterograde motor proteins, may be a functional target of miR-92a. Behavioral studies that employed expression of khc73 with and without its 3' untranslated region (UTR) containing miR-92a target sites, luciferase assays in HEK cells with reporters containing wild-type and mutant target sequences in the khc73 3'UTR, and immunohistochemistry experiments involving KHC73 expression with and without the wild-type khc73 3'UTR, all point to the conclusion that khc73 is a major target of miR-92a in its functional role as a miRNA memory suppressor gene.
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11
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Freudenthal RAM, Romano A, Baez MV. Editorial: Changes in Molecular Expression After Memory Acquisition and Plasticity. Looking for the Memory Trace. Front Mol Neurosci 2020; 13:50. [PMID: 32317930 PMCID: PMC7146821 DOI: 10.3389/fnmol.2020.00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ramiro A M Freudenthal
- CONICET Institute of Physiology, Molecular Biology and Neurosciences (IFIBYNE), Buenos Aires, Argentina.,Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - Arturo Romano
- CONICET Institute of Cell Biology and Neuroscience (IBCN), Buenos Aires, Argentina
| | - Maria Veronica Baez
- CONICET Institute of Cell Biology and Neuroscience (IBCN), Buenos Aires, Argentina.,Faculty of Medicine, University of Buenos Aires, Buenos Aires, Argentina
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12
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Abstract
Locomotion is an ancient and fundamental output of the nervous system required for animals to perform many other complex behaviors. Although the formation of motor circuits is known to be under developmental control of transcriptional mechanisms that define the fates and connectivity of the many neurons, glia and muscle constituents of these circuits, relatively little is known about the role of post-transcriptional regulation of locomotor behavior. MicroRNAs have emerged as a potentially rich source of modulators for neural development and function. In order to define the microRNAs required for normal locomotion in Drosophila melanogaster, we utilized a set of transgenic Gal4-dependent competitive inhibitors (microRNA sponges, or miR-SPs) to functionally assess ca. 140 high-confidence Drosophila microRNAs using automated quantitative movement tracking systems followed by multiparametric analysis. Using ubiquitous expression of miR-SP constructs, we identified a large number of microRNAs that modulate aspects of normal baseline adult locomotion. Addition of temperature-dependent Gal80 to identify microRNAs that act during adulthood revealed that the majority of these microRNAs play developmental roles. Comparison of ubiquitous and neural-specific miR-SP expression suggests that most of these microRNAs function within the nervous system. Parallel analyses of spontaneous locomotion in adults and in larvae also reveal that very few of the microRNAs required in the adult overlap with those that control the behavior of larval motor circuits. These screens suggest that a rich regulatory landscape underlies the formation and function of motor circuits and that many of these mechanisms are stage and/or parameter-specific.
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13
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Bi J, Zheng Y, Wang RF, Ai H, Haynes PR, Brownlie JC, Yu XQ, Wang YF. Wolbachia infection may improve learning and memory capacity of Drosophila by altering host gene expression through microRNA. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 106:47-54. [PMID: 30468769 DOI: 10.1016/j.ibmb.2018.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Wolbachia are endosymbiotic bacteria present in a wide range of invertebrates. Although their dramatic effects on host reproductive biology have been well studied, little is known about the effects of Wolbachia on the learning and memory capacity (LMC) of hosts, despite their distribution in the host nervous system, including brain. In this study, we found that Wolbachia infection significantly enhanced LMC in both Drosophila melanogaster and D. simulans. Expression of LMC-related genes was significantly increased in the head of D. melanogaster infected with the wMel strain, and among these genes, crebA was up-regulated the most. Knockdown of crebA in Wolbachia-infected flies significantly decreased LMC, while overexpression of crebA in Wolbachia-free flies significantly enhanced the LMC of flies. More importantly, a microRNA (miRNA), dme-miR-92b, was identified to be complementary to the 3'UTR of crebA. Wolbachia infection was correlated with reduced expression of dme-miR-92b in D. melanogaster, and dme-miR-92b negatively regulated crebA through binding to its 3'UTR region. Overexpression of dme-miR-92b in Wolbachia-infected flies by microinjection of agomirs caused a significant decrease in crebA expression and LMC, while inhibition of dme-miR-92b in Wolbachia-free flies by microinjection of antagomirs resulted in a significant increase in crebA expression and LMC. These results suggest that Wolbachia may improve LMC in Drosophila by altering host gene expression through a miRNA-target pathway. Our findings help better understand the host-endosymbiont interactions and, in particular, the impact of Wolbachia on cognitive processes in invertebrate hosts.
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Affiliation(s)
- Jie Bi
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Ya Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Rui-Fang Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Hui Ai
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Paula R Haynes
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeremy C Brownlie
- School of Natural Science, Griffith University, Nathan, QLD 4111, Australia
| | - Xiao-Qiang Yu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China; School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Yu-Feng Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China.
