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Human RNAi pathway: crosstalk with organelles and cells

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Abstract

Understanding gene regulation mechanisms has been a serious challenge in biology. As a novel mechanism, small non-coding RNAs are an alternative means of gene regulation in a specific and efficient manner. There are growing reports on regulatory roles of these RNAs including transcriptional gene silencing/activation and post-transcriptional gene silencing events. Also, there are several known small non-coding RNAs which all work through RNA interference pathway. Interestingly, these small RNAs are secreted from cells toward targeted cells presenting new communication approach in cell–cell or cell–organ signal transduction. In fact, understanding cellular and molecular basis of these pathways will strongly improve developing targeted therapies and potent and specific regulatory tools. This study will review some of the most recent findings in this subject and will introduce a super-pathway RNA interference-based small RNA silencing network.

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References

  • Adkin CF et al (2012) Multiple exon skipping strategies to by-pass dystrophin mutations. Neuromuscul Disord 22(4):297–305

    PubMed Central  PubMed  Google Scholar 

  • Ahlenstiel CL et al (2012) Direct evidence of nuclear Argonaute distribution during transcriptional silencing links the actin cytoskeleton to nuclear RNAi machinery in human cells. Nucleic Acids Res 40(4):1579–1595

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ando Y et al (2011) Two-step cleavage of hairpin RNA with 5′ overhangs by human DICER. BMC Mol Biol 12:6

    PubMed Central  PubMed  CAS  Google Scholar 

  • Aravin AA et al (2001) Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr Biol 11(13):1017–1027

    PubMed  CAS  Google Scholar 

  • Aravin AA et al (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell 5(2):337–350

    PubMed  CAS  Google Scholar 

  • Aravin A et al (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442(7099):203–207

    PubMed  CAS  Google Scholar 

  • Aravin AA, Hannon GJ, Brennecke J (2007a) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318(5851):761–764

    PubMed  CAS  Google Scholar 

  • Aravin AA et al (2007b) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316(5825):744–747

    PubMed  CAS  Google Scholar 

  • Arroyo JD et al (2011) Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci U S A 108(12):5003–5008

    PubMed Central  PubMed  CAS  Google Scholar 

  • Azimzadeh Jamalkandi S, Masoudi-Nejad A (2009) Reconstruction of Arabidopsis thaliana fully integrated small RNA pathway. Funct Integr Genomics 9(4):419–432

    Google Scholar 

  • Azimzadeh Jamalkandi S, Masoudi-Nejad A (2011) RNAi pathway integration in Caenorhabditis elegans development. Funct Integr Genomics 11(3):389–405

    PubMed  Google Scholar 

  • Azuma-Mukai A et al (2008) Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc Natl Acad Sci U S A 105(23):7964–7969

    PubMed Central  PubMed  CAS  Google Scholar 

  • Bandres E et al (2009) MicroRNA-451 regulates macrophage migration inhibitory factor production and proliferation of gastrointestinal cancer cells. Clin Cancer Res 15(7):2281–2290

    PubMed  CAS  Google Scholar 

  • Barr I et al (2011) DiGeorge critical region 8 (DGCR8) is a double-cysteine-ligated heme protein. J Biol Chem 286(19):16716–16725

    PubMed Central  PubMed  CAS  Google Scholar 

  • Barr I et al (2012) Ferric, not ferrous, heme activates RNA-binding protein DGCR8 for primary microRNA processing. Proc Natl Acad Sci U S A 109(6):1919–1924

    PubMed Central  PubMed  CAS  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297

    PubMed  CAS  Google Scholar 

  • Benhamed M et al (2012) Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells. Nat Cell Biol 14(3):266–275

    PubMed  CAS  Google Scholar 

  • Bennasser Y et al (2011) Competition for XPO5 binding between Dicer mRNA, pre-miRNA and viral RNA regulates human Dicer levels. Nat Struct Mol Biol 18(3):323–327

    PubMed Central  PubMed  CAS  Google Scholar 

  • Bogerd HP et al (2010) A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. Mol Cell 37(1):135–142

    PubMed Central  PubMed  CAS  Google Scholar 

  • Bohnsack MT, Czaplinski K, Gorlich D (2004) Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10(2):185–191

    PubMed Central  PubMed  CAS  Google Scholar 

  • Boonyaratanakornkit J et al (2011) The C proteins of human parainfluenza virus type 1 limit double-stranded RNA accumulation that would otherwise trigger activation of MDA5 and protein kinase R. J Virol 85(4):1495–1506

    PubMed Central  PubMed  CAS  Google Scholar 

  • Brennecke J et al (2005) Principles of microRNA-target recognition. PLoS Biol 3(3):e85

    PubMed Central  PubMed  Google Scholar 

  • Brodersen P, Voinnet O (2009) Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 10(2):141–148

