651
|
Ross JP, Kassir Z. The varied roles of nuclear argonaute-small RNA complexes and avenues for therapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e203. [PMID: 25313622 PMCID: PMC4217078 DOI: 10.1038/mtna.2014.54] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/22/2014] [Indexed: 12/14/2022]
Abstract
Argonautes are highly conserved proteins found in almost all eukaryotes and some bacteria and archaea. In humans, there are eight argonaute proteins evenly distributed across two clades, the Ago clade (AGO1-4) and the Piwi clade (PIWIL1-4). The function of Ago proteins is best characterized by their role in RNA interference (RNAi) and cytoplasmic post-transcriptional gene silencing (PTGS) – which involves the loading of siRNA or miRNA into argonaute to direct silencing of genes at the posttranscriptional or translational level. However, nuclear-localized, as opposed to cytoplasmic, argonaute-small RNA complexes may also orchestrate the mechanistically very different process of transcriptional gene silencing, which results in prevention of transcription from a gene locus by the formation of silent chromatin domains. More recently, the role of argonaute in other aspects of epigenetic regulation of chromatin, alternative splicing and DNA repair is emerging. This review focuses on the activity of nuclear-localized short RNA-argonaute complexes in a mammalian setting and discusses recent in vivo studies employing nuclear-directed sRNA for therapeutic interventions. These studies heed the potential development of RNA-based drugs which induce epigenetic changes in the cell.
Collapse
Affiliation(s)
- Jason P Ross
- CSIRO Food and Nutrition Flagship, Sydney, New South Wales, Australia
| | - Zena Kassir
- 1] CSIRO Food and Nutrition Flagship, Sydney, New South Wales, Australia [2] Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| |
Collapse
|
652
|
Hisanaga T, Miyashima S, Nakajima K. Small RNAs as positional signal for pattern formation. CURRENT OPINION IN PLANT BIOLOGY 2014; 21:37-42. [PMID: 25005923 DOI: 10.1016/j.pbi.2014.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/12/2014] [Accepted: 06/13/2014] [Indexed: 06/03/2023]
Abstract
Pattern formation in plant relies on intimate cell-cell communication exchanging positional information. While ligand-receptor interaction is commonly used by plants and animals as a means to transmit positional information, plant cells can directly exchange regulatory molecules such as transcription factors through a cytoplasmic continuum called the plasmodesmata. Recently endogenous small RNAs (sRNAs) of various biogenetic origins have been shown to function non-cell-autonomously. To date, non-cell-autonomous sRNAs have been shown to regulate leaf polarity, root vascular patterning, meristem formation in embryos, shoot meristem maintenance and female gametogenesis. All these developmental processes are fundamental to the life cycle and architecture of flowering plants, suggesting that sRNA-mediated cell-to-cell signaling has been adopted to achieve novel morphology in the course of plant evolution.
Collapse
Affiliation(s)
- Tetsuya Hisanaga
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shunsuke Miyashima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Keiji Nakajima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan.
| |
Collapse
|
653
|
Hauptmann J, Kater L, Löffler P, Merkl R, Meister G. Generation of catalytic human Ago4 identifies structural elements important for RNA cleavage. RNA (NEW YORK, N.Y.) 2014; 20:1532-1538. [PMID: 25114291 PMCID: PMC4174435 DOI: 10.1261/rna.045203.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/18/2014] [Indexed: 06/03/2023]
Abstract
Argonaute proteins bind small RNAs and mediate cleavage of complementary target RNAs. The human Argonaute protein Ago4 is catalytically inactive, although it is highly similar to catalytic Ago2. Here, we have generated Ago2-Ago4 chimeras and analyzed their cleavage activity in vitro. We identify several specific features that inactivate Ago4: the catalytic center, short sequence elements in the N-terminal domain, and an Ago4-specific insertion in the catalytic domain. In addition, we show that Ago2-mediated cleavage of the noncanonical miR-451 precursor can be carried out by any catalytic human Ago protein. Finally, phylogenetic analyses establish evolutionary distances between the Ago proteins. Interestingly, these distances do not fully correlate with the structural changes inactivating them, suggesting functional adaptations of individual human Ago proteins.
Collapse
Affiliation(s)
- Judith Hauptmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Lukas Kater
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Patrick Löffler
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| |
Collapse
|
654
|
Five children with deletions of 1p34.3 encompassing AGO1 and AGO3. Eur J Hum Genet 2014; 23:761-5. [PMID: 25271087 DOI: 10.1038/ejhg.2014.202] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/14/2014] [Accepted: 08/20/2014] [Indexed: 01/06/2023] Open
Abstract
Small RNAs (miRNA, siRNA, and piRNA) regulate gene expression through targeted destruction or translational repression of specific messenger RNA in a fundamental biological process called RNA interference (RNAi). The Argonaute proteins, which derive from a highly conserved family of genes found in almost all eukaryotes, are critical mediators of this process. Four AGO genes are present in humans, three of which (AGO 1, 3, and 4) reside in a cluster on chromosome 1p35p34. The effects of germline AGO variants or dosage alterations in humans are not known, however, prior studies have implicated dysregulation of the RNAi mechanism in the pathogenesis of several neurodevelopmental disorders. We describe five patients with hypotonia, poor feeding, and developmental delay who were found to have microdeletions of chromosomal region 1p34.3 encompassing the AGO1 and AGO3 genes. We postulate that haploinsufficiency of AGO1 and AGO3 leading to impaired RNAi may be responsible for the neurocognitive deficits present in these patients. However, additional studies with rigorous phenotypic characterization of larger cohorts of affected individuals and systematic investigation of the underlying molecular defects will be necessary to confirm this.
Collapse
|
655
|
Co-option of the piRNA pathway for germline-specific alternative splicing of C. elegans TOR. Cell Rep 2014; 8:1609-1616. [PMID: 25220461 DOI: 10.1016/j.celrep.2014.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 07/02/2014] [Accepted: 08/07/2014] [Indexed: 12/12/2022] Open
Abstract
Many eukaryotic genes contain embedded antisense transcripts and repetitive sequences of unknown function. We report that male germline-specific expression of an antisense transcript contained in an intron of C. elegans Target of Rapamycin (TOR, let-363) is associated with (1) accumulation of endo-small interfering RNAs (siRNAs) against an embedded Helitron transposon and (2) activation of an alternative 3' splice site of TOR. The germline-specific Argonaute proteins PRG-1 and CSR-1, which participate in self/nonself RNA recognition, antagonistically regulate the generation of these endo-siRNAs, TOR mRNA levels, and 3' splice-site selection. Supply of exogenous double-stranded RNA against the region of sense/antisense overlap reverses changes in TOR expression and splicing and suppresses the progressive multigenerational sterility phenotype of prg-1 mutants. We propose that recognition of a "nonself" intronic transposon by endo-siRNAs/the piRNA system provides physiological regulation of expression and alternative splicing of a host gene that, in turn, contributes to the maintenance of germline function across generations.
Collapse
|
656
|
Yang M, Haase AD, Huang FK, Coulis G, Rivera KD, Dickinson BC, Chang CJ, Pappin DJ, Neubert TA, Hannon GJ, Boivin B, Tonks NK. Dephosphorylation of tyrosine 393 in argonaute 2 by protein tyrosine phosphatase 1B regulates gene silencing in oncogenic RAS-induced senescence. Mol Cell 2014; 55:782-90. [PMID: 25175024 PMCID: PMC4159145 DOI: 10.1016/j.molcel.2014.07.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/29/2014] [Accepted: 07/21/2014] [Indexed: 11/20/2022]
Abstract
Oncogenic RAS (H-RAS(V12)) induces premature senescence in primary cells by triggering production of reactive oxygen species (ROS), but the molecular role of ROS in senescence remains elusive. We investigated whether inhibition of protein tyrosine phosphatases by ROS contributed to H-RAS(V12)-induced senescence. We identified protein tyrosine phosphatase 1B (PTP1B) as a major target of H-RAS(V12)-induced ROS. Inactivation of PTP1B was necessary and sufficient to induce premature senescence in H-RAS(V12)-expressing IMR90 fibroblasts. We identified phospho-Tyr 393 of argonaute 2 (AGO2) as a direct substrate of PTP1B. Phosphorylation of AGO2 at Tyr 393 inhibited loading with microRNAs (miRNAs) and thus miRNA-mediated gene silencing, which counteracted the function of H-RAS(V12)-induced oncogenic miRNAs. Overall, our data illustrate that premature senescence in H-RAS(V12)-transformed primary cells is a consequence of oxidative inactivation of PTP1B and inhibition of miRNA-mediated gene silencing.