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14
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Anreiter I, Biergans SD, Sokolowski MB. Epigenetic regulation of behavior in Drosophila melanogaster. Curr Opin Behav Sci 2019. [DOI: 10.1016/j.cobeha.2018.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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The Role of miRNAs in Drosophila melanogaster Male Courtship Behavior. Genetics 2019; 211:925-942. [PMID: 30683757 DOI: 10.1534/genetics.118.301901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 01/19/2019] [Indexed: 11/18/2022] Open
Abstract
Drosophila melanogaster courtship, although stereotypical, continually changes based on cues received from the courtship subject. Such adaptive responses are mediated via rapid and widespread transcriptomic reprogramming, a characteristic now widely attributed to microRNAs (miRNAs), along with other players. Here, we conducted a large-scale miRNA knockout screen to identify miRNAs that affect various parameters of male courtship behavior. Apart from identifying miRNAs that impact male-female courtship, we observed that miR-957 mutants performed significantly increased male-male courtship and "chaining" behavior, whereby groups of males court one another. We tested the effect of miR-957 reduction in specific neuronal cell clusters, identifying miR-957 activity in Doublesex (DSX)-expressing and mushroom body clusters as an important regulator of male-male courtship interactions. We further characterized the behavior of miR-957 mutants and found that these males court male subjects vigorously, but do not elicit courtship. Moreover, they fail to lower courtship efforts toward females with higher levels of antiaphrodisiac pheromones. At the level of individual pheromones, miR-957 males show a reduced inhibitory response to both 7-Tricosene (7-T) and cis-vaccenyl acetate, with the effect being more pronounced in the case of 7-T. Overall, our results indicate that a single miRNA can contribute to the regulation of complex behaviors, including detection or processing of chemicals that control important survival strategies such as chemical mate-guarding, and the maintenance of sex- and species-specific courtship barriers.
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16
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Menzel P, McCorkindale AL, Stefanov SR, Zinzen RP, Meyer IM. Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis. RNA Biol 2019; 16:69-81. [PMID: 30582411 PMCID: PMC6380339 DOI: 10.1080/15476286.2018.1558907] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 01/20/2023] Open
Abstract
During Drosophila melanogaster embryogenesis, tight regulation of gene expression in time and space is required for the orderly emergence of specific cell types. While the general importance of microRNAs in regulating eukaryotic gene expression has been well-established, their role in early neurogenesis remains to be addressed. In this survey, we investigate the transcriptional dynamics of microRNAs and their target transcripts during neurogenesis of Drosophila melanogaster. To this end, we use the recently developed DIV-MARIS protocol, a method for enriching specific cell types from the Drosophila embryo in vivo, to sequence cell type-specific transcriptomes. We generate dedicated small and total RNA-seq libraries for neuroblasts, neurons and glia cells at early (6-8 h after egg laying (AEL)) and late (18-22 h AEL) stage. This allows us to directly compare these transcriptomes and investigate the potential functional roles of individual microRNAs with spatiotemporal resolution genome-wide, which is beyond the capabilities of existing in situ hybridization methods. Overall, we identify 74 microRNAs that are significantly differentially expressed between the three cell types and the two developmental stages. In all cell types, predicted target genes of down-regulated microRNAs show a significant enrichment of Gene Ontology terms related to neurogenesis. We also investigate how microRNAs regulate the transcriptome by targeting transcription factors and find many candidate microRNAs with putative roles in neurogenesis. Our survey highlights the roles of microRNAs as regulators of differentiation and glioneurognesis in the fruit fly and provides distinct starting points for dedicated functional follow-up studies.
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Affiliation(s)
- Peter Menzel
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Alexandra L. McCorkindale
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Stefan R. Stefanov
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Biochemistry, Department of Biology, Chemistry, and Pharmacology, Freie Universität Berlin, Berlin, Germany
| | - Robert P. Zinzen
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Irmtraud M. Meyer
- Berlin Institute for Molecular and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Biochemistry, Department of Biology, Chemistry, and Pharmacology, Freie Universität Berlin, Berlin, Germany
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17
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Amyloid Beta 1-42 Alters the Expression of miRNAs in Cortical Neurons. J Mol Neurosci 2018; 67:181-192. [PMID: 30515701 DOI: 10.1007/s12031-018-1223-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/18/2018] [Indexed: 02/08/2023]
Abstract
Recently, Aβ1-42 was demonstrated to have the potential to translocate into the nucleus and to be involved in the transcriptional regulation of certain neurodegeneration-related genes. This data raises the question of whether Aβ-induced neurodegeneration might include the expression of miRNAs. Thus, our aim in this study was to investigate the effects of Aβ1-42 on certain miRNAs which are related with vitamin D metabolism, neuronal differentiation, development, and memory. This question was investigated in primary cortical neurons that were treated with 10 μM Aβ and/or 10-8 M 1,25-dihydroxyvitamin D3 at different time points by expression analysis of let-7a-5p, miR-26b-5p, miR-27b-3p, miR-31a-5p, miR-125b-5p, and miR-192-5p with qRT-PCR. Our data indicate that amyloid pathology has effects on the expression of miRNAs. Furthermore, some of these miRNAs simultaneously regulate the proteins or the enzymes involved in neuronal metabolism. The experimental setup that we used and the data we acquired supply valuable information about the miRNAs that play a part in the Aβ pathology and suggested Aβ as a counterpart of vitamin D at the crossroads of neuronal differentiation, development, and memory.
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18
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Regulation of Circadian Behavior by Astroglial MicroRNAs in Drosophila. Genetics 2018; 208:1195-1207. [PMID: 29487148 DOI: 10.1534/genetics.117.300342] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/08/2018] [Indexed: 11/18/2022] Open
Abstract
We describe a genome-wide microRNA (miRNA)-based screen to identify brain glial cell functions required for circadian behavior. To identify glial miRNAs that regulate circadian rhythmicity, we employed a collection of "miR-sponges" to inhibit miRNA function in a glia-specific manner. Our initial screen identified 20 glial miRNAs that regulate circadian behavior. We studied two miRNAs, miR-263b and miR-274, in detail and found that both function in adult astrocytes to regulate behavior. Astrocyte-specific inhibition of miR-263b or miR-274 in adults acutely impairs circadian locomotor activity rhythms with no effect on glial or clock neuronal cell viability. To identify potential RNA targets of miR-263b and miR-274, we screened 35 predicted miRNA targets, employing RNA interference-based approaches. Glial knockdown of two putative miR-274 targets, CG4328 and MESK2, resulted in significantly decreased rhythmicity. Homology of the miR-274 targets to mammalian counterparts suggests mechanisms that might be relevant for the glial regulation of rhythmicity.