    PubMed  CAS  Google Scholar 

  • Brownawell AM, Macara IG (2002) Exportin-5, a novel karyopherin, mediates nuclear export of double-stranded RNA binding proteins. J Cell Biol 156(1):53–64

    PubMed Central  PubMed  CAS  Google Scholar 

  • Calado A et al (2002) Exportin-5-mediated nuclear export of eukaryotic elongation factor 1A and tRNA. EMBO J 21(22):6216–6224

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chakravarthy S et al (2010) Substrate-specific kinetics of Dicer-catalyzed RNA processing. J Mol Biol 404(3):392–402

    PubMed Central  PubMed  CAS  Google Scholar 

  • Cheloufi S et al (2010) A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 465(7298):584–589

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chen T, Brownawell AM, Macara IG (2004) Nucleocytoplasmic shuttling of JAZ, a new cargo protein for exportin-5. Mol Cell Biol 24(15):6608–6619

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chen X et al (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18(10):997–1006

    PubMed  CAS  Google Scholar 

  • Chendrimada TP et al (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436(7051):740–744

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chi YH, Semmes OJ, Jeang KT (2011) A proteomic study of TAR-RNA binding protein (TRBP)-associated factors. Cell Biosci 1(1):9

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chu Y et al (2010) Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter. Nucleic Acids Res 38(21):7736–7748

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chu Y et al (2012) Transcriptional silencing by hairpin RNAs complementary to a gene promoter. Nucleic Acid Ther 22(3):147–151

    PubMed Central  PubMed  CAS  Google Scholar 

  • Chueh AC et al (2009) LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin. PLoS Genet 5(1):e1000354

    PubMed Central  PubMed  Google Scholar 

  • Cocucci E, Racchetti G, Meldolesi J (2009) Shedding microvesicles: artefacts no more. Trends Cell Biol 19(2):43–51

    PubMed  CAS  Google Scholar 

  • Corcoran DL et al (2009) Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One 4(4):e5279

    PubMed Central  PubMed  Google Scholar 

  • Courts C, Madea B (2011) Specific micro-RNA signatures for the detection of saliva and blood in forensic body-fluid identification. J Forensic Sci 56(6):1464–1470

    PubMed  CAS  Google Scholar 

  • Curtis HJ, Sibley CR, Wood MJ (2012) Mirtrons, an emerging class of atypical miRNA. Wiley Interdiscip Rev RNA 3:617–632

    Google Scholar 

  • Daher A et al (2009) TRBP control of PACT-induced phosphorylation of protein kinase R is reversed by stress. Mol Cell Biol 29(1):254–265

    PubMed Central  PubMed  CAS  Google Scholar 

  • Dallas A et al (2012) Right- and left-loop short shRNAs have distinct and unusual mechanisms of gene silencing. Nucleic Acids Res Advance access:1–17

    Google Scholar 

  • Daniels SM et al (2009) Characterization of the TRBP domain required for dicer interaction and function in RNA interference. BMC Mol Biol 10:38

    PubMed Central  PubMed  Google Scholar 

  • Detzer A et al (2011) Cell stress is related to re-localization of Argonaute 2 and to decreased RNA interference in human cells. Nucleic Acids Res 39(7):2727–2741

    PubMed Central  PubMed  CAS  Google Scholar 

  • Doench JG, Sharp PA (2004) Specificity of microRNA target selection in translational repression. Genes Dev 18(5):504–511

    PubMed Central  PubMed  CAS  Google Scholar 

  • El-Hefnawy T et al (2004) Characterization of amplifiable, circulating RNA in plasma and its potential as a tool for cancer diagnostics. Clin Chem 50(3):564–573

    PubMed  CAS  Google Scholar 

  • Elkayam E et al (2012) The structure of human argonaute-2 in complex with miR-20a. Cell 150(1):100–110

    PubMed Central  PubMed  CAS  Google Scholar 

  • Espada-Murao LA, Morita K (2011) Delayed cytosolic exposure of Japanese encephalitis virus double-stranded RNA impedes interferon activation and enhances viral dissemination in porcine cells. J Virol 85(13):6736–6749

    PubMed Central  PubMed  CAS  Google Scholar 

  • Esposito T et al (2011) piR_015520 belongs to Piwi-associated RNAs regulates expression of the human melatonin receptor 1A gene. PLoS One 6(7):e22727

    PubMed Central  PubMed  CAS  Google Scholar 

  • Faller M et al (2010) DGCR8 recognizes primary transcripts of microRNAs through highly cooperative binding and formation of higher-order structures. RNA 16(8):1570–1583

    PubMed Central  PubMed  CAS  Google Scholar 

  • Feng Y et al (2011) Drosha processing controls the specificity and efficiency of global microRNA expression. Biochim Biophys Acta 1809(11–12):700–707

    PubMed Central  PubMed  CAS  Google Scholar 

  • Fleischhacker M, Schmidt B (2007) Circulating nucleic acids (CNAs) and cancer—a survey. Biochim Biophys Acta 1775(1):181–232