Collapse
Affiliation(s)
- Ming Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11790, USA
| | - Astrid D Haase
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute
| | - Fang-Ke Huang
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Langone School of Medicine, New York, NY 10016, USA
| | - Gérald Coulis
- Department of Biochemistry and Department of Medicine, Université de Montréal, Montréal, H3C 3J7 QC, Canada; Montreal Heart Institute, Montréal, H1T 1C8 QC, Canada
| | - Keith D Rivera
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bryan C Dickinson
- Howard Hughes Medical Institute; Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher J Chang
- Howard Hughes Medical Institute; Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Darryl J Pappin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Thomas A Neubert
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Langone School of Medicine, New York, NY 10016, USA
| | - Gregory J Hannon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute
| | - Benoit Boivin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Biochemistry and Department of Medicine, Université de Montréal, Montréal, H3C 3J7 QC, Canada; Montreal Heart Institute, Montréal, H1T 1C8 QC, Canada.
| | - Nicholas K Tonks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
657
|
Role of miRNA let-7 and its major targets in prostate cancer. BIOMED RESEARCH INTERNATIONAL 2014; 2014:376326. [PMID: 25276782 PMCID: PMC4168040 DOI: 10.1155/2014/376326] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/11/2014] [Accepted: 08/18/2014] [Indexed: 12/21/2022]
Abstract
Prostate cancer is worldwide the sixth leading cause of cancer related death in men thus early detection and successful treatment are still of major interest. The commonly performed screening of the prostate-specific antigen (PSA) is controversially discussed, as in many patients the prostate-specific antigen levels are chronically elevated in the absence of cancer. Due to the unsatisfying efficiency of available prostate cancer screening markers and the current treatment outcome of the aggressive hormone refractory prostate cancer, the evaluation of novel molecular markers and targets is considered an issue of high importance. MicroRNAs are relatively stable in body fluids orchestrating simultaneously the expression of many genes. These molecules are currently discussed to bear a greater diagnostic potential than protein-coding genes, being additionally promising therapeutic drugs and/or targets. Herein we review the potential impact of the microRNA let-7 family on prostate cancer and show how deregulation of several of its target genes could influence the cellular equilibrium in the prostate gland, promoting cancer development as they do in a variety of other human malignant neoplasias.
Collapse
|
658
|
Non-coding RNA regulation of synaptic plasticity and memory: implications for aging. Ageing Res Rev 2014; 17:34-42. [PMID: 24681292 DOI: 10.1016/j.arr.2014.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 12/31/2022]
Abstract
Advancing age is associated with the loss of cognitive ability and vulnerability to debilitating mental diseases. Although much is known about the development of cognitive processes in the brain, the study of the molecular mechanisms governing memory decline with aging is still in its infancy. Recently, it has become apparent that most of the human genome is transcribed into non-coding RNAs (ncRNAs) rather than protein-coding mRNAs. Multiple types of ncRNAs are enriched in the central nervous system, and this large group of molecules may regulate the molecular complexity of the brain, its neurons, and synapses. Here, we review the current knowledge on the role of ncRNAs in synaptic plasticity, learning, and memory in the broader context of the aging brain and associated memory loss. We also discuss future directions to study the role of ncRNAs in the aging process.
Collapse
|
659
|
Import routes and nuclear functions of Argonaute and other small RNA-silencing proteins. Trends Biochem Sci 2014; 39:420-31. [DOI: 10.1016/j.tibs.2014.07.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 02/06/2023]
|
660
|
Masciarelli S, Quaranta R, Iosue I, Colotti G, Padula F, Varchi G, Fazi F, Del Rio A. A small-molecule targeting the microRNA binding domain of argonaute 2 improves the retinoic acid differentiation response of the acute promyelocytic leukemia cell line NB4. ACS Chem Biol 2014; 9:1674-9. [PMID: 24914804 DOI: 10.1021/cb500286b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Argonaute proteins are pivotal regulators of gene expression mediating miRNAs function. Modulating their activity would be extremely useful to elucidate the processes governing small-RNAs-guided gene silencing. We report the identification of a chemical compound able to compete with Argonaute 2 miRNAs binding, and we demonstrate that this functional inhibition determines effects similar to Argonaute 2 shRNA-mediated down-regulation, favoring granulocytic differentiation of the acute promyelocytic leukemia cell line NB4 in response to retinoic acid.
Collapse
Affiliation(s)
| | | | | | | | | | - Greta Varchi
- CNR-National
Research
Council of Italy, Institute for Organic Chemistry and Photoreactivity, 40129 Bologna, Italy
| | | | - Alberto Del Rio
- CNR-National
Research
Council of Italy, Institute for Organic Chemistry and Photoreactivity, 40129 Bologna, Italy
- Department
of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| |
Collapse
|
661
|
Weidmann CA, Raynard NA, Blewett NH, Van Etten J, Goldstrohm AC. The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation. RNA (NEW YORK, N.Y.) 2014; 20:1298-319. [PMID: 24942623 PMCID: PMC4105754 DOI: 10.1261/rna.046029.114] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/20/2014] [Indexed: 05/24/2023]
Abstract
PUF proteins are potent repressors that serve important roles in stem cell maintenance, neurological processes, and embryonic development. These functions are driven by PUF protein recognition of specific binding sites within the 3' untranslated regions of target mRNAs. In this study, we investigated mechanisms of repression by the founding PUF, Drosophila Pumilio, and its human orthologs. Here, we evaluated a previously proposed model wherein the Pumilio RNA binding domain (RBD) binds Argonaute, which in turn blocks the translational activity of the eukaryotic elongation factor 1A. Surprisingly, we found that Argonautes are not necessary for repression elicited by Drosophila and human PUFs in vivo. A second model proposed that the RBD of Pumilio represses by recruiting deadenylases to shorten the mRNA's polyadenosine tail. Indeed, the RBD binds to the Pop2 deadenylase and accelerates deadenylation; however, this activity is not crucial for regulation. Rather, we determined that the poly(A) is necessary for repression by the RBD. Our results reveal that poly(A)-dependent repression by the RBD requires the poly(A) binding protein, pAbp. Furthermore, we show that repression by the human PUM2 RBD requires the pAbp ortholog, PABPC1. Pumilio associates with pAbp but does not disrupt binding of pAbp to the mRNA. Taken together, our data support a model wherein the Pumilio RBD antagonizes the ability of pAbp to promote translation. Thus, the conserved function of the PUF RBD is to bind specific mRNAs, antagonize pAbp function, and promote deadenylation.
Collapse
Affiliation(s)
- Chase A Weidmann
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Genetics Training Program, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Nathan A Raynard
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Genetics Training Program, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Nathan H Blewett
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Jamie Van Etten
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Aaron C Goldstrohm
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Genetics Training Program, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| |
Collapse
|
662
|
Mohammed J, Bortolamiol-Becet D, Flynt AS, Gronau I, Siepel A, Lai EC. Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila. RNA (NEW YORK, N.Y.) 2014; 20:1195-209. [PMID: 24942624 PMCID: PMC4105746 DOI: 10.1261/rna.044644.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/11/2014] [Indexed: 05/09/2023]
Abstract
The propensity of animal miRNAs to regulate targets bearing modest complementarity, most notably via pairing with miRNA positions ∼2-8 (the "seed"), is believed to drive major aspects of miRNA evolution. First, minimal targeting requirements have allowed most conserved miRNAs to acquire large target cohorts, thus imposing strong selection on miRNAs to maintain their seed sequences. Second, the modest pairing needed for repression suggests that evolutionarily nascent miRNAs may generally induce net detrimental, rather than beneficial, regulatory effects. Hence, levels and activities of newly emerged miRNAs are expected to be limited to preserve the status quo of gene expression. In this study, we unexpectedly show that Drosophila testes specifically express a substantial miRNA population that contravenes these tenets. We find that multiple genomic clusters of testis-restricted miRNAs harbor recently evolved miRNAs, whose experimentally verified orthologs exhibit divergent sequences, even within seed regions. Moreover, this class of miRNAs exhibits higher expression and greater phenotypic capacities in transgenic misexpression assays than do non-testis-restricted miRNAs of similar evolutionary age. These observations suggest that these testis-restricted miRNAs may be evolving adaptively, and several methods of evolutionary analysis provide strong support for this notion. Consistent with this, proof-of-principle tests show that orthologous miRNAs with divergent seeds can distinguish target sensors in a species-cognate manner. Finally, we observe that testis-restricted miRNA clusters exhibit extraordinary dynamics of miRNA gene flux in other Drosophila species. Altogether, our findings reveal a surprising tissue-directed influence of miRNA evolution, involving a distinct mode of miRNA function connected to adaptive gene regulation in the testis.
Collapse
Affiliation(s)
- Jaaved Mohammed
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
| | - Diane Bortolamiol-Becet
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Alex S Flynt
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Ilan Gronau
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| |
Collapse
|
663
|
Fukuoka M, Yoshida M, Eda A, Takahashi M, Hohjoh H. Gene silencing mediated by endogenous microRNAs under heat stress conditions in mammalian cells. PLoS One 2014; 9:e103130. [PMID: 25068899 PMCID: PMC4113354 DOI: 10.1371/journal.pone.0103130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/27/2014] [Indexed: 12/21/2022] Open
Abstract
Heat shock, sudden change in temperature, triggers various responses in cells for protecting the cells from such a severe circumstance. Here we investigated gene silencing mediated by endogenous microRNAs (miRNAs) in mammalian cells exposed to a mild hyperthermia, by means of miRNA activity assay using a luciferase reporter gene as well as miRNA expression analysis using a DNA microarray. Our findings indicated that the gene silencing activities involving miRNAs were enhanced without increasing in their expression levels under heat-stress conditions. Additionally, the gene silencing activity appeared to be independent of the cytoprotective action involving heat shock proteins that are immediately activated in heat-shocked cells and that function as molecular chaperons for restoring heat-denatured proteins to normal proteins. Our current findings suggested the possibility that gene silencing involving endogenous miRNAs might play a subsidiary role in heat-shocked cells for an aggressive inhibition of the expression of heat-denatured proteins.