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19
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The Drosophila Receptor Tyrosine Kinase Alk Constrains Long-Term Memory Formation. J Neurosci 2018; 38:7701-7712. [PMID: 30030398 DOI: 10.1523/jneurosci.0784-18.2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/21/2018] [Accepted: 07/03/2018] [Indexed: 02/06/2023] Open
Abstract
In addition to mechanisms promoting protein-synthesis-dependent long-term memory (PSD-LTM), the process appears to also be specifically constrained. We present evidence that the highly conserved receptor tyrosine kinase dAlk is a novel PSD-LTM attenuator in Drosophila Reduction of dAlk levels in adult α/β mushroom body (MB) neurons during conditioning elevates LTM, whereas its overexpression impairs it. Unlike other memory suppressor proteins and miRNAs, dAlk within the MBs constrains PSD-LTM specifically but constrains learning outside the MBs as previously shown. Dendritic dAlk levels rise rapidly in MB neurons upon conditioning, a process apparently controlled by the 3'UTR of its mRNA, and interruption of the 3'UTR leads to enhanced LTM. Because its activating ligand Jeb is dispensable for LTM attenuation, we propose that postconditioning elevation of dAlk within α/β dendrites results in its autoactivation and constrains formation of the energy costly PSD-LTM, acting as a novel memory filter.SIGNIFICANCE STATEMENT In addition to the widely studied molecular mechanisms promoting protein-synthesis-dependent long-term memory (PSD-LTM), recent discoveries indicate that the process is also specifically constrained. We describe a role in PSD-LTM constraint for the first receptor tyrosine kinase (RTK) involved in olfactory memory in Drosophila Unlike other memory suppressor proteins and miRNAs, dAlk limits specifically PSD-LTM formation as it does not affect 3 h, or anesthesia-resistant memory. Significantly, we show conditioning-dependent dAlk elevation within the mushroom body dendrites and propose that its local abundance may activate its kinase activity, to mediate imposition of PSD-LTM constraints through yet unknown mechanisms.
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20
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Engineered Hsp70 chaperones prevent Aβ42-induced memory impairments in a Drosophila model of Alzheimer's disease. Sci Rep 2018; 8:9915. [PMID: 29967544 PMCID: PMC6028656 DOI: 10.1038/s41598-018-28341-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/14/2018] [Indexed: 11/09/2022] Open
Abstract
Proteinopathies constitute a group of diseases in which certain proteins are abnormally folded leading to aggregation and eventual cell failure. Most neurodegenerative diseases belong to protein misfolding disorders and, among them, Alzheimer’s disease (AD) is the most prevalent. AD is characterized by accumulation of the amyloid-β42 (Aβ42) peptide in the extracellular space. Hence, we genetically engineered a molecular chaperone that was selectively delivered to this cellular location. It has been reported that the heat shock protein 70 (Hsp70) binds Aβ42 preventing self-aggregation. Here, we employed two isoforms of the Hsp70, cytosolic and extracellular, to evaluate their potential protective effect against the memory decline triggered by extracellular deposition of Aβ42. Both Hsp70 isoforms significantly improved memory performance of flies expressing Aβ42, irrespective of their age or the level of Aβ42 load. Using olfactory classical conditioning, we established a Drosophila model of AD based on Aβ42 neurotoxicity and monitored memory decline through aging. The onset of the memory impairment observed was proportional to the cumulative level of Aβ42 in the Drosophila brain. These data support the use of this Drosophila model of AD to further investigate molecules with a protective activity against Aβ42-induced memory loss, contributing to the development of palliative therapies for AD.
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21
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Deshmukh S, Ponnaluri VKC, Dai N, Pradhan S, Deobagkar D. Levels of DNA cytosine methylation in the Drosophila genome. PeerJ 2018; 6:e5119. [PMID: 30002967 PMCID: PMC6033079 DOI: 10.7717/peerj.5119] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/07/2018] [Indexed: 01/16/2023] Open
Abstract
Insects provide an accessible system to study the contribution of DNA methylation to complex epigenetic phenotypes created to regulate gene expression, chromatin states, imprinting and dosage compensation. The members of genus Drosophila have been used as a model system to study aspects of biology like development, behaviour and genetics. Despite the popularity of Drosophila melanogaster as a genetic and epigenetic model organism, DNA methylation studies are limited due to low levels of genomic 5-methylcytosine. Our study employs a sensitive liquid chromatography-mass spectrometry (LCMS) based method to quantify the levels of 5-methylcytosine from the genomic DNA in different members of the genus Drosophila. Our results reveal that, despite being phylogenetically related, there is a marked variation in the levels of 5-methylcytosine between the genomes of the members of genus Drosophila. Also, there is a change in the genomic levels of 5-methylcytosine through each life cycle stage of holometabolous development in D. melanogaster.