    PubMed  CAS  Google Scholar 

  • Fletcher S et al (2012) Targeted exon skipping to address “leaky” mutations in the dystrophin gene. Mol Ther Nucleic Acids 1:e48

    PubMed Central  PubMed  Google Scholar 

  • Franks TM, Lykke-Andersen J (2008) The control of mRNA decapping and P-body formation. Mol Cell 32(5):605–615

    PubMed Central  PubMed  CAS  Google Scholar 

  • Fukagawa T et al (2004) Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat Cell Biol 6(8):784–791

    PubMed  CAS  Google Scholar 

  • Galitskii VA (2008) Hypothesis of the initiation of DNA methylation de novo and allelic exclusion by small RNA. Tsitologiia 50(4):277–286

    PubMed  CAS  Google Scholar 

  • Gallo A et al (2012) The majority of microRNAs detectable in serum and saliva is concentrated in exosomes. PLoS One 7(3):e30679

    PubMed Central  PubMed  CAS  Google Scholar 

  • Gao Q, Frohman MA (2012) Roles for the lipid-signaling enzyme MitoPLD in mitochondrial dynamics, piRNA biogenesis, and spermatogenesis. BMB Rep 45(1):7–13

    PubMed Central  PubMed  CAS  Google Scholar 

  • Gidlof O et al (2011) Cardiospecific microRNA plasma levels correlate with troponin and cardiac function in patients with ST elevation myocardial infarction, are selectively dependent on renal elimination, and can be detected in urine samples. Cardiology 118(4):217–226

    PubMed  Google Scholar 

  • Gokhale S et al (2012) A simple method for incorporating dynamic effects of intronic miRNA mediated regulation. Mol Biosyst 8(8):2145–2152

    PubMed  CAS  Google Scholar 

  • Gomez-Cabello D et al (2010) Regulation of the microRNA processor DGCR8 by the tumor suppressor ING1. Cancer Res 70(5):1866–1874

    PubMed  CAS  Google Scholar 

  • Gong M et al (2012) Caspases cleave and inhibit the microRNA processing protein DiGeorge Critical Region 8. Protein Sci 21(6):797–808

    PubMed Central  PubMed  CAS  Google Scholar 

  • Gregory RI et al (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432(7014):235–240

    PubMed  CAS  Google Scholar 

  • Gu A et al (2010) Genetic variants in Piwi-interacting RNA pathway genes confer susceptibility to spermatogenic failure in a Chinese population. Hum Reprod 25(12):2955–2961

    PubMed  CAS  Google Scholar 

  • Gupta A et al (2006) Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature 442(7098):82–85

    PubMed  CAS  Google Scholar 

  • Gwizdek C et al (2004) Minihelix-containing RNAs mediate exportin-5-dependent nuclear export of the double-stranded RNA-binding protein ILF3. J Biol Chem 279(2):884–891

    PubMed  CAS  Google Scholar 

  • Han J et al (2004) The Drosha–DGCR8 complex in primary microRNA processing. Genes Dev 18(24):3016–3027

    PubMed Central  PubMed  CAS  Google Scholar 

  • Han J, Kim D, Morris KV (2007) Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc Natl Acad Sci U S A 104(30):12422–12427

    PubMed Central  PubMed  CAS  Google Scholar 

  • Han J et al (2009) Posttranscriptional crossregulation between Drosha and DGCR8. Cell 136(1):75–84

    PubMed Central  PubMed  CAS  Google Scholar 

  • Hanke M et al (2010) A robust methodology to study urine microRNA as tumor marker: microRNA-126 and microRNA-182 are related to urinary bladder cancer. Urol Oncol 28(6):655–661

    PubMed  CAS  Google Scholar 

  • Hausser J et al (2009) Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome Res 19(11):2009–2020

    PubMed Central  PubMed  CAS  Google Scholar 

  • Havens MA et al (2012) Biogenesis of mammalian microRNAs by a non-canonical processing pathway. Nucleic Acids Res 40(10):4626–4640

    PubMed Central  PubMed  CAS  Google Scholar 

  • Hawkins PG et al (2009) Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res 37(9):2984–2995

    PubMed Central  PubMed  CAS  Google Scholar 

  • Huang V et al (2010) RNAa is conserved in mammalian cells. PLoS One 5(1):e8848

    PubMed Central  PubMed  Google Scholar 

  • Huang H et al (2011) piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling. Dev Cell 20(3):376–387

    PubMed Central  PubMed  CAS  Google Scholar 

  • Huang V et al (2012) Upregulation of cyclin B1 by miRNA and its implications in cancer. Nucleic Acids Res 40(4):1695–1707

    PubMed Central  PubMed  CAS  Google Scholar 

  • Iguchi H, Kosaka N, Ochiya T (2010) Secretory microRNAs as a versatile communication tool. Commun Integr Biol 3(5):478–481