Collapse
Affiliation(s)
- Masashi Fukuoka
- Department of Molecular Pharmacology, National Institute of Neuroscience, NCNP, Kodaira, Tokyo, Japan
| | - Mariko Yoshida
- Department of Molecular Pharmacology, National Institute of Neuroscience, NCNP, Kodaira, Tokyo, Japan
| | - Akiko Eda
- Department of Molecular Pharmacology, National Institute of Neuroscience, NCNP, Kodaira, Tokyo, Japan
| | - Masaki Takahashi
- Department of Molecular Pharmacology, National Institute of Neuroscience, NCNP, Kodaira, Tokyo, Japan
| | - Hirohiko Hohjoh
- Department of Molecular Pharmacology, National Institute of Neuroscience, NCNP, Kodaira, Tokyo, Japan
- * E-mail:
| |
Collapse
|
664
|
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function as guide molecules in RNA silencing. Targeting most protein-coding transcripts, miRNAs are involved in nearly all developmental and pathological processes in animals. The biogenesis of miRNAs is under tight temporal and spatial control, and their dysregulation is associated with many human diseases, particularly cancer. In animals, miRNAs are ∼22 nucleotides in length, and they are produced by two RNase III proteins--Drosha and Dicer. miRNA biogenesis is regulated at multiple levels, including at the level of miRNA transcription; its processing by Drosha and Dicer in the nucleus and cytoplasm, respectively; its modification by RNA editing, RNA methylation, uridylation and adenylation; Argonaute loading; and RNA decay. Non-canonical pathways for miRNA biogenesis, including those that are independent of Drosha or Dicer, are also emerging.
Collapse
|
665
|
Designing Ago2-specific siRNA/shRNA to Avoid Competition with Endogenous miRNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e176. [PMID: 25025466 PMCID: PMC4121517 DOI: 10.1038/mtna.2014.27] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 05/23/2014] [Indexed: 12/22/2022]
Abstract
Relatively large amounts of transfected siRNA can compete for Ago proteins and thus compromise endogenous miRNA function, potentially leading to toxicities. Here, we show that shRNA can also perturb endogenous miRNA function similarly. More importantly, we also show that the problem can be solved by designing shRNAs in the context of pre-miR-451 structure with completely complementary stem, which significantly improves the Ago2 specificity. This shRNA was shown to be Ago2-specific, and maintain target-silencing ability while avoiding competition with endogenous miRNAs by not competing for Agos 1, 3, and 4. We conclude that modified pre-miR-451 structure provides a general platform to design shRNAs that significantly reduce perturbation of miRNA function.
Collapse
|
666
|
Chang RCA, Ying W, Bazer FW, Zhou B. MicroRNAs Control Macrophage Formation and Activation: The Inflammatory Link between Obesity and Cardiovascular Diseases. Cells 2014; 3:702-12. [PMID: 25014161 PMCID: PMC4197627 DOI: 10.3390/cells3030702] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 12/16/2022] Open
Abstract
Activation and recruitment of resident macrophages in tissues in response to physiological stress are crucial regulatory processes in promoting the development of obesity-associated metabolic disorders and cardiovascular diseases. Recent studies have provided compelling evidence that microRNAs play important roles in modulating monocyte formation, macrophage maturation, infiltration into tissues and activation. Macrophage-dependent systemic physiological and tissue-specific responses also involve cell-cell interactions between macrophages and host tissue niche cell components, including other tissue-resident immune cell lineages, adipocytes, vascular smooth muscle and others. In this review, we highlight the roles of microRNAs in regulating the development and function of macrophages in the context of obesity, which could provide insights into the pathogenesis of obesity-related metabolic syndrome and cardiovascular diseases.
Collapse
Affiliation(s)
- Richard Cheng-An Chang
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Wei Ying
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
| | - Fuller W Bazer
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
| | - Beiyan Zhou
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
667
|
Reeves ME, Firek M, Chen ST, Amaar YG. Evidence that RASSF1C stimulation of lung cancer cell proliferation depends on IGFBP-5 and PIWIL1 expression levels. PLoS One 2014; 9:e101679. [PMID: 25007054 PMCID: PMC4090148 DOI: 10.1371/journal.pone.0101679] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 06/11/2014] [Indexed: 12/24/2022] Open
Abstract
RASSF1C is a major isoform of the RASSF1 gene, and is emerging as an oncogene. This is in contradistinction to the RASSF1A isoform, which is an established tumor suppressor. We have previously shown that RASSF1C promotes lung cancer cell proliferation and have identified RASSF1C target genes with growth promoting functions. Here, we further report that RASSF1C promotes lung cancer cell migration and enhances lung cancer cell tumor sphere formation. We also show that RASSF1C over-expression reduces the inhibitory effects of the anti-cancer agent, betulinic acid (BA), on lung cancer cell proliferation. In previous work, we demonstrated that RASSF1C up-regulates piwil1 gene expression, which is a stem cell self-renewal gene that is over-expressed in several human cancers, including lung cancer. Here, we report on the effects of BA on piwil1 gene expression. Cells treated with BA show decreased piwil1 expression. Also, interaction of IGFBP-5 with RASSF1C appears to prevent RASSF1C from up-regulating PIWIL1 protein levels. These findings suggest that IGFBP-5 may be a negative modulator of RASSF1C/ PIWIL1 growth-promoting activities. In addition, we found that inhibition of the ATM-AMPK pathway up-regulates RASSF1C gene expression.
Collapse
Affiliation(s)
- Mark E. Reeves
- Surgical Oncology Laboratory, Loma Linda VA Medical Center, Loma Linda, California, United States of America
- Department of Surgery, Loma Linda University School of Medicine, Loma Linda, California, United States of America
| | - Matthew Firek
- Surgical Oncology Laboratory, Loma Linda VA Medical Center, Loma Linda, California, United States of America
| | - Shin-Tai Chen
- Musculoskeletal Disease Center, Loma Linda VA Medical Center, Loma Linda, California, United States of America
| | - Yousef G. Amaar
- Surgical Oncology Laboratory, Loma Linda VA Medical Center, Loma Linda, California, United States of America
- Department of Surgery, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- * E-mail:
| |
Collapse
|
668
|
Micol-Ponce R, Aguilera V, Ponce MR. A genetic screen for suppressors of a hypomorphic allele of Arabidopsis ARGONAUTE1. Sci Rep 2014; 4:5533. [PMID: 24985352 PMCID: PMC4078309 DOI: 10.1038/srep05533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/13/2014] [Indexed: 12/28/2022] Open
Abstract
ARGONAUTE1 (AGO1) encodes a key component of the complexes mediating microRNA (miRNA) function in Arabidopsis. To study the regulation, action and interactions of AGO1, we conducted a genetic screen to identify second-site mutations modifying the morphological phenotype of ago1-52, a partial loss-of-function allele of AGO1. Unlike null ago1 mutations, the hypomorphic ago1-52 allele does not cause lethality or sterility; however, ago1-52 does produce a morphological phenotype clearly distinct from wild type. In our screen for modifiers of ago1-52, we identified suppressor mutations that partially restore wild-type morphology in the ago1-52 background and we termed these mas (morphology of argonaute1-52 suppressed). We focused on 23 of these putative suppressors. Linkage analysis of the mas mutations together with sequencing of the AGO1 gene in genomic DNA and cDNA from ago1-52 mas plants indicated that 22 of the mas lines contain extragenic suppressors, and one contains an intragenic suppressor that affects splicing of ago1-52. In the presence of the wild-type allele of AGO1, most of the mas mutations cause a mild or no mutant phenotype on their own, indicating that the ago1-52 mutant may provide a sensitized background for examining the interactions of AGO1.
Collapse
Affiliation(s)
- Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
- These authors contributed equally to this work
| | - Verónica Aguilera
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
- These authors contributed equally to this work
- Current address: Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| |
Collapse
|
669
|
van Wolfswinkel JC. Piwi and Potency: PIWI Proteins in Animal Stem Cells and Regeneration. Integr Comp Biol 2014; 54:700-13. [DOI: 10.1093/icb/icu084] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
670
|
Uddin MN, Dunoyer P, Schott G, Akhter S, Shi C, Lucas WJ, Voinnet O, Kim JY. The protein kinase TOUSLED facilitates RNAi in Arabidopsis. Nucleic Acids Res 2014; 42:7971-80. [PMID: 24920830 PMCID: PMC4081062 DOI: 10.1093/nar/gku422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RNA silencing is an evolutionarily conserved mechanism triggered by double-stranded RNA that is processed into 21- to 24-nt small interfering (si)RNA or micro (mi)RNA by RNaseIII-like enzymes called Dicers. Gene regulations by RNA silencing have fundamental implications in a large number of biological processes that include antiviral defense, maintenance of genome integrity and the orchestration of cell fates. Although most generic or core components of the various plant small RNA pathways have been likely identified over the past 15 years, factors involved in RNAi regulation through post-translational modifications are just starting to emerge, mostly through forward genetic studies. A genetic screen designed to identify factors required for RNAi in Arabidopsis identified the serine/threonine protein kinase, TOUSLED (TSL). Mutations in TSL affect exogenous and virus-derived siRNA activity in a manner dependent upon its kinase activity. By contrast, despite their pleiotropic developmental phenotype, tsl mutants show no defect in biogenesis or activity of miRNA or endogenous trans-acting siRNA. These data suggest a possible role for TSL phosphorylation in the specific regulation of exogenous and antiviral RNA silencing in Arabidopsis and identify TSL as an intrinsic regulator of RNA interference.