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Affiliation(s)
- Saniya Deshmukh
- Molecular Biology Research Laboratory; Department of Zoology (Centre for Advanced Studies), Savitribai Phule Pune University (formerly University of Pune), Pune, Maharashtra, India
| | | | - Nan Dai
- New England Biolabs, Ipswich, MA, United States of America
| | | | - Deepti Deobagkar
- Molecular Biology Research Laboratory; Department of Zoology (Centre for Advanced Studies), Savitribai Phule Pune University (formerly University of Pune), Pune, Maharashtra, India
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22
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Jia X, Zhou M, Zou Z, Lin P, Wang Y, Zhang Z. Identification and comparative analysis of the ovary and testis microRNAome of mud crab Scylla paramamosain. Mol Reprod Dev 2018; 85:519-531. [DOI: 10.1002/mrd.22989] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/19/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Xiwei Jia
- Fisheries College; Jimei University; Xiamen China
| | - Mingcan Zhou
- Fisheries College; Jimei University; Xiamen China
| | - Zhihua Zou
- Fisheries College; Jimei University; Xiamen China
| | - Peng Lin
- Fisheries College; Jimei University; Xiamen China
| | - Yilei Wang
- Fisheries College; Jimei University; Xiamen China
| | - Ziping Zhang
- College of Animal Science; Fujian Agriculture and Forestry University; Fuzhou China
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23
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Wei G, Sun L, Li R, Li L, Xu J, Ma F. Dynamic miRNA-mRNA regulations are essential for maintaining Drosophila immune homeostasis during Micrococcus luteus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 81:210-224. [PMID: 29198775 DOI: 10.1016/j.dci.2017.11.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/15/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
Pathogen bacteria infections can lead to dynamic changes of microRNA (miRNA) and mRNA expression profiles, which may control synergistically the outcome of immune responses. To reveal the role of dynamic miRNA-mRNA regulation in Drosophila innate immune responses, we have detailedly analyzed the paired miRNA and mRNA expression profiles at three time points during Drosophila adult males with Micrococcus luteus (M. luteus) infection using RNA- and small RNA-seq data. Our results demonstrate that differentially expressed miRNAs and mRNAs represent extensively dynamic changes over three time points during Drosophila with M. luteus infection. The pathway enrichment analysis indicates that differentially expressed genes are involved in diverse signaling pathways, including Toll and Imd as well as orther signaling pathways at three time points during Drosophila with M. luteus infection. Remarkably, the dynamic change of miRNA expression is delayed by compared to mRNA expression change over three time points, implying that the "time" parameter should be considered when the function of miRNA/mRNA is further studied. In particular, the dynamic miRNA-mRNA regulatory networks have shown that miRNAs may synergistically regulate gene expressions of different signaling pathways to promote or inhibit innate immune responses and maintain homeostasis in Drosophila, and some new regulators involved in Drosophila innate immune response have been identified. Our findings strongly suggest that miRNA regulation is a key mechanism involved in fine-tuning cooperatively gene expressions of diverse signaling pathways to maintain innate immune response and homeostasis in Drosophila. Taken together, the present study reveals a novel role of dynamic miRNA-mRNA regulation in immune response to bacteria infection, and provides a new insight into the underlying molecular regulatory mechanism of Drosophila innate immune responses.
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Affiliation(s)
- Guanyun Wei
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Lianjie Sun
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Ruimin Li
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Lei Li
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China; Laboratory of Intelligent Computation, School of Computer Science, Nanjing Normal University, Nanjing 210046, China
| | - Jiao Xu
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China.
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24
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Lim DH, Lee S, Han JY, Choi MS, Hong JS, Seong Y, Kwon YS, Lee YS. Ecdysone-responsive microRNA-252-5p controls the cell cycle by targeting Abi in Drosophila. FASEB J 2018. [PMID: 29543534 DOI: 10.1096/fj.201701185rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The steroid hormone ecdysone has a central role in the developmental transitions of insects through its control of responsive protein-coding and microRNA (miRNA) gene expression. However, the complete regulatory network controlling the expression of these genes remains to be elucidated. In this study, we performed cross-linking immunoprecipitation coupled with deep sequencing of endogenous Argonaute 1 (Ago1) protein, the core effector of the miRNA pathway, in Drosophila S2 cells. We found that regulatory interactions between miRNAs and their cognate targets were substantially altered by Ago1 in response to ecdysone signaling. Additionally, during the larva-to-adult metamorphosis, miR-252-5p was up-regulated via the canonical ecdysone-signaling pathway. Moreover, we provide evidence that miR-252-5p targets Abelson interacting protein ( Abi) to decrease the protein levels of cyclins A and B, controlling the cell cycle. Overall, our data suggest a potential role for the ecdysone/miR-252-5p/Abi regulatory axis partly in cell-cycle control during metamorphosis in Drosophila.-Lim, D.-H., Lee, S., Han, J. Y., Choi, M.-S., Hong, J.-S., Seong, Y., Kwon, Y.-S., Lee, Y. S. Ecdysone-responsive microR-252-5p controls the cell cycle by targeting Abi in Drosophila.