    PubMed Central  PubMed  Google Scholar 

  • Ikeda K et al (2006) Detection of the argonaute protein Ago2 and microRNAs in the RNA induced silencing complex (RISC) using a monoclonal antibody. J Immunol Methods 317(1–2):38–44

    PubMed Central  PubMed  CAS  Google Scholar 

  • Iwasaki S, Tomari Y (2009) Argonaute-mediated translational repression (and activation). Fly (Austin) 3(3):204–206

    Google Scholar 

  • Jagannath A, Wood MJ (2009) Localization of double-stranded small interfering RNA to cytoplasmic processing bodies is Ago2 dependent and results in up-regulation of GW182 and Argonaute-2. Mol Biol Cell 20(1):521–529

    PubMed Central  PubMed  CAS  Google Scholar 

  • Janowski BA et al (2006) Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat Struct Mol Biol 13(9):787–792

    PubMed  CAS  Google Scholar 

  • Janowski BA et al (2007) Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat Chem Biol 3(3):166–173

    PubMed  CAS  Google Scholar 

  • Jiang F et al (2011) Structural basis of RNA recognition and activation by innate immune receptor RIG-I. Nature 479(7373):423–427

    PubMed Central  PubMed  CAS  Google Scholar 

  • Johnston M et al (2010) HSP90 protein stabilizes unloaded argonaute complexes and microscopic P-bodies in human cells. Mol Biol Cell 21(9):1462–1469

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kedersha NL et al (1999) RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2 alpha to the assembly of mammalian stress granules. J Cell Biol 147(7):1431–1442

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kim DH et al (2006) Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat Struct Mol Biol 13(9):793–797

    PubMed  CAS  Google Scholar 

  • Kim DH et al (2008) MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A 105(42):16230–16235

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kok KH et al (2007) Human TRBP and PACT directly interact with each other and associate with dicer to facilitate the production of small interfering RNA. J Biol Chem 282(24):17649–17657

    PubMed  CAS  Google Scholar 

  • Koscianska E, Starega-Roslan J, Krzyzosiak WJ (2011) The role of Dicer protein partners in the processing of microRNA precursors. PLoS One 6(12):e28548

    PubMed Central  PubMed  CAS  Google Scholar 

  • Kowalinski E et al (2011) Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA. Cell 147(2):423–435

    PubMed  CAS  Google Scholar 

  • Kozaki K, Inazawa J (2012) Tumor-suppressive microRNA silenced by tumor-specific DNA hypermethylation in cancer cells. Cancer Sci 103(5):837–845

    PubMed  CAS  Google Scholar 

  • Kuwabara T et al (2005) The NRSE smRNA specifies the fate of adult hippocampal neural stem cells. Nucleic Acids Symp Ser (Oxf) (49):87–88

  • Kwak PB, Tomari Y (2012) The N domain of Argonaute drives duplex unwinding during RISC assembly. Nat Struct Mol Biol 19(2):145–151

    PubMed  CAS  Google Scholar 

  • Laraki G et al (2008) Interactions between the double-stranded RNA-binding proteins TRBP and PACT define the Medipal domain that mediates protein-protein interactions. RNA Biol 5(2):92–103

    PubMed  CAS  Google Scholar 

  • Lau PW et al (2009) Structure of the human Dicer-TRBP complex by electron microscopy. Structure 17(10):1326–1332

    PubMed Central  PubMed  CAS  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854

    PubMed  CAS  Google Scholar 

  • Lee YS et al (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23(22):2639–2649

    PubMed Central  PubMed  CAS  Google Scholar 

  • Lemaire PA et al (2008) Mechanism of PKR activation by dsRNA. J Mol Biol 381(2):351–360

    PubMed Central  PubMed  CAS  Google Scholar 

  • Leung AK, Calabrese JM, Sharp PA (2006) Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules. Proc Natl Acad Sci U S A 103(48):18125–18130

    PubMed Central  PubMed  CAS  Google Scholar 

  • Li LC et al (2006) Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A 103(46):17337–17342

    PubMed Central  PubMed  CAS  Google Scholar 

  • Li SC, Tang P, Lin WC (2007) Intronic microRNA: discovery and biological implications. DNA Cell Biol 26(4):195–207

    PubMed  Google Scholar 

  • Liao JY et al (2010) Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3′ trailers. PLoS One 5(5):e10563

    PubMed Central  PubMed  Google Scholar 

  • Lin YT, Sullivan CS (2011) Expanding the role of Drosha to the regulation of viral gene expression. Proc Natl Acad Sci U S A 108(27):11229–11234

    PubMed Central  PubMed  CAS  Google Scholar 

  • Liu J et al (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305(5689):1437–1441

    PubMed  CAS  Google Scholar 

  • Lung B et al (2006) Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res 34(14):3842–3852

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ma N et al (2011) Coexpression of an intronic microRNA and its host gene reveals a potential role for miR-483-5p as an IGF2 partner. Mol Cell Endocrinol 333(1):96–101