Collapse
Affiliation(s)
- Mohammad Nazim Uddin
- Division of Applied Life Science (BK21+/WCU program), PMBBRC, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Patrice Dunoyer
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Gregory Schott
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Salina Akhter
- Division of Applied Life Science (BK21+/WCU program), PMBBRC, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - Chunlin Shi
- Division of Applied Life Science (BK21+/WCU program), PMBBRC, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| | - William J Lucas
- Division of Applied Life Science (BK21+/WCU program), PMBBRC, Graduate School of Gyeongsang National University, Jinju 660-701, Korea Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, U.S.A
| | - Olivier Voinnet
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zurich, Switzerland
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21+/WCU program), PMBBRC, Graduate School of Gyeongsang National University, Jinju 660-701, Korea
| |
Collapse
|
671
|
Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Couté Y, Conn S, Kadlec J, Sachidanandam R, Kaksonen M, Cusack S, Ephrussi A, Pillai RS. RNA clamping by Vasa assembles a piRNA amplifier complex on transposon transcripts. Cell 2014; 157:1698-711. [PMID: 24910301 DOI: 10.1016/j.cell.2014.05.018] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/28/2014] [Accepted: 05/15/2014] [Indexed: 01/25/2023]
Abstract
Germline-specific Piwi-interacting RNAs (piRNAs) protect animal genomes against transposons and are essential for fertility. piRNAs targeting active transposons are amplified by the ping-pong cycle, which couples Piwi endonucleolytic slicing of target RNAs to biogenesis of new piRNAs. Here, we describe the identification of a transient Amplifier complex that mediates biogenesis of secondary piRNAs in insect cells. Amplifier is nucleated by the DEAD box RNA helicase Vasa and contains the two Piwi proteins participating in the ping-pong loop, the Tudor protein Qin/Kumo and antisense piRNA guides. These components assemble on the surface of Vasa's helicase domain, which functions as an RNA clamp to anchor Amplifier onto transposon transcripts. We show that ATP-dependent RNP remodeling by Vasa facilitates transfer of 5' sliced piRNA precursors between ping-pong partners, and loss of this activity causes sterility in Drosophila. Our results reveal the molecular basis for the small RNA amplification that confers adaptive immunity against transposons.
Collapse
Affiliation(s)
- Jordi Xiol
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Pietro Spinelli
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Maike A Laussmann
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Cell Biology and Biophysics Unit, EMBL, 69117 Heidelberg, Germany
| | - David Homolka
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Zhaolin Yang
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Elisa Cora
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Yohann Couté
- Laboratoire Biologie à Grande Echelle, IRTSV, CEA, 38054 Grenoble, France
| | - Simon Conn
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Jan Kadlec
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Sinai, New York, NY 10029, USA
| | - Marko Kaksonen
- Cell Biology and Biophysics Unit, EMBL, 69117 Heidelberg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Anne Ephrussi
- Developmental Biology Unit, EMBL, 69117 Heidelberg, Germany
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France.
| |
Collapse
|
672
|
Cora E, Pandey RR, Xiol J, Taylor J, Sachidanandam R, McCarthy AA, Pillai RS. The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs. RNA (NEW YORK, N.Y.) 2014; 20:773-81. [PMID: 24757166 PMCID: PMC4024632 DOI: 10.1261/rna.044701.114] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here, we examined the contribution of structural domains in Piwi proteins toward defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5' uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5' end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the transposon strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis.
Collapse
Affiliation(s)
- Elisa Cora
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Radha R. Pandey
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Jordi Xiol
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Josh Taylor
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
| | - Ramesh S. Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France
- Corresponding authorE-mail
| |
Collapse
|
673
|
Dueck A, Meister G. Assembly and function of small RNA – Argonaute protein complexes. Biol Chem 2014; 395:611-29. [DOI: 10.1515/hsz-2014-0116] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/28/2014] [Indexed: 01/05/2023]
Abstract
Abstract
Small RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs) or Piwi-interacting RNAs (piRNAs) are important regulators of gene expression in various organisms. Small RNAs bind to a member of the Argonaute protein family and are incorporated into larger structures that mediate diverse gene silencing events. The loading of Argonaute proteins with small RNAs is aided by a number of auxiliary factors as well as ATP hydrolysis. This review will focus on the mechanisms of Argonaute loading in different organisms. Furthermore, we highlight the versatile functions of small RNA-Argonaute protein complexes in organisms from all three kingdoms of life.
Collapse
|
674
|
|
675
|
Hannus M, Beitzinger M, Engelmann JC, Weickert MT, Spang R, Hannus S, Meister G. siPools: highly complex but accurately defined siRNA pools eliminate off-target effects. Nucleic Acids Res 2014; 42:8049-61. [PMID: 24875475 PMCID: PMC4081087 DOI: 10.1093/nar/gku480] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Short interfering RNAs (siRNAs) are widely used as tool for gene inactivation in basic research and therapeutic applications. One of the major shortcomings of siRNA experiments are sequence-specific off-target effects. Such effects are largely unpredictable because siRNAs can affect partially complementary sequences and function like microRNAs (miRNAs), which inhibit gene expression on mRNA stability or translational levels. Here we demonstrate that novel, enzymatically generated siRNA pools—referred to as siPools—containing up to 60 accurately defined siRNAs eliminate off-target effects. This is achieved by the low concentration of each individual siRNA diluting sequence-specific off-target effects below detection limits. In fact, whole transcriptome analyses reveal that single siRNA transfections can severely affect global gene expression. However, when complex siRNA pools are transfected, almost no transcriptome alterations are observed. Taken together, we present enzymatically produced complex but accurately defined siRNA pools with potent on-target silencing but without detectable off-target effects.
Collapse
Affiliation(s)
- Michael Hannus
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany Intana Biosciences GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany siTools Biotech GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany
| | - Michaela Beitzinger
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany siTools Biotech GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany
| | - Julia C Engelmann
- Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany
| | - Marie-Theresa Weickert
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Rainer Spang
- Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany
| | - Stefan Hannus
- Intana Biosciences GmbH, Lochhamerstrasse 29A, 82152 Martinsried/Planegg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| |
Collapse
|
676
|
Jee D, Lai EC. Alteration of miRNA activity via context-specific modifications of Argonaute proteins. Trends Cell Biol 2014; 24:546-53. [PMID: 24865524 DOI: 10.1016/j.tcb.2014.04.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 12/12/2022]
Abstract
miRNAs are enclosed within Argonaute (Ago) proteins, the downstream effectors of small RNA-mediated gene silencing. Because miRNAs mediate extensive networks of post-transcriptional control, cells have evolved multiple strategies to control their activity with precision. A growing theme of recent years is how post-translational modifications of Ago proteins, such as prolyl hydroxylation, phosphorylation, ubiquitination, and poly-ADP-ribosylation, alter miRNA activity at global or specific levels. In this review, we discuss recent advances in Ago modifications in mammalian cells and emphasize how such alterations modulate small RNA function to coordinate appropriate downstream cellular responses. These findings provide a framework to understand how Ago protein modifications are linked to reorganization of post-transcriptional regulatory networks, enabling dynamic responses to diverse external stimuli and changing environmental conditions.
Collapse
Affiliation(s)
- David Jee
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA; Program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA.