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Affiliation(s)
- Do-Hwan Lim
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Seungjae Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Jee Yun Han
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Min-Seok Choi
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Jae-Sang Hong
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
| | - Youngmo Seong
- Department of Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - Young-Soo Kwon
- Department of Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - Young Sik Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.,Institute of Animal Molecular Biotechnology, Korea University, Seoul, South Korea
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25
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Korneev SA, Vavoulis DV, Naskar S, Dyakonova VE, Kemenes I, Kemenes G. A CREB2-targeting microRNA is required for long-term memory after single-trial learning. Sci Rep 2018; 8:3950. [PMID: 29500383 PMCID: PMC5834643 DOI: 10.1038/s41598-018-22278-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/12/2018] [Indexed: 02/01/2023] Open
Abstract
Although single-trial induced long-term memories (LTM) have been of major interest in neuroscience, how LTM can form after a single episode of learning remains largely unknown. We hypothesized that the removal of molecular inhibitory constraints by microRNAs (miRNAs) plays an important role in this process. To test this hypothesis, first we constructed small non-coding RNA (sncRNA) cDNA libraries from the CNS of Lymnaea stagnalis subjected to a single conditioning trial. Then, by next generation sequencing of these libraries, we identified a specific pool of miRNAs regulated by training. Of these miRNAs, we focussed on Lym-miR-137 whose seed region shows perfect complementarity to a target sequence in the 3' UTR of the mRNA for CREB2, a well-known memory repressor. We found that Lym-miR-137 was transiently up-regulated 1 h after single-trial conditioning, preceding a down-regulation of Lym-CREB2 mRNA. Furthermore, we discovered that Lym-miR-137 is co-expressed with Lym-CREB2 mRNA in an identified neuron with an established role in LTM. Finally, using an in vivo loss-of-function approach we demonstrated that Lym-miR-137 is required for single-trial induced LTM.
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Affiliation(s)
- Sergei A Korneev
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.
| | - Dimitris V Vavoulis
- RDM Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Clifton, BS8 1UB, UK
| | - Souvik Naskar
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Varvara E Dyakonova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Ildikó Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - György Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
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26
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Anti-Aβ single-chain variable fragment antibodies restore memory acquisition in a Drosophila model of Alzheimer's disease. Sci Rep 2017; 7:11268. [PMID: 28900185 PMCID: PMC5595865 DOI: 10.1038/s41598-017-11594-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/25/2017] [Indexed: 11/23/2022] Open
Abstract
Alzheimer’s disease (AD) is a prevalent neurodegenerative disorder triggered by the accumulation of soluble assemblies of the amyloid-β42 (Aβ42) peptide. Despite remarkable advances in understanding the pathogenesis of AD, the development of palliative therapies is still lacking. Engineered anti-Aβ42 antibodies are a promising strategy to stall the progression of the disease. Single-chain variable fragment (scFv) antibodies increase brain penetration and offer flexible options for delivery while maintaining the epitope targeting of full antibodies. Here, we examined the ability of two anti-Aβ scFv antibodies targeting the N-terminal (scFv9) and C-terminal (scFv42.2) regions of Aβ42 to suppress the progressive memory decline induced by extracellular deposition of Aβ42 in Drosophila. Using olfactory classical conditioning, we observe that both scFv antibodies significantly improve memory performance in flies expressing Aβ42 in the mushroom body neurons, which are intimately involved in the coding and storage of olfactory memories. The scFvs effectively restore memory at all ages, from one-day post-eclosion to thirty-day-old flies, proving their ability to prevent the toxicity of different pathogenic assemblies. These data support the application of this paradigm of Aβ42-induced memory loss in Drosophila to investigate the protective activity of Aβ42–binding agents in an AD-relevant functional assay.
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27
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Saldaña MA, Etebari K, Hart CE, Widen SG, Wood TG, Thangamani S, Asgari S, Hughes GL. Zika virus alters the microRNA expression profile and elicits an RNAi response in Aedes aegypti mosquitoes. PLoS Negl Trop Dis 2017; 11:e0005760. [PMID: 28715413 PMCID: PMC5531668 DOI: 10.1371/journal.pntd.0005760] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/27/2017] [Accepted: 06/29/2017] [Indexed: 01/18/2023] Open
Abstract
Zika virus (ZIKV), a flavivirus transmitted primarily by Aedes aegypti, has recently spread globally in an unprecedented fashion, yet we have a poor understanding of host-microbe interactions in this system. To gain insights into the interplay between ZIKV and the mosquito, we sequenced the small RNA profiles in ZIKV-infected and non-infected Ae. aegypti mosquitoes at 2, 7 and 14 days post-infection. ZIKA induced an RNAi response in the mosquito with virus-derived short interfering RNAs and PIWI-interacting RNAs dramatically increased in abundance post-infection. Further, we found 17 host microRNAs (miRNAs) that were modulated by ZIKV infection at all time points. Strikingly, many of these regulated miRNAs have been reported to have their expression altered by dengue and West Nile viruses, while the response was divergent from that induced by the alphavirus Chikungunya virus in mosquitoes. This suggests that conserved miRNA responses occur within mosquitoes in response to flavivirus infection. This study expands our understanding of ZIKV-vector interactions and provides potential avenues to be further investigated to target ZIKV in the mosquito host.