    PubMed  CAS  Google Scholar 

  • Ma E et al (2012) Coordinated activities of human dicer domains in regulatory RNA processing. J Mol Biol 422:466–476

    Google Scholar 

  • Maroney PA, Yu Y, Nilsen TW (2006) MicroRNAs, mRNAs, and translation. Cold Spring Harb Symp Quant Biol 71:531–535

    PubMed  CAS  Google Scholar 

  • Matranga C et al (2005) Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123(4):607–620

    PubMed  CAS  Google Scholar 

  • Meckes DG Jr et al (2010) Human tumor virus utilizes exosomes for intercellular communication. Proc Natl Acad Sci U S A 107(47):20370–20375

    PubMed Central  PubMed  Google Scholar 

  • Meister G et al (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell 15(2):185–197

    PubMed  CAS  Google Scholar 

  • Michael A et al (2010) Exosomes from human saliva as a source of microRNA biomarkers. Oral Dis 16(1):34–38

    PubMed Central  PubMed  CAS  Google Scholar 

  • Minor J et al (2012) Methylation of microRNA-9 is a specific and sensitive biomarker for oral and oropharyngeal squamous cell carcinomas. Oral Oncol 48(1):73–78

    PubMed Central  PubMed  CAS  Google Scholar 

  • Mitchell JP et al (2008) Increased exosome production from tumour cell cultures using the Integra CELLine Culture System. J Immunol Methods 335(1–2):98–105

    PubMed  CAS  Google Scholar 

  • Mitrpant C et al (2013) Improved antisense oligonucleotide design to suppress aberrant SMN2 gene transcript processing: towards a treatment for spinal muscular atrophy. PLoS One 8(4):e62114

    PubMed Central  PubMed  CAS  Google Scholar 

  • Mohammad F et al (2012) Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing. Development 139(15):2792–2803

    PubMed  CAS  Google Scholar 

  • Monteys AM et al (2010) Structure and activity of putative intronic miRNA promoters. RNA 16(3):495–505

    PubMed Central  PubMed  Google Scholar 

  • Morris KV et al (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305(5688):1289–1292

    PubMed  CAS  Google Scholar 

  • Mueller C et al (2012) Sustained miRNA-mediated knockdown of mutant AAT with simultaneous augmentation of wild-type AAT has minimal effect on global liver miRNA profiles. Mol Ther 20(3):590–600

    PubMed Central  PubMed  CAS  Google Scholar 

  • Noland CL, Ma E, Doudna JA (2011) siRNA repositioning for guide strand selection by human Dicer complexes. Mol Cell 43(1):110–121

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ohrt T et al (2006) In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5. Nucleic Acids Res 34(5):1369–1380

    PubMed Central  PubMed  CAS  Google Scholar 

  • Okamura K, Lai EC (2008) Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol 9(9):673–678

    PubMed Central  PubMed  CAS  Google Scholar 

  • Omel’ianchuk NA, Ponomarenko PM, Ponomarenko MP (2011) The nucleotide sequence features of the mature microRNA seem to be responsible for the affinity to human Ago2 AND Ago3 proteins. Mol Biol (Mosk) 45(2):366–375

    Google Scholar 

  • Ono M et al (2011) Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res 39(9):3879–3891

    PubMed Central  PubMed  CAS  Google Scholar 

  • Pan W et al (2010) MicroRNA-21 and microRNA-148a contribute to DNA hypomethylation in lupus CD4+ T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol 184(12):6773–6781

    PubMed  CAS  Google Scholar 

  • Papachristou DJ et al (2012) Immunohistochemical analysis of the endoribonucleases Drosha, Dicer and Ago2 in smooth muscle tumours of soft tissues. Histopathology 60(6B):E28–E36

    PubMed  Google Scholar 

  • Pare JM et al (2009) Hsp90 regulates the function of argonaute 2 and its recruitment to stress granules and P-bodies. Mol Biol Cell 20(14):3273–3284

    PubMed Central  PubMed  CAS  Google Scholar 

  • Park NJ et al (2009) Salivary microRNA: discovery, characterization, and clinical utility for oral cancer detection. Clin Cancer Res 15(17):5473–5477

    PubMed Central  PubMed  CAS  Google Scholar 

  • Park JE et al (2011) Dicer recognizes the 5′ end of RNA for efficient and accurate processing. Nature 475(7355):201–205

    PubMed  CAS  Google Scholar 

  • Parsi S et al (2012) Experimental verification of a predicted intronic microRNA in human NGFR gene with a potential pro-apoptotic function. PLoS One 7(4):e35561

    PubMed Central  PubMed  CAS  Google Scholar 

  • Patel RS et al (2011) High resolution of microRNA signatures in human whole saliva. Arch Oral Biol 56(12):1506–1513