| |
Collapse
|
677
|
Ohyama H, Sakai T, Agari Y, Fukui K, Nakagawa N, Shinkai A, Masui R, Kuramitsu S. The role of ribonucleases in regulating global mRNA levels in the model organism Thermus thermophilus HB8. BMC Genomics 2014; 15:386. [PMID: 24884843 PMCID: PMC4229858 DOI: 10.1186/1471-2164-15-386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 05/08/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA metabolism, including RNA synthesis and RNA degradation, is one of the most conserved biological systems and has been intensively studied; however, the degradation network of ribonucleases (RNases) and RNA substrates is not fully understood. RESULTS The genome of the extreme thermophile, Thermus thermophilus HB8 includes 15 genes that encode RNases or putative RNases. Using DNA microarray analyses, we examined the effects of disruption of each RNase on mRNA abundance. Disruption of the genes encoding RNase J, RecJ-like protein and RNase P could not be isolated, indicating that these RNases are essential for cell viability. Disruption of the TTHA0252 gene, which was not previously considered to be involved in mRNA degradation, affected mRNA abundance, as did disruption of the putative RNases, YbeY and PhoH-like proteins, suggesting that they have RNase activity. The effects on mRNA abundance of disruption of several RNase genes were dependent on the phase of cell growth. Disruption of the RNase Y and RNase HII genes affected mRNA levels only during the log phase, whereas disruption of the PhoH-like gene affected mRNA levels only during the stationary phase. Moreover, disruption of the RNase R and PNPase genes had a greater impact on mRNA abundance during the stationary phase than the log phase, whereas the opposite was true for the TTHA0252 gene disruptant. Similar changes in mRNA levels were observed after disruption of YbeY or PhoH-like genes. The changes in mRNA levels in the bacterial Argonaute disruptant were similar to those in the RNase HI and RNase HII gene disruptants, suggesting that bacterial Argonaute is a functional homolog of RNase H. CONCLUSION This study suggests that T. thermophilus HB8 has 13 functional RNases and that each RNase has a different function in the cell. The putative RNases, TTHA0252, YbeY and PhoH-like proteins, are suggested to have RNase activity and to be involved in mRNA degradation. In addition, PhoH-like and YbeY proteins may act cooperatively in the stationary phase. This study also suggests that endo-RNases function mainly during the log phase, whereas exo-RNases function mainly during the stationary phase. RNase HI and RNase HII may have similar substrate selectivity.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
| |
Collapse
|
678
|
|
679
|
Rehfeld F, Rohde AM, Nguyen DTT, Wulczyn FG. Lin28 and let-7: ancient milestones on the road from pluripotency to neurogenesis. Cell Tissue Res 2014; 359:145-60. [PMID: 24825413 DOI: 10.1007/s00441-014-1872-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/11/2014] [Indexed: 11/25/2022]
Abstract
Beginning with their discovery in the context of stem cell fate choice in Caenorhabditis elegans, the microRNA (miRNA) let-7 and the RNA-binding protein Lin28 have been recognized as a regulatory pair with far-reaching impact on stem cell behavior in a wide range of organisms and tissues, including the mammalian brain. In this review, we describe molecular interactions between Lin28 and let-7 and the biological role that each plays in implementing stem cell programs that either maintain stem cell self-renewal and plasticity or drive lineage commitment and differentiation. For Lin28, considerable progress has been made in defining let-7-dependent and let-7-independent functions in the maintenance of pluripotency, somatic cell reprogramming, tissue regeneration, and neural stem cell plasticity. For the pro-differentiation activity of let-7, we focus on emerging roles in mammalian neurogenesis and neuronal function. Specific targets and pathways for let-7 have been identified in embryonic and adult neurogenesis, including corticogenesis, retinal specification, and adult neurogenic niches. Special emphasis is given to examples of feedback and feedforward regulation, in particular within the miRNA biogenesis pathway.
Collapse
Affiliation(s)
- Frederick Rehfeld
- Institute for Cell and Neurobiology, Charité University Medicine Berlin, Berlin, Germany
| | | | | | | |
Collapse
|
680
|
Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis. Cell Res 2014; 24:680-700. [PMID: 24787618 PMCID: PMC4042167 DOI: 10.1038/cr.2014.41] [Citation(s) in RCA: 267] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 02/26/2014] [Accepted: 03/02/2014] [Indexed: 12/12/2022] Open
Abstract
Spermatogenesis in mammals is characterized by two waves of piRNA expression: one corresponds to classic piRNAs responsible for silencing retrotransponsons and the second wave is predominantly derived from nontransposon intergenic regions in pachytene spermatocytes, but the function of these pachytene piRNAs is largely unknown. Here, we report the involvement of pachytene piRNAs in instructing massive mRNA elimination in mouse elongating spermatids (ES). We demonstrate that a piRNA-induced silencing complex (pi-RISC) containing murine PIWI (MIWI) and deadenylase CAF1 is selectively assembled in ES, which is responsible for inducing mRNA deadenylation and decay via a mechanism that resembles the action of miRNAs in somatic cells. Such a highly orchestrated program appears to take full advantage of the enormous repertoire of diversified targeting capacity of pachytene piRNAs derived from nontransposon intergenic regions. These findings suggest that pachytene piRNAs are responsible for inactivating vast cellular programs in preparation for sperm production from ES.
Collapse
|
681
|
Hirose T, Mishima Y, Tomari Y. Elements and machinery of non-coding RNAs: toward their taxonomy. EMBO Rep 2014; 15:489-507. [PMID: 24731943 PMCID: PMC4210095 DOI: 10.1002/embr.201338390] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/04/2014] [Accepted: 03/10/2014] [Indexed: 12/26/2022] Open
Abstract
Although recent transcriptome analyses have uncovered numerous non-coding RNAs (ncRNAs), their functions remain largely unknown. ncRNAs assemble with proteins and operate as ribonucleoprotein (RNP) machineries, formation of which is thought to be determined by specific fundamental elements embedded in the primary RNA transcripts. Knowledge about the relationships between RNA elements, RNP machinery, and molecular and physiological functions is critical for understanding the diverse roles of ncRNAs and may eventually allow their systematic classification or "taxonomy." In this review, we catalog and discuss representative small and long non-coding RNA classes, focusing on their currently known (and unknown) RNA elements and RNP machineries.
Collapse
Affiliation(s)
- Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido UniversitySapporo, Hokkaido, Japan
| | - Yuichiro Mishima
- Institute of Molecular and Cellular Biosciences, The University of TokyoBunkyo-ku, Tokyo, Japan
- Department of Medical Genome Sciences, The University of TokyoBunkyo-ku, Tokyo, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of TokyoBunkyo-ku, Tokyo, Japan
- Department of Medical Genome Sciences, The University of TokyoBunkyo-ku, Tokyo, Japan
| |
Collapse
|
682
|
Chen N, Wang J, Hu Y, Cui B, Li W, Xu G, Liu L, Liu S. MicroRNA-410 reduces the expression of vascular endothelial growth factor and inhibits oxygen-induced retinal neovascularization. PLoS One 2014; 9:e95665. [PMID: 24777200 PMCID: PMC4002426 DOI: 10.1371/journal.pone.0095665] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 03/28/2014] [Indexed: 11/18/2022] Open
Abstract
Retinal neovascularization (RNV) is an eye disease that can cause retinal detachment and even lead to blindness. RNV mainly occurs in the elderly population. The pathogenesis of RNV has been previously reported to be highly related to the expression of vascular endothelial growth factor A (VEGFA), basic fibroblast growth factor (bFGF) and other angiogenic factors. It has also been reported that VEGFA and other factors associated with RNV could be regulated by certain microRNAs (miRNA), a group of small non-coding RNAs which are able to regulate the expression of many genes in vivo. Here, we demonstrate that the miRNA miR-410 is highly expressed in mice within two weeks after birth. miR-410 could suppress VEGFA expression through interaction with the 3′UTR of the VEGFA messenger RNA. Overexpressing a miR-410 mimic effectively suppresses VEGFA expression in various cell lines. Further experiments on oxygen-induced retinopathy (OIR) in mice revealed that eye drops containing large amounts of miR-410 efficiently downregulate VEGFA expression, prevent retinal angiogenesis and effectively treat RNV. These results not only show the underlying mechanism of how miR-410 targets VEGFA but also provide a potential treatment strategy for RNV that might be used in the near future.
Collapse
Affiliation(s)
- Na Chen
- Department of Ophthalmology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Ophthalmology, First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Jiaqi Wang
- Clinical Research Center, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yijun Hu
- Clinical Research Center, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bei Cui
- Department of Sea-Air Examination Center, Navy General Hospital, Beijing, China
| | - Wenjie Li
- Department of Laboratory Diagnosis, First Affiliated Hospital of Second Military Medical University, Shanghai, China
| | - Guixia Xu
- Clinical Research Center, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Lin Liu
- Department of Ophthalmology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (LL); (SL)
| | - Shanrong Liu
- Clinical Research Center, Changhai Hospital, Second Military Medical University, Shanghai, China
- * E-mail: (LL); (SL)
| |
Collapse
|
683
|
Zinovyeva AY, Bouasker S, Simard MJ, Hammell CM, Ambros V. Mutations in conserved residues of the C. elegans microRNA Argonaute ALG-1 identify separable functions in ALG-1 miRISC loading and target repression. PLoS Genet 2014; 10:e1004286. [PMID: 24763381 PMCID: PMC3998888 DOI: 10.1371/journal.pgen.1004286] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 02/18/2014] [Indexed: 11/19/2022] Open
Abstract
microRNAs function in diverse developmental and physiological processes by regulating target gene expression at the post-transcriptional level. ALG-1 is one of two Caenorhabditis elegans Argonautes (ALG-1 and ALG-2) that together are essential for microRNA biogenesis and function. Here, we report the identification of novel antimorphic (anti) alleles of ALG-1 as suppressors of lin-28(lf) precocious developmental phenotypes. The alg-1(anti) mutations broadly impair the function of many microRNAs and cause dosage-dependent phenotypes that are more severe than the complete loss of ALG-1. ALG-1(anti) mutant proteins are competent for promoting Dicer cleavage of microRNA precursors and for associating with and stabilizing microRNAs. However, our results suggest that ALG-1(anti) proteins may sequester microRNAs in immature and functionally deficient microRNA Induced Silencing Complexes (miRISCs), and hence compete with ALG-2 for access to functional microRNAs. Immunoprecipitation experiments show that ALG-1(anti) proteins display an increased association with Dicer and a decreased association with AIN-1/GW182. These findings suggest that alg-1(anti) mutations impair the ability of ALG-1 miRISC to execute a transition from Dicer-associated microRNA processing to AIN-1/GW182 associated effector function, and indicate an active role for ALG/Argonaute in mediating this transition. microRNAs are small non-coding RNAs that function in diverse processes by post-transcriptionally regulating gene expression. Argonautes form the core of the microRNA Induced Silencing Complex (miRISC) and are required for microRNA biogenesis and function. Here we describe the identification and characterization of a novel set of mutations in alg-1, a Caenorhabditis elegans microRNA specific Argonaute. This new class of alg-1 mutations causes phenotypes more severe than the complete loss of alg-1. Interestingly, the mutant ALG-1 proteins are able to promote microRNA biogenesis, but are defective in mediating microRNA target gene repression. We found that mutant ALG-1 associates more with Dicer, but less with miRISC effector AIN-1, compared to wild type ALG-1. We propose that these mutant ALG-1 proteins assemble nonfunctional complexes that effectively compete with the paralogous ALG-2 for critical miRISC components, including mature microRNAs. This new class of Argonaute mutants highlights the role of Argonaute in mediating a functional transition for miRISC from microRNA processing phase to target repression phase.