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Affiliation(s)
- Miguel A. Saldaña
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Kayvan Etebari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Charles E. Hart
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Steven G. Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Thomas G. Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Saravanan Thangamani
- Department of Pathology, Institute for Human Infections and Immunity, Center for Tropical Diseases, Center for Biodefense and Emerging Infectious Disease. University of Texas Medical Branch, Galveston, TX, United States of America
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
- * E-mail: (SA); (GLH)
| | - Grant L. Hughes
- Department of Pathology, Institute for Human Infections and Immunity, Center for Tropical Diseases, Center for Biodefense and Emerging Infectious Disease. University of Texas Medical Branch, Galveston, TX, United States of America
- * E-mail: (SA); (GLH)
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Raab-Graham KF, Niere F. mTOR referees memory and disease through mRNA repression and competition. FEBS Lett 2017; 591:1540-1554. [PMID: 28493559 DOI: 10.1002/1873-3468.12675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/11/2022]
Abstract
Mammalian target of rapamycin (mTOR) activity is required for memory and is dysregulated in disease. Activation of mTOR promotes protein synthesis; however, new studies are demonstrating that mTOR activity also represses the translation of mRNAs. Almost three decades ago, Kandel and colleagues hypothesised that memory was due to the induction of positive regulators and removal of negative constraints. Are these negative constraints repressed mRNAs that code for proteins that block memory formation? Herein, we will discuss the mRNAs coded by putative memory suppressors, how activation/inactivation of mTOR repress protein expression at the synapse, how mTOR activity regulates RNA binding proteins, mRNA stability, and translation, and what the possible implications of mRNA repression are to memory and neurodegenerative disorders.
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Affiliation(s)
- Kimberly F Raab-Graham
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Farr Niere
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston Salem, NC, USA
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Pervasive Behavioral Effects of MicroRNA Regulation in Drosophila. Genetics 2017; 206:1535-1548. [PMID: 28468905 PMCID: PMC5500149 DOI: 10.1534/genetics.116.195776] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/23/2017] [Indexed: 11/18/2022] Open
Abstract
Picao-Osorio et al. reveal pervasive effects of microRNA regulation on complex locomotor behaviors in Drosophila larvae: over 40% of microRNAs display... The effects of microRNA (miRNA) regulation on the genetic programs underlying behavior remain largely unexplored. Despite this, recent work in Drosophila shows that mutation of a single miRNA locus (miR-iab4/iab8) affects the capacity of the larva to correct its orientation if turned upside down (self-righting, SR), suggesting that other miRNAs might also be involved in behavioral control. Here we explore this possibility, studying early larval SR behavior in a collection of 81 Drosophila miRNA mutants covering almost the entire miRNA complement of the late embryo. Unexpectedly, we observe that >40% of all miRNAs tested significantly affect SR time, revealing pervasive behavioral effects of miRNA regulation in the early larva. Detailed analyses of those miRNAs affecting SR behavior (SR-miRNAs) show that individual miRNAs can affect movement in different ways, suggesting that specific molecular and cellular elements are affected by individual miRNA mutations. Furthermore, gene expression analysis shows that the Hox gene Abdominal-B (Abd-B) represents one of the targets deregulated by several SR-miRNAs. Our work thus reveals pervasive effects of miRNA regulation on a complex innate behavior in Drosophila and suggests that miRNAs may be core components of the genetic programs underlying behavioral control in other animals too.
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Nadim WD, Simion V, Bénédetti H, Pichon C, Baril P, Morisset-Lopez S. MicroRNAs in Neurocognitive Dysfunctions: New Molecular Targets for Pharmacological Treatments? Curr Neuropharmacol 2017; 15:260-275. [PMID: 27396304 PMCID: PMC5412695 DOI: 10.2174/1570159x14666160709001441] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/31/2016] [Accepted: 07/01/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Neurodegenerative and cognitive disorders are multifactorial diseases (i.e., involving neurodevelopmental, genetic, age or environmental factors) characterized by an abnormal development that affects neuronal function and integrity. Recently, an increasing number of studies revealed that the dysregulation of microRNAs (miRNAs) may be involved in the etiology of cognitive disorders as Alzheimer, Parkinson, and Huntington's diseases, Schizophrenia and Autism spectrum disorders. METHODS From an extensive search in bibliographic databases of peer-reviewed research literature, we identified relevant published studies related to specific key words such as memory, cognition, neurodegenerative disorders, neurogenesis and miRNA. We then analysed, evaluated and summerized scientific evidences derived from these studies. RESULTS We first briefly summarize the basic molecular events involved in memory, a process inherent to cognitive disease, and then describe the role of miRNAs in neurodevelopment, synaptic plasticity and memory. Secondly, we provide an overview of the impact of miRNA dysregulation in the pathogenesis of different neurocognitive disorders, and lastly discuss the feasibility of miRNA-based therapeutics in the treatment of these disorders. CONCLUSION This review highlights the molecular basis of neurodegenerative and cognitive disorders by focusing on the impact of miRNAs dysregulation in these pathological phenotypes. Altogether, the published reports suggest that miRNAs-based therapy could be a viable therapeutic alternative to current treatment options in the future.
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Affiliation(s)
- Wissem Deraredj Nadim
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Viorel Simion
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Hélène Bénédetti
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Patrick Baril
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
| | - Séverine Morisset-Lopez
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d’Orléans France, 45071 Orléans Cedex, France
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Busto GU, Guven-Ozkan T, Davis RL. MicroRNA function in Drosophila memory formation. Curr Opin Neurobiol 2016; 43:15-24. [PMID: 27837663 DOI: 10.1016/j.conb.2016.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/19/2016] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRs) are small non-coding RNAs that regulate protein expression through post-transcriptional mechanisms. They participate in broad aspects of biology from the control of developmental processes to tumorigenesis. Recent studies in Drosophila show that they also regulate activity-dependent and sensory-specific protein expression and support olfactory memory formation. Among the hundreds of miRs described, several have been demonstrated to be required for normal learning, memory, or for the development of neuronal circuits that support memory formation. Fly models of human diseases offer promise of identifying miRs whose expression becomes dysregulated and part of the pathological state, providing models for understanding brain disorders and drug discovery.