    PubMed Central  PubMed  CAS  Google Scholar 

  • Pauler FM, Koerner MV, Barlow DP (2007) Silencing by imprinted noncoding RNAs: is transcription the answer? Trends Genet 23(6):284–292

    PubMed Central  PubMed  CAS  Google Scholar 

  • Perron MP, Provost P (2009) Protein components of the microRNA pathway and human diseases. Methods Mol Biol 487:369–385

    PubMed Central  PubMed  CAS  Google Scholar 

  • Place RF et al (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A 105(5):1608–1613

    PubMed Central  PubMed  CAS  Google Scholar 

  • Place RF et al (2010) Defining features and exploring chemical modifications to manipulate RNAa activity. Curr Pharm Biotechnol 11(5):518–526

    PubMed Central  PubMed  CAS  Google Scholar 

  • Portnoy V et al (2011) Small RNA and transcriptional upregulation. Wiley Interdiscip Rev RNA 2(5):748–760

    PubMed Central  PubMed  CAS  Google Scholar 

  • Regazzi R, Widmann C (2012) Genetics and molecular biology: miRNAs take the HDL ride. Curr Opin Lipidol 23(2):165–166

    PubMed  CAS  Google Scholar 

  • Rintahaka J et al (2011) Recognition of cytoplasmic RNA results in cathepsin-dependent inflammasome activation and apoptosis in human macrophages. J Immunol 186(5):3085–3092

    PubMed  CAS  Google Scholar 

  • Ro S et al (2013) The mitochondrial genome encodes abundant small noncoding RNAs. Cell Res 23(6):759–774

    PubMed  CAS  Google Scholar 

  • Rosenfeld JA et al (2009) Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics 10:143

    PubMed Central  PubMed  Google Scholar 

  • Ruby JG, Jan CH, Bartel DP (2007) Intronic microRNA precursors that bypass Drosha processing. Nature 448(7149):83–86

    PubMed Central  PubMed  CAS  Google Scholar 

  • Rudel S, Meister G (2008) Phosphorylation of Argonaute proteins: regulating gene regulators. Biochem J 413(3):e7–e9

    PubMed  Google Scholar 

  • Rudel S et al (2008) A multifunctional human Argonaute2-specific monoclonal antibody. RNA 14(6):1244–1253

    PubMed Central  PubMed  Google Scholar 

  • Rudel S et al (2011) Phosphorylation of human Argonaute proteins affects small RNA binding. Nucleic Acids Res 39(6):2330–2343

    PubMed Central  PubMed  Google Scholar 

  • Sakurai K et al (2011) A role for human Dicer in pre-RISC loading of siRNAs. Nucleic Acids Res 39(4):1510–1525

    PubMed Central  PubMed  CAS  Google Scholar 

  • Sarkar SN, Sen GC (2004) Novel functions of proteins encoded by viral stress-inducible genes. Pharmacol Ther 103(3):245–259

    PubMed  CAS  Google Scholar 

  • Schirle NT, MacRae IJ (2012) The crystal structure of human Argonaute2. Science 336(6084):1037–1040

    PubMed Central  PubMed  CAS  Google Scholar 

  • Schopman NC et al (2010) A miRNA-tRNA mix-up: tRNA origin of proposed miRNA. RNA Biol 7(5):573–576

    PubMed  CAS  Google Scholar 

  • Scian MJ et al (2011) MicroRNA profiles in allograft tissues and paired urines associate with chronic allograft dysfunction with IF/TA. Am J Transplant 11(10):2110–2122

    PubMed Central  PubMed  CAS  Google Scholar 

  • Scott MS, Ono M (2011) From snoRNA to miRNA: dual function regulatory non-coding RNAs. Biochimie 93(11):1987–1992

    PubMed Central  PubMed  CAS  Google Scholar 

  • Sen GL, Blau HM (2005) Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat Cell Biol 7(6):633–636

    PubMed  CAS  Google Scholar 

  • Shenoy A, Blelloch R (2009) Genomic analysis suggests that mRNA destabilization by the microprocessor is specialized for the auto-regulation of Dgcr8. PLoS One 4(9):e6971

    PubMed Central  PubMed  Google Scholar 

  • Sigurdsson MI et al (2012) The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system. BMC Genet 13:31

    PubMed Central  PubMed  CAS  Google Scholar 

  • Singh M et al (2011) Stress-induced phosphorylation of PACT reduces its interaction with TRBP and leads to PKR activation. Biochemistry 50(21):4550–4560

    PubMed  CAS  Google Scholar 

  • Skalsky RL et al (2012) The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog 8(1):e1002484

    PubMed Central  PubMed  CAS  Google Scholar 

  • Stefani G, Slack FJ (2012) A ‘pivotal’ new rule for microRNA-mRNA interactions. Nat Struct Mol Biol 19(3):265–266

    PubMed  CAS  Google Scholar 

  • Stern-Ginossar N et al (2007) Host immune system gene targeting by a viral miRNA. Science 317(5836):376–381