Collapse
Affiliation(s)
- Anna Y. Zinovyeva
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Samir Bouasker
- St-Patrick Research Group in Basic Oncology, Hôtel-Dieu de Québec (Centre Hospitalier Universitaire de Québec), Laval University Cancer Research Centre, Quebec City, Québec, Canada
| | - Martin J. Simard
- St-Patrick Research Group in Basic Oncology, Hôtel-Dieu de Québec (Centre Hospitalier Universitaire de Québec), Laval University Cancer Research Centre, Quebec City, Québec, Canada
| | | | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
684
|
Hu W, Wang T, Yue E, Zheng S, Xu JH. Flexible microRNA arm selection in rice. Biochem Biophys Res Commun 2014; 447:526-30. [PMID: 24746469 DOI: 10.1016/j.bbrc.2014.04.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
MicroRNAs act at the post-transcriptional level and guide Argonaute proteins to cleave their corresponding target transcripts. However, little attention has been paid to arm selection in miRNA precursors. In this study, small RNA high-throughput sequencing data from 29 different rice libraries were pooled to investigate tissue- and abiotic stress-specific dynamic expression of miRNAs. We found that more than half of pre-miRNAs showed changes in arm selection in different tissues and/or under different abiotic stresses. Our findings suggest that miRNA selection is remarkably prevalent in plants, providing new insights into the role of miRNAs in plant growth and development.
Collapse
Affiliation(s)
- Wangxiong Hu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingzhang Wang
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Erkui Yue
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shu Zheng
- Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, China.
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| |
Collapse
|
685
|
Inefficient SRP interaction with a nascent chain triggers a mRNA quality control pathway. Cell 2014; 156:146-57. [PMID: 24439374 DOI: 10.1016/j.cell.2013.12.017] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 08/01/2013] [Accepted: 12/18/2013] [Indexed: 11/22/2022]
Abstract
Misfolded proteins are often cytotoxic, unless cellular systems prevent their accumulation. Data presented here uncover a mechanism by which defects in secretory proteins lead to a dramatic reduction in their mRNAs and protein expression. When mutant signal sequences fail to bind to the signal recognition particle (SRP) at the ribosome exit site, the nascent chain instead contacts Argonaute2 (Ago2), and the mutant mRNAs are specifically degraded. Severity of signal sequence mutations correlated with increased proximity of Ago2 to nascent chain and mRNA degradation. Ago2 knockdown inhibited degradation of the mutant mRNA, while overexpression of Ago2 or knockdown of SRP54 promoted degradation of secretory protein mRNA. The results reveal a previously unappreciated general mechanism of translational quality control, in which specific mRNA degradation preemptively regulates aberrant protein production (RAPP).
Collapse
|
686
|
Wedeles CJ, Wu MZ, Claycomb JM. Silent no more: Endogenous small RNA pathways promote gene expression. WORM 2014; 3:e28641. [PMID: 25254148 DOI: 10.4161/worm.28641] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 03/24/2014] [Indexed: 11/19/2022]
Abstract
Endogenous small RNA pathways related to RNA interference (RNAi) play a well-documented role in protecting host genomes from the invasion of foreign nucleic acids. In C. elegans, the PIWI type Argonaute, PRG-1, through an association with 21U-RNAs, mediates a genome surveillance process by constantly scanning the genome for potentially deleterious invading elements. Upon recognition of foreign nucleic acids, PRG-1 initiates a cascade of cytoplasmic and nuclear events that results in heritable epigenetic silencing of these transcripts and their coding genomic loci. If the PRG-1/21U-RNA genome surveillance pathway has the capacity to target most of the C. elegans transcriptome, what mechanisms exist to protect endogenous transcripts from being silenced by this pathway? In this commentary, we discuss three recent publications that implicate the CSR-1 small RNA pathway in the heritable activation of germline transcripts, propose a model as to why not all epialleles behave similarly, and touch on the practical implications of these findings.
Collapse
Affiliation(s)
| | - Monica Z Wu
- Department of Molecular Genetics; University of Toronto; Toronto, ON Canada
| | - Julie M Claycomb
- Department of Molecular Genetics; University of Toronto; Toronto, ON Canada
| |
Collapse
|
687
|
Kim YJ, Maizel A, Chen X. Traffic into silence: endomembranes and post-transcriptional RNA silencing. EMBO J 2014; 33:968-80. [PMID: 24668229 PMCID: PMC4193931 DOI: 10.1002/embj.201387262] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
microRNAs (miRNAs) and small interfering RNAs (siRNAs) are small RNAs that repress gene expression at the post-transcriptional level in plants and animals. Small RNAs guide Argonaute-containing RNA-induced silencing complexes to target RNAs in a sequence-specific manner, resulting in mRNA deadenylation followed by exonucleolytic decay, mRNA endonucleolytic cleavage, or translational inhibition. Although our knowledge of small RNA biogenesis, turnover, and mechanisms of action has dramatically expanded in the past decade, the subcellular location of small RNA-mediated RNA silencing still needs to be defined. In contrast to the prevalent presumption that RNA silencing occurs in the cytosol, emerging evidence reveals connections between the endomembrane system and small RNA activities in plants and animals. Here, we summarize the work that uncovered this link between small RNAs and endomembrane compartments and present an overview of the involvement of the endomembrane system in various aspects of RNA silencing. We propose that the endomembrane system is an integral component of RNA silencing that has been long overlooked and predict that a marriage between cell biology and RNA biology holds the key to a full understanding of post-transcriptional gene regulation by small RNAs.
Collapse
Affiliation(s)
- Yun Ju Kim
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology University of California, Riverside, CA, USA
| | | | | |
Collapse
|
688
|
Palanichamy JK, Rao DS. miRNA dysregulation in cancer: towards a mechanistic understanding. Front Genet 2014; 5:54. [PMID: 24672539 PMCID: PMC3957189 DOI: 10.3389/fgene.2014.00054] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/02/2014] [Indexed: 12/17/2022] Open
Abstract
It is now well known that gene expression is intricately regulated inside each cell especially in mammals. There are multiple layers of gene regulation active inside a cell at a given point of time. Gene expression is regulated post-transcriptionally by microRNAs and other factors. Mechanistically, microRNAs are known to bind to the 3’ UTR of mRNAs and cause repression of gene expression and the number of known microRNAs continues to increase every day. Dysregulated microRNA signatures in different types of cancer are being uncovered consistently implying their importance in cellular homeostasis. However when studied in isolation in mouse models, clear-cut cellular and molecular mechanisms have been described only for a select few microRNAs. What is the reason behind this discrepancy? Are microRNAs small players in gene regulation helping only to fine tune gene expression? Or are their roles tissue and cell type-specific with single-cell level effects on mRNA expression and microRNA threshold levels? Or does it all come down to the technical limitations of high-throughput techniques, resulting in false positive results? In this review, we will assess the challenges facing the field and potential avenues for resolving the cellular and molecular mechanisms of these small but important regulators of gene expression.
Collapse
Affiliation(s)
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, CA, USA ; Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA, USA ; Broad Stem Cell Research Center, University of California Los Angeles, CA, USA ; Division of Biology, California Institute of Technology Pasadena, CA, USA
| |
Collapse
|
689
|
Iyer AN, Bellon A, Baudet ML. microRNAs in axon guidance. Front Cell Neurosci 2014; 8:78. [PMID: 24672429 PMCID: PMC3953822 DOI: 10.3389/fncel.2014.00078] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/23/2014] [Indexed: 01/01/2023] Open
Abstract
Brain wiring is a highly intricate process in which trillions of neuronal connections are established. Its initial phase is particularly crucial in establishing the general framework of neuronal circuits. During this early step, differentiating neurons extend axons, which reach their target by navigating through a complex environment with extreme precision. Research in the past 20 years has unraveled a vast and complex array of chemotropic cues that guide the leading tip of axons, the growth cone, throughout its journey. Tight regulation of these cues, and of their receptors and signaling pathways, is necessary for the high degree of accuracy required during circuit formation. However, little is known about the nature of regulatory molecules or mechanisms fine-tuning axonal cue response. Here we review recent, and somewhat fragmented, research on the possibility that microRNAs (miRNAs) could be key fine-tuning regulatory molecules in axon guidance. miRNAs appear to shape long-range axon guidance, fasciculation and targeting. We also present several lines of evidence suggesting that miRNAs could have a compartmentalized and differential action at the cell soma, and within axons and growth cones.