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Affiliation(s)
- Germain U Busto
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Tugba Guven-Ozkan
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Ronald L Davis
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA.
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Busto GU, Guven-Ozkan T, Chakraborty M, Davis RL. Developmental inhibition of miR-iab8-3p disrupts mushroom body neuron structure and adult learning ability. Dev Biol 2016; 419:237-249. [PMID: 27634569 PMCID: PMC5204246 DOI: 10.1016/j.ydbio.2016.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/08/2016] [Accepted: 09/10/2016] [Indexed: 01/15/2023]
Abstract
MicroRNAs are small non-coding RNAs that inhibit protein expression post-transcriptionally. They have been implicated in many different physiological processes, but little is known about their individual involvement in learning and memory. We recently identified several miRNAs that either increased or decreased intermediate-term memory when inhibited in the central nervous system, including miR-iab8-3p. We report here a new developmental role for this miRNA. Blocking the expression of miR-iab8-3p during the development of the organism leads to hypertrophy of individual mushroom body neuron soma, a reduction in the field size occupied by axonal projections, and adult intellectual disability. We further identified four potential mRNA targets of miR-iab8-3p whose inhibition modulates intermediate-term memory including ceramide phosphoethanolamine synthase, which may account for the behavioral effects produced by miR-iab8-3p inhibition. Our results offer important new information on a microRNA required for normal neurodevelopment and the capacity to learn and remember normally.
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Affiliation(s)
- Germain U Busto
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter FL 33458, USA.
| | - Tugba Guven-Ozkan
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter FL 33458, USA
| | - Molee Chakraborty
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter FL 33458, USA
| | - Ronald L Davis
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter FL 33458, USA.
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Roberts AC, Pearce KC, Choe RC, Alzagatiti JB, Yeung AK, Bill BR, Glanzman DL. Long-term habituation of the C-start escape response in zebrafish larvae. Neurobiol Learn Mem 2016; 134 Pt B:360-8. [PMID: 27555232 DOI: 10.1016/j.nlm.2016.08.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/10/2016] [Accepted: 08/18/2016] [Indexed: 01/01/2023]
Abstract
The cellular and molecular basis of long-term memory in vertebrates remains poorly understood. Knowledge regarding long-term memory has been impeded by the enormous complexity of the vertebrate brain, particularly the mammalian brain, as well as by the relative complexity of the behavioral alterations examined in most studies of long-term memory in vertebrates. Here, we demonstrate a long-term form of nonassociative learning-specifically, long-term habituation (LTH)-of a simple reflexive escape response, the C-start, in zebrafish larvae. The C-start is triggered by the activation of one of a pair of giant neurons in the zebrafish's hindbrain, the Mauthner cells. We show that LTH of the C-start requires the activity of NMDA receptors and involves macromolecular synthesis. We further show that the long-term habituated reflex can by rapidly dishabituated by a brief tactile stimulus. Our results set the stage for rigorous, mechanistic investigations of the long-term memory for habituation of a reflexive behavioral response, one that is mediated by a relatively simple, neurobiologically tractable, neural circuit. Moreover, the demonstration of NMDAR and transcriptionally dependent LTH in a translucent vertebrate organism should facilitate the use of optical recording, and optogenetic manipulation, of neuronal activity to elucidate the cellular basis of a long-term vertebrate memory.
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Affiliation(s)
- Adam C Roberts
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, United States
| | - Kaycey C Pearce
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, United States
| | - Ronny C Choe
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, United States
| | - Joseph B Alzagatiti
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, United States
| | - Anthony K Yeung
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, United States
| | - Brent R Bill
- Center for Autism Research and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior at UCLA, Los Angeles, CA, United States; Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States; Department of Biology, University of Texas at Tyler, Tyler, TX, United States
| | - David L Glanzman
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, United States; Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States; Integrative Center for Learning and Memory, Brain Research Institute, University of California Los Angeles, Los Angeles, CA, United States.
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Gao YE, Wang Y, Chen FQ, Feng JY, Yang G, Feng GX, Yang Z, Ye LH, Zhang XD. Post-transcriptional modulation of protein phosphatase PPP2CA and tumor suppressor PTEN by endogenous siRNA cleaved from hairpin within PTEN mRNA 3'UTR in human liver cells. Acta Pharmacol Sin 2016; 37:898-907. [PMID: 27133296 PMCID: PMC4933753 DOI: 10.1038/aps.2016.18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/03/2016] [Indexed: 01/08/2023] Open
Abstract
Aim: Increasing evidence shows that mRNAs exert regulatory function along with coding proteins. Recently we report that a hairpin within YAP mRNA 3′UTR can modulate the Hippo signaling pathway. PTEN is a tumor suppressor, and is mutated in human cancers. In this study we examined whether PTEN mRNA 3′UTR contained a hairpin structure that could regulate gene regulation at the post-transcriptional level. Methods: The secondary structure of PTEN mRNA 3′UTR was analyzed using RNAdraw and RNAstructure. Function of hairpin structure derived from the PTEN mRNA 3′UTR was examined using luciferase reporter assay, RT-PCR and Western blotting. RNA-immunoprecipitation (RIP) assay was used to analyze the interaction between PTEN mRNA and microprocessor Drosha and DGCR8. Endogenous siRNA (esiRNA) derived from PTEN mRNA 3′UTR was identified by RT-PCR and rt-PCR, and its target genes were predicted using RNAhybrid. Results: A bioinformatics analysis revealed that PTEN mRNA contained a hairpin structure (termed PTEN-sh) within 3′UTR, which markedly increased the reporter activities of AP-1 and NF-κB in 293T cells. Moreover, treatment with PTEN-sh (1 and 2 μg) dose-dependently inhibited the expression of PTEN in human liver L-O2 cells. RIP assay demonstrated that the microprocessor Drosha and DGCR8 was bound to PTEN-sh in L-O2 cells, leading to the cleavage of PTEN-sh from PTEN mRNA 3′UTR. In addition, microprocessor Dicer was involved in the processing of PTEN-sh. Interestingly, esiRNA (termed PTEN-sh-3p21) cleaved from PTEN-sh was identified in 293T cells and human liver tissues, which was found to target the mRNA 3′UTRs of protein phosphatase PPP2CA and PTEN in L-O2 cells. Treatment of L-O2 or Chang liver cells with PTEN-sh-3p21 (50, 100 nmol/L) promoted the cell proliferation in dose- and time-dependent manners. Conclusion: The endogenous siRNA (PTEN-sh-3p21) cleaved from PTEN-sh within PTEN mRNA 3′UTR modulates PPP2CA and PTEN at the post-transcriptional level in liver cells.
