1,110
Views
7
CrossRef citations to date
0
Altmetric
Research Paper

Short versus long double-stranded RNA activation of a post-transcriptional gene knockdown pathway

, , , , , , & show all
Pages 1766-1775 | Received 26 Apr 2017, Accepted 11 Jul 2017, Published online: 03 Nov 2017

References

  • Saleh MC, Tassetto M, van Rij RP, Goic B, Gausson V, Berry B, Jacquier C, Antoniewski C, Andino R. Antiviral immunity in Drosophila requires systemic RNA interference spread. Nature. 2009;458:346–50. doi:10.1038/nature07712.
  • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998;391:806–11. doi:10.1038/35888.
  • Sagi A, Manor R, Ventura T. Gene silencing in crustaceans: From basic research to biotechnologies. Genes. 2013;4:620–45. doi:10.3390/genes4040620.
  • Czech MP, Aouadi M, Tesz GJ. RNAi-based therapeutic strategies for metabolic disease. Nat Rev Endocrinol. 2011;7:473–84. doi:10.1038/nrendo.2011.57.
  • Winston WM, Molodowitch C, Hunter CP. Systemic RNAi in C-elegans requires the putative transmembrane protein SID-1. Science. 2002;295:2456–9. doi:10.1126/science.1068836.
  • Feinberg EH, Hunter CP. Transport of dsRNA into cells by the transmembrane protein SID-1. Science. 2003;301:1545–7. doi:10.1126/science.1087117.
  • Shih JD, Hunter CP. SID-1 is a dsRNA-selective dsRNA-gated channel. Rna-a Publication of the Rna Society. 2011;17:1057–65. doi:10.1261/rna.2596511.
  • Saleh M-C, van Rij RP, Hekele A, Gillis A, Foley E, O'Farrell PH, Andino R. The endocytic pathway mediates cell entry of dsRNA to induce RNAi silencing. Nat Cell Biol. 2006;8:793–802. doi:10.1038/ncb1439.
  • Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21-and 22-nucleotide RNAs. Gene Dev. 2001;15:188–200. doi:10.1101/gad.862301.
  • Dykxhoorn DM, Novina CD, Sharp PA. Killing the messenger: Short RNAs that silence gene expression. Nat Rev Mol Cell Biol. 2003;4:457–67. doi:10.1038/nrm1129.
  • Carthew RW, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs. Cell. 2009;136:642–55. doi:10.1016/j.cell.2009.01.035.
  • Ender C, Meister G. Argonaute proteins at a glance. J Cell Sci. 2010;123:1819–23. doi:10.1242/jcs.055210.
  • Lee Y, Ahn C, Han JJ, Choi H, Kim J, Yim J, Lee J, Provost P, Rådmark O, Kim S, et al. The nuclear RNase III Drosha initiates microRNA processing. Nature. 2003;425:415–9. doi:10.1038/nature01957.
  • Kadener S, Rodriguez J, Abruzzi KC, Khodor YL, Sugino K, Marr MT, Nelson S, Rosbash M. Genome-wide identification of targets of the drosha-pasha/DGCR8 complex. Rna-a Publication of the Rna Society. 2009;15:537–45. doi:10.1261/rna.1319309.
  • Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol. 2009;10:126–39. doi:10.1038/nrm2632.
  • Okamura K, Ishizuka A, Siomi H, Siomi MC. Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Gene Dev. 2004;18:1655–6. doi:10.1101/gad.1210204.
  • Janowski BA, Huffman KE, Schwartz JC, Ram R, Nordsell R, Shames DS, Minna JD, Corey DR. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat Struct Mol Biol. 2006;13:787–92. doi:10.1038/nsmb1140.
  • Noma K, Sugiyama T, Cam H, Verdel A, Zofall M, Jia ST, Moazed D, Grewal SI. RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat Genet. 2004;36:1174–80. doi:10.1038/ng1452.
  • Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature. 2009;457:413–20. doi:10.1038/nature07756.
  • Verdel A, Jia ST, Gerber S, Sugiyama T, Gygi S, Grewal SIS, Martienssen RA, Yanagida M. RNAi-mediated targeting of heterochromatin by the RITS complex. Science. 2004;303:672–6. doi:10.1126/science.1093686.
  • Thomson T, Lin HF. The biogenesis and function of PIWI proteins and piRNAs: progress and prospect. Annu Rev Cell Dev Biol. 2009;25:355–76. doi:10.1146/annurev.cellbio.24.110707.175327.
  • Ventura T, Manor R, Aflalo ED, Weil S, Rosen O, Sagi A. Timing sexual differentiation: Full functional sex reversal achieved through silencing of a single insulin-like gene in the prawn, Macrobrachium rosenbergii. Biol Reprod. 2012;86:90. doi:10.1095/biolreprod.111.097261.
  • Shpak N, Manor R, Aflalo ED, Sagi A. Three generations of cultured prawn without W chromosome. Aquaculture. 2017;467:41–8. doi:10.1016/j.aquaculture.2016.06.008
  • Aflalo E, Hoang T, Nguyen V, Lam Q, Nguyen D, Trinh Q, Raviv S, Sagi A. A novel two-step procedure for mass production of all-male populations of the giant freshwater prawn Macrobrachium rosenbergii. Aquaculture. 2006;256:468–78. doi:10.1016/j.aquaculture.2006.01.035
  • Nair CM, Salin KR, Raju MS, Sebastian M. Economic analysis of monosex culture of giant freshwater prawn (Macrobrachium rosenbergii De Man): A case study. Aquac Res. 2006;37:949–54. doi:10.1111/j.1365-2109.2006.01521.x.
  • Manor R, Weil S, Oren S, Glazer L, Aflalo ED, Ventura T, Chalifa-Caspi V, Lapidot M, Sagi A. Insulin and gender: An insulin-like gene expressed exclusively in the androgenic gland of the male crayfish. Gen Comp Endocrinol. 2007;150:326–36. doi:10.1016/j.ygcen.2006.09.006.
  • Ventura T, Rosen O, Sagi A. From the discovery of the crustacean androgenic gland to the insulin-like hormone in six decades. Gen Comp Endocrinol. 2011;173:381–8. doi:10.1016/j.ygcen.2011.05.018.
  • Ventura T, Manor R, Aflalo ED, Weil S, Raviv S, Glazer L, Sagi A. Temporal silencing of an androgenic gland-specific insulin-like gene affecting phenotypical gender differences and spermatogenesis. Endocrinology. 2009;150:1278–86. doi:10.1210/en.2008-0906.
  • Labreuche Y, Warr GW. Insights into the antiviral functions of the RNAi machinery in penaeid shrimp. Fish Shellfish Immunol. 2013;34:1002–10. doi:10.1016/j.fsi.2012.06.008.
  • Dowling D, Pauli