Collapse
Affiliation(s)
- Archana N Iyer
- Center for Integrative Biology, University of Trento Trento, Italy
| | - Anaïs Bellon
- Department of Physiology, Development and Neuroscience, University of Cambridge Cambridge, UK
| | | |
Collapse
|
690
|
Kumar S, Mapa K, Maiti S. Understanding the effect of locked nucleic acid and 2'-O-methyl modification on the hybridization thermodynamics of a miRNA-mRNA pair in the presence and absence of AfPiwi protein. Biochemistry 2014; 53:1607-15. [PMID: 24564489 DOI: 10.1021/bi401677d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
miRNAs are some of the key epigenetic regulators of gene expression. They act through hybridization with their target mRNA and modulate the level of respective proteins via different mechanisms. Various cancer conditions are known to be associated with up- and downregulation of the oncogenic and tumor suppressor miRNAs, respectively. The levels of aberrantly expressed oncogenic miRNAs can be downregulated in different ways. Similarly, restoration of tumor suppressor miRNAs to their normal levels can be achieved using miRNA mimics. However, the use of miRNA mimics is limited by their reduced biostability and function. We have studied the hybridization thermodynamics of the miRNA 26a (11-mer, including the seed sequence) guide strand with the mRNA (11-mer) target strand in the absence and presence of AfPiwi protein. We have also inserted locked nucleic acids (LNAs) and 2'-O-methyl-modified nucleotides into the guide strand, in a walk-through manner, to assess their effect on the binding efficiency between guide and target RNA. Insertion of LNA and 2'-O-methyl-modified nucleotides into the guide strand helped to strengthen the binding affinity irrespective of the position of insertion. However, in the presence of AfPiwi protein, these modifications reduced the binding affinity to different extents depending on the position of insertion. Insertion of a modification leads to an increase in the enthalpic contribution with an increased unfavorable entropic contribution, which negatively compensates for the higher favorable enthalpy.
Collapse
Affiliation(s)
- Santosh Kumar
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mall Road, Delhi 110 007, India
| | | | | |
Collapse
|
691
|
Nakamoto K, Ueno Y. Diazirine-Containing RNA Photo-Cross-Linking Probes for Capturing microRNA Targets. J Org Chem 2014; 79:2463-72. [DOI: 10.1021/jo402738t] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kosuke Nakamoto
- Course of Applied Life Science, Faculty of
Applied Biological Sciences and ‡United Graduate
School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yoshihito Ueno
- Course of Applied Life Science, Faculty of
Applied Biological Sciences and ‡United Graduate
School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| |
Collapse
|
692
|
Ward AJ, Norrbom M, Chun S, Bennett CF, Rigo F. Nonsense-mediated decay as a terminating mechanism for antisense oligonucleotides. Nucleic Acids Res 2014; 42:5871-9. [PMID: 24589581 PMCID: PMC4027159 DOI: 10.1093/nar/gku184] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are synthetic oligonucleotides that alter expression of disease-associated transcripts via Watson-Crick hybridization. ASOs that function through RNase H or the RNA-induced silencing complex (RISC) result in enzymatic degradation of target RNA. ASOs designed to sterically block access of proteins to the RNA modulate mRNA metabolism but do not typically cause degradation. Here, we rationally design steric blocking ASOs to promote mRNA reduction and characterize the terminating mechanism. Transfection of ASOs complementary to constitutive exons in STAT3 and Sod1 results in greater than 70% reduction of mRNA and protein. The ASOs promote aberrant exon skipping and generation of premature termination codon (PTC)-containing mRNAs. We inhibit the nonsense-mediated mRNA decay (NMD) pathway and show that the PTC-containing mRNAs are recognized by the UPF1 ATPase, cleaved by the SMG6 endonuclease and degraded by the XRN1 cytoplasmic exonuclease. NMD surveillance, however, does not entirely explain the mechanism of decreased STAT3 expression. In addition to exon skipping, ASO treatment causes intron retention and reduction of chromatin-associated STAT3 mRNA. The application of steric blocking ASOs to promote RNA degradation allows one to explore more nucleotide modifications than tolerated by RNase H or RISC-dependent ASOs, with the goal of improving ASO drug properties.
Collapse
Affiliation(s)
- Amanda J Ward
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Michaela Norrbom
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Seung Chun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - C Frank Bennett
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Frank Rigo
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| |
Collapse
|
693
|
Zimmermann J, Latta L, Beck A, Leidinger P, Fecher-Trost C, Schlenstedt G, Meese E, Wissenbach U, Flockerzi V. Trans-activation response (TAR) RNA-binding protein 2 is a novel modulator of transient receptor potential canonical 4 (TRPC4) protein. J Biol Chem 2014; 289:9766-80. [PMID: 24563462 DOI: 10.1074/jbc.m114.557066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TRPC4 proteins function as Ca(2+) conducting, non-selective cation channels in endothelial, smooth muscle, and neuronal cells. To further characterize the roles of TRPC4 in vivo, detailed information about the molecular composition of native channel complexes and their association with cellular signaling networks is needed. Therefore, a mouse brain cDNA library was searched for novel TRPC4-interacting proteins using a modified yeast two-hybrid assay. This screen identified Trans-activation Response RNA-binding protein 2 (Tarpb2), a protein that recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Tarbp2 was found to bind to the C terminus of TRPC4 and TRPC5 and to modulate agonist-dependent TRPC4-induced Ca(2+) entry. A stretch of basic residues within the Tarbp2 protein is required for these actions. Tarbp2 binding to and modulation of TRPC4 occurs in the presence of endogenously expressed Dicer but is no longer detectable when the Dicer cDNA is overexpressed. Dicer activity in crude cell lysates is increased in the presence of Ca(2+), most probably by Ca(2+)-dependent proteolytic activation of Dicer. Apparently, Tarbp2 binding to TRPC4 promotes changes of cytosolic Ca(2+) and, thereby, leads to a dynamic regulation of Dicer activity, essentially at low endogenous Dicer concentrations.
Collapse
Affiliation(s)
- Jasmin Zimmermann
- From the Institut für Experimentelle und Klinische Pharmakologie und Toxikologie
| | | | | | | | | | | | | | | | | |
Collapse
|
694
|
Speth C, Laubinger S. RACK1 and the microRNA pathway: is it déjà-vu all over again? PLANT SIGNALING & BEHAVIOR 2014; 9:e27909. [PMID: 24521556 PMCID: PMC4091593 DOI: 10.4161/psb.27909] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 01/19/2014] [Indexed: 05/30/2023]
Abstract
MicroRNAs (miRNAs) control many aspects of development and adaption in plants and in animals by post-transcriptional control of mRNA stability and translatability. Over the last years numerous proteins have been identified in the miRNA pathway. The versatile scaffold protein RACK1 has been associated with efficient miRNA production and function in plants and metazoans. Here, we briefly summarize the differences of RACK1 function in the plant and animal miRNA pathways and discuss putative mechanisms and functional roles of RACK1 in miRNA biogenesis and action.
Collapse
Affiliation(s)
- Corinna Speth
- Center for Plant Molecular Biology (ZMBP); University of Tübingen; Tübingen, Germany
- Chemical Genomics Centre (CGC) of the Max Planck Society; Dortmund, Germany, & MPI for Developmental Biology; Tübingen, Germany
| | - Sascha Laubinger
- Center for Plant Molecular Biology (ZMBP); University of Tübingen; Tübingen, Germany
- Chemical Genomics Centre (CGC) of the Max Planck Society; Dortmund, Germany, & MPI for Developmental Biology; Tübingen, Germany
| |
Collapse
|
695
|
Barca-Mayo O, De Pietri Tonelli D. Convergent microRNA actions coordinate neocortical development. Cell Mol Life Sci 2014; 71:2975-95. [PMID: 24519472 PMCID: PMC4111863 DOI: 10.1007/s00018-014-1576-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/11/2014] [Accepted: 01/27/2014] [Indexed: 12/19/2022]
Abstract
Neocortical development is a complex process that, at the cellular level, involves tight control of self-renewal, cell fate commitment, survival, differentiation and delamination/migration. These processes require, at the molecular level, the precise regulation of intrinsic signaling pathways and extrinsic factors with coordinated action in a spatially and temporally specific manner. Transcriptional regulation plays an important role during corticogenesis; however, microRNAs (miRNAs) are emerging as important post-transcriptional regulators of various aspects of central nervous system development. miRNAs are a class of small, single-stranded noncoding RNA molecules that control the expression of the majority of protein coding genes (i.e., targets). How do different miRNAs achieve precise control of gene networks during neocortical development? Here, we critically review all the miRNA–target interactions validated in vivo, with relevance to the generation and migration of pyramidal-projection glutamatergic neurons, and for the initial formation of cortical layers in the embryonic development of rodent neocortex. In particular, we focus on convergent miRNA actions, which are still a poorly understood layer of complexity in miRNA signaling, but potentially one of the keys to disclosing how miRNAs achieve the precise coordination of complex biological processes such as neocortical development.