    PubMed  CAS  Google Scholar 

  • Su H et al (2009) Essential and overlapping functions for mammalian Argonautes in microRNA silencing. Genes Dev 23(3):304–317

    PubMed Central  PubMed  CAS  Google Scholar 

  • Suzuki Y et al (2009) The Hsp90 inhibitor geldanamycin abrogates colocalization of eIF4E and eIF4E-transporter into stress granules and association of eIF4E with eIF4G. J Biol Chem 284(51):35597–35604

    PubMed Central  PubMed  CAS  Google Scholar 

  • Svoboda P et al (2004) RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos. Dev Biol 269(1):276–285

    PubMed  CAS  Google Scholar 

  • Tahbaz N et al (2004) Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer. EMBO Rep 5(2):189–194

    PubMed Central  PubMed  CAS  Google Scholar 

  • Takimoto K, Wakiyama M, Yokoyama S (2009) Mammalian GW182 contains multiple Argonaute-binding sites and functions in microRNA-mediated translational repression. RNA 15(6):1078–1089

    PubMed Central  PubMed  CAS  Google Scholar 

  • Tang R et al (2012) Mouse miRNA-709 directly regulates miRNA-15a/16-1 biogenesis at the posttranscriptional level in the nucleus: evidence for a microRNA hierarchy system. Cell Res 22(3):504–515

    PubMed Central  PubMed  CAS  Google Scholar 

  • Ting AH et al (2008) A requirement for DICER to maintain full promoter CpG island hypermethylation in human cancer cells. Cancer Res 68(8):2570–2575

    PubMed Central  PubMed  CAS  Google Scholar 

  • Triboulet R et al (2009) Post-transcriptional control of DGCR8 expression by the Microprocessor. RNA 15(6):1005–1011

    PubMed Central  PubMed  CAS  Google Scholar 

  • Tsuchiya S et al (2009) MicroRNA-338-3p and microRNA-451 contribute to the formation of basolateral polarity in epithelial cells. Nucleic Acids Res 37(11):3821–3827

    PubMed Central  PubMed  CAS  Google Scholar 

  • Turner AM et al (2012) Characterization of an HIV-targeted transcriptional gene-silencing RNA in primary cells. Hum Gene Ther 23(5):473–483

    PubMed Central  PubMed  CAS  Google Scholar 

  • Valadi H et al (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 9(6):654–659

    PubMed  CAS  Google Scholar 

  • Valdmanis PN et al (2012) Expression determinants of mammalian argonaute proteins in mediating gene silencing. Nucleic Acids Res 40(8):3704–3713

    PubMed Central  PubMed  CAS  Google Scholar 

  • Vickers KC et al (2011) MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins. Nat Cell Biol 13(4):423–433

    PubMed Central  PubMed  CAS  Google Scholar 

  • von Brandenstein M et al (2012) MicroRNA 15a, inversely correlated to PKCalpha, is a potential marker to differentiate between benign and malignant renal tumors in biopsy and urine samples. Am J Pathol 180(5):1787–1797

    Google Scholar 

  • Wada T, Kikuchi J, Furukawa Y (2012) Histone deacetylase 1 enhances microRNA processing via deacetylation of DGCR8. EMBO Rep 13(2):142–149

    PubMed Central  PubMed  CAS  Google Scholar 

  • Wang Z et al (2011) DNA hypermethylation of microRNA-34b/c has prognostic value for stage non-small cell lung cancer. Cancer Biol Ther 11(5):490–496

    PubMed  CAS  Google Scholar 

  • Wang LL et al (2012a) The potential role of microRNA-146 in Alzheimer’s disease: biomarker or therapeutic target? Med Hypotheses 78(3):398–401

    PubMed  CAS  Google Scholar 

  • Wang X et al (2012b) Induction of NANOG expression by targeting promoter sequence with small activating RNA antagonizes retinoic acid-induced differentiation. Biochem J 443(3):821–828

    PubMed Central  PubMed  CAS  Google Scholar 

  • Watanabe T et al (2006) Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 20(13):1732–1743

    PubMed Central  PubMed  CAS  Google Scholar 

  • Wee EJ et al (2012) Mapping the regulatory sequences controlling 93 breast cancer-associated miRNA genes leads to the identification of two functional promoters of the Hsa-mir-200b cluster, methylation of which is associated with metastasis or hormone receptor status in advanced breast cancer. Oncogene 31:4182–4195

    Google Scholar 

  • Weinberg MS et al (2006) The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12(2):256–262

    PubMed Central  PubMed  CAS  Google Scholar 

  • Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75(5):855–862

    PubMed  CAS  Google Scholar 

  • Wong KY, Huang X, Chim C (2012) DNA methylation of microRNA genes in multiple myeloma. Carcinogenesis. doi:10.1093/carcin/bgs212

  • Wu YL et al (2011) A non-coding RNA of insect HzNV-1 virus establishes latent viral infection through microRNA. Sci Rep 1:60