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Report on the 13th symposium on invertebrate neurobiology held 26-30 August 2015 at the Balaton Limnological Institute, MTA Centre for ecological research of the Hungarian Academy of Sciences, Tihany, Hungary. INVERTEBRATE NEUROSCIENCE 2016; 16:3. [PMID: 27149972 DOI: 10.1007/s10158-016-0186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This report summarizes the lectures and posters presented at the International Society for Invertebrate Neurobiology's 13th symposium held 26-30 August 2015, at the Balaton Limnological Institute, MTA Centre for Ecological Research, Tihany, Hungary. The symposium provided an opportunity for scientists working on a range of topics in invertebrate neurobiology to meet and present their research and discuss ways to advance the discipline.
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36
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Steinkraus BR, Toegel M, Fulga TA. Tiny giants of gene regulation: experimental strategies for microRNA functional studies. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2016; 5:311-62. [PMID: 26950183 PMCID: PMC4949569 DOI: 10.1002/wdev.223] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/19/2015] [Accepted: 11/28/2015] [Indexed: 12/11/2022]
Abstract
The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA-target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high-throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA-target binding events in vivo drove the emergence of a slew of high-throughput multiplex strategies, which now provide a viable prospect for elucidating genome-wide miRNA-target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post-transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high-precision interference with their direct, endogenous targets. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Bruno R Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Markus Toegel
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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Carthew RW, Agbu P, Giri R. MicroRNA function in Drosophila melanogaster. Semin Cell Dev Biol 2016; 65:29-37. [PMID: 27000418 DOI: 10.1016/j.semcdb.2016.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 12/19/2022]
Abstract
Over the last decade, microRNAs have emerged as critical regulators in the expression and function of animal genomes. This review article discusses the relationship between microRNA-mediated regulation and the biology of the fruit fly Drosophila melanogaster. We focus on the roles that microRNAs play in tissue growth, germ cell development, hormone action, and the development and activity of the central nervous system. We also discuss the ways in which microRNAs affect robustness. Many gene regulatory networks are robust; they are relatively insensitive to the precise values of reaction constants and concentrations of molecules acting within the networks. MicroRNAs involved in robustness appear to be nonessential under uniform conditions used in conventional laboratory experiments. However, the robust functions of microRNAs can be revealed when environmental or genetic variation otherwise has an impact on developmental outcomes.
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Affiliation(s)
- Richard W Carthew
- Department of Molecular Biosciences, Northwestern University Evanston, IL 60208, USA; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Chicago, IL 60611, USA.
| | - Pamela Agbu
- Department of Molecular Biosciences, Northwestern University Evanston, IL 60208, USA
| | - Ritika Giri
- Department of Molecular Biosciences, Northwestern University Evanston, IL 60208, USA
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Guven-Ozkan T, Busto GU, Schutte SS, Cervantes-Sandoval I, O'Dowd DK, Davis RL. MiR-980 Is a Memory Suppressor MicroRNA that Regulates the Autism-Susceptibility Gene A2bp1. Cell Rep 2016; 14:1698-1709. [PMID: 26876166 DOI: 10.1016/j.celrep.2016.01.040] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/26/2015] [Accepted: 01/09/2016] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs have been associated with many different biological functions, but little is known about their roles in conditioned behavior. We demonstrate that Drosophila miR-980 is a memory suppressor gene functioning in multiple regions of the adult brain. Memory acquisition and stability were both increased by miR-980 inhibition. Whole cell recordings and functional imaging experiments indicated that miR-980 regulates neuronal excitability. We identified the autism susceptibility gene, A2bp1, as an mRNA target for miR-980. A2bp1 levels varied inversely with miR-980 expression; memory performance was directly related to A2bp1 levels. In addition, A2bp1 knockdown reversed the memory gains produced by miR-980 inhibition, consistent with A2bp1 being a downstream target of miR-980 responsible for the memory phenotypes. Our results indicate that miR-980 represses A2bp1 expression to tune the excitable state of neurons, and the overall state of excitability translates to memory impairment or improvement.
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Affiliation(s)
- Tugba Guven-Ozkan
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Germain U Busto
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
| | - Soleil S Schutte
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Diane K O'Dowd
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA; Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Ronald L Davis
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA.
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