Collapse
Affiliation(s)
- Olga Barca-Mayo
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | | |
Collapse
|
696
|
Al-Janabi O, Wach S, Nolte E, Weigelt K, Rau TT, Stöhr C, Legal W, Schick S, Greither T, Hartmann A, Wullich B, Taubert H. Piwi-like 1 and 4 gene transcript levels are associated with clinicopathological parameters in renal cell carcinomas. Biochim Biophys Acta Mol Basis Dis 2014; 1842:686-90. [PMID: 24509249 DOI: 10.1016/j.bbadis.2014.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/24/2014] [Accepted: 01/30/2014] [Indexed: 12/14/2022]
Abstract
Piwi-like gene family members (Piwil 1-4) are considered stem cell-associated genes/proteins. These are expressed predominantly in germline cells, but are re-expressed in different tumors. Piwil 1-4 gene expression has not previously been studied and correlated with clinicopathological parameters in renal cell carcinomas (RCC). The Piwil 1-4 transcript levels were analyzed by quantitative real-time PCR in 73 clear cell RCC (ccRCC) tissues and corresponding normal tissues. The transcript levels of Piwil 1, 2 and 4 were strongly and significantly correlated with each other, in both the tumor tissues and the normal tissues (P<0.001; Spearman's rank test). Piwil 4 gene expression was significantly higher in the ccRCC tissues than that in the corresponding normal renal tissues (P<0.001; Wilcoxon signed-rank test). When the ccRCC patient cohort was divided according to the median Piwil 1-4 expression into low- and high-expression groups and according to age into younger (≤64years) and older patient groups (>64years), the younger patients displayed significantly higher levels of Piwil 1 mRNA in comparison to the older patients (P=0.010; Fisher's exact test). Interestingly, Piwil 1 expression was left-right polarized in the normal tissues but not in the tumor tissues (P=0.004; Fisher's exact test). Altogether, associations were determined between the Piwi-like family member expression levels and clinicopathological parameters of ccRCC, suggesting a potential role for these genes/proteins in ccRCC diagnostics and tumorigenesis as well as in renal tissue embryology.
Collapse
Affiliation(s)
- Omar Al-Janabi
- Department of Urology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Sven Wach
- Department of Urology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Elke Nolte
- Department of Urology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Katrin Weigelt
- Department of Urology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Tilman T Rau
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Christine Stöhr
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Wolfgang Legal
- Department of Urology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Stefan Schick
- Tumour Centre at the Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
| | - Thomas Greither
- Center for Reproductive Medicine and Andrology, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | - Arndt Hartmann
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Bernd Wullich
- Department of Urology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| | - Helge Taubert
- Department of Urology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
| |
Collapse
|
697
|
Stroynowska-Czerwinska A, Fiszer A, Krzyzosiak WJ. The panorama of miRNA-mediated mechanisms in mammalian cells. Cell Mol Life Sci 2014; 71:2253-70. [PMID: 24468964 PMCID: PMC4031385 DOI: 10.1007/s00018-013-1551-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/02/2013] [Accepted: 12/30/2013] [Indexed: 12/21/2022]
Abstract
MicroRNAs comprise a large family of short, non-coding RNAs that are present in most eukaryotic organisms and are typically involved in downregulating the expression of protein-coding genes. The detailed mechanisms of miRNA functioning in animals and plants have been under investigation for more than decade. In mammalian cells, miRNA guides the effector complex miRISC to bind with partially complementary sequences, usually within the 3′UTR of mRNAs, and inhibit protein synthesis with or without transcript degradation. In addition to these main mechanisms, several other modes of miRNA-mediated gene expression regulation have been described, but their scale and importance remain a matter of debate. In this review, we briefly summarize the pathway of miRNA precursor processing during miRNA biogenesis and continue with the description of the miRISC assembly process. Then, we present the miRNA-mediated mechanisms of gene expression regulation in detail, and we gather information concerning the proteins involved in these processes. In addition, we briefly refer to the current applications of miRNA mechanisms in therapeutic strategies. Finally, we highlight some of the remaining controversies surrounding the regulation of mammalian gene expression by miRNAs.
Collapse
Affiliation(s)
- Anna Stroynowska-Czerwinska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704, Poznan, Poland
| | | | | |
Collapse
|
698
|
Dueck A, Eichner A, Sixt M, Meister G. A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS Lett 2014; 588:632-40. [PMID: 24444604 DOI: 10.1016/j.febslet.2014.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/30/2013] [Accepted: 01/03/2014] [Indexed: 01/02/2023]
Abstract
MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct influence of miR-155 on the expression levels of other miRNAs. For example, miR-455 is negatively regulated in miR-155-deficient cells possibly due to inhibition of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data sets, we propose a model of hierarchical miRNA expression dominated by miR-155 in DCs and macrophages.
Collapse
Affiliation(s)
- Anne Dueck
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Alexander Eichner
- IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Michael Sixt
- IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
| |
Collapse
|
699
|
Pai B, Siripornmongcolchai T, Berentsen B, Pakzad A, Vieuille C, Pallesen S, Pajak M, Simpson TI, Armstrong JD, Wibrand K, Bramham CR. NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo. Front Cell Neurosci 2014; 7:285. [PMID: 24454279 PMCID: PMC3888942 DOI: 10.3389/fncel.2013.00285] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 12/19/2013] [Indexed: 01/02/2023] Open
Abstract
microRNAs (miRNAs) are major regulators of protein synthesis in the brain. A major goal is to identify changes in miRNA expression underlying protein synthesis-dependent forms of synaptic plasticity such as long-term potentiation (LTP). Previous analyses focused on changes in miRNA levels in total lysate samples. Here, we asked whether changes in total miRNA accurately reflect changes in the amount of miRNA bound to Argonaute protein within the miRNA-induced silencing complex (miRISC). Ago2 immunoprecipitation was used to isolate RISC-associated miRNAs following high-frequency stimulation (HFS)-induced LTP in the dentate gyrus of anesthetized rats. Using locked-nucleic acid-based PCR cards for high-throughput screening and independent validation by quantitative TaqMan RT-PCR, we identified differential regulation of Ago2-associated and total miRNA expression. The ratio of Ago2/total miRNA expression was regulated bidirectionally in a miRNA-specific manner and was largely dependent on N-methyl-D-aspartate receptor (NMDA) activation during LTP induction. The present results identify miRNA association with Ago2 as a potential control point in activity-dependent synaptic plasticity in the adult brain. Finally, novel computational analysis for targets of the Ago2-associated miRNAs identifies 21 pathways that are enriched and differentially targeted by the miRNAs including axon guidance, mTOR, MAPK, Ras, and LTP.
Collapse
Affiliation(s)
- Balagopal Pai
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Taweeporn Siripornmongcolchai
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Birgitte Berentsen
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Ashraf Pakzad
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Christel Vieuille
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Ståle Pallesen
- Department of Psychosocial Science, University of Bergen Bergen, Norway
| | - Maciej Pajak
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh Edinburgh, UK
| | - T Ian Simpson
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh Edinburgh, UK ; Biomathematics and Statistics Scotland JCMB, Edinburgh, UK
| | - J Douglas Armstrong
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh Edinburgh, UK
| | - Karin Wibrand
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| | - Clive R Bramham
- Department of Biomedicine and K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen Bergen, Norway
| |
Collapse
|
700
|
Gene and MicroRNA transcriptome analysis of Parkinson's related LRRK2 mouse models. PLoS One 2014; 9:e85510. [PMID: 24427314 PMCID: PMC3888428 DOI: 10.1371/journal.pone.0085510] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/28/2013] [Indexed: 12/12/2022] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of genetic Parkinson’s disease (PD). The biological function of LRRK2 and how mutations lead to disease remain poorly defined. It has been proposed that LRRK2 could function in gene transcription regulation; however, this issue remains controversial. Here, we investigated in parallel gene and microRNA (miRNA) transcriptome profiles of three different LRRK2 mouse models. Striatal tissue was isolated from adult LRRK2 knockout (KO) mice, as well as mice expressing human LRRK2 wildtype (hLRRK2-WT) or the PD-associated R1441G mutation (hLRRK2-R1441G). We identified a total of 761 genes and 24 miRNAs that were misregulated in the absence of LRRK2 when a false discovery rate of 0.2 was applied. Notably, most changes in gene expression were modest (i.e., <2 fold). By real-time quantitative RT-PCR, we confirmed the variations of selected genes (e.g., adra2, syt2, opalin) and miRNAs (e.g., miR-16, miR-25). Surprisingly, little or no changes in gene expression were observed in mice expressing hLRRK2-WT or hLRRK2-R1441G when compared to non-transgenic controls. Nevertheless, a number of miRNAs were misexpressed in these models. Bioinformatics analysis identified several miRNA-dependent and independent networks dysregulated in LRRK2-deficient mice, including PD-related pathways. These results suggest that brain LRRK2 plays an overall modest role in gene transcription regulation in mammals; however, these effects seem context and RNA type-dependent. Our data thus set the stage for future investigations regarding LRRK2 function in PD development.
Collapse
|