    PubMed Central  PubMed  Google Scholar 

  • Yan L et al (2011) Intronic microRNA suppresses endothelial nitric oxide synthase expression and endothelial cell proliferation via inhibition of STAT3 signaling. Mol Cell Biochem 357(1–2):9–19

    PubMed  CAS  Google Scholar 

  • Yang JS et al (2010) Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis. Proc Natl Acad Sci U S A 107(34):15163–15168

    PubMed Central  PubMed  CAS  Google Scholar 

  • Yang C et al (2012) Identification of seven serum microRNAs from a genome-wide serum microRNA expression profile as potential noninvasive biomarkers for malignant astrocytomas. Int J Cancer

  • Yi R et al (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17(24):3011–3016

    PubMed Central  PubMed  CAS  Google Scholar 

  • Yi R et al (2005) Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. RNA 11(2):220–226

    PubMed Central  PubMed  CAS  Google Scholar 

  • Younger ST, Corey DR (2009) The puzzle of RNAs that target gene promoters. Chembiochem 10(7):1135–1139

    PubMed Central  PubMed  CAS  Google Scholar 

  • Younger ST, Corey DR (2011) Transcriptional gene silencing in mammalian cells by miRNA mimics that target gene promoters. Nucleic Acids Res 39(13):5682–5691

    PubMed Central  PubMed  CAS  Google Scholar 

  • Younger ST, Pertsemlidis A, Corey DR (2009) Predicting potential miRNA target sites within gene promoters. Bioorg Med Chem Lett 19(14):3791–3794

    PubMed Central  PubMed  CAS  Google Scholar 

  • Yu N et al (2011) Double-stranded RNA induces melanocyte death via activation of Toll-like receptor 3. Exp Dermatol 20(2):134–139

    PubMed  CAS  Google Scholar 

  • Yu F et al (2012) MicroRNA 34c gene down-regulation via DNA methylation promotes self-renewal and epithelial-mesenchymal transition in breast tumor-initiating cells. J Biol Chem 287(1):465–473

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zahm AM et al (2012) Circulating MicroRNA is a biomarker of biliary Atresia. J Pediatr Gastroenterol Nutr 55:366–369

    Google Scholar 

  • Zampetaki A et al (2012) Profiling of circulating microRNAs: from single biomarkers to re-wired networks. Cardiovasc Res 93(4):555–562

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zen K, Zhang CY (2012) Circulating microRNAs: a novel class of biomarkers to diagnose and monitor human cancers. Med Res Rev 32(2):326–348

    PubMed  Google Scholar 

  • Zeng Y, Cullen BR (2004) Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res 32(16):4776–4785

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zeng Y et al (2008) Phosphorylation of Argonaute 2 at serine-387 facilitates its localization to processing bodies. Biochem J 413(3):429–436

    PubMed  CAS  Google Scholar 

  • Zhang X, Zeng Y (2010) The terminal loop region controls microRNA processing by Drosha and Dicer. Nucleic Acids Res 38(21):7689–7697

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zhang X et al (2009) Alterations in miRNA processing and expression in pleomorphic adenomas of the salivary gland. Int J Cancer 124(12):2855–2863

    PubMed  CAS  Google Scholar 

  • Zhang Y et al (2010) Secreted monocytic miR-150 enhances targeted endothelial cell migration. Mol Cell 39(1):133–144

    PubMed  CAS  Google Scholar 

  • Zhao Z et al (2012) Circulating microRNA miR-323-3p as a biomarker of ectopic pregnancy. Clin Chem 58(5):896–905

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zhou H, Huang C, Xia XG (2008) A tightly regulated Pol III promoter for synthesis of miRNA genes in tandem. Biochim Biophys Acta 1779(11):773–779

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zhou X et al (2012a) MicroRNA-9 as potential biomarker for breast cancer local recurrence and tumor estrogen receptor status. PLoS One 7(6):e39011

    PubMed Central  PubMed  CAS  Google Scholar 

  • Zhou J et al (2012b) Transcriptional gene silencing of HPV16 E6/E7 induces growth inhibition via apoptosis in vitro and in vivo. Gynecol Oncol 124(2):296–302

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran

    Sadegh Azimzadeh Jamalkandi

  2. Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran

    Esmaeel Azadian & Ali Masoudi-Nejad

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  1. Sadegh Azimzadeh Jamalkandi
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  2. Esmaeel Azadian
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  3. Ali Masoudi-Nejad
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Correspondence to Ali Masoudi-Nejad.

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Sadegh Azimzadeh Jamalkandi and Esmaeel Azadian contributed equally to the manuscript.

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Azimzadeh Jamalkandi, S., Azadian, E. & Masoudi-Nejad, A. Human RNAi pathway: crosstalk with organelles and cells. Funct Integr Genomics 14, 31–46 (2014). https://doi.org/10.1007/s10142-013-0344-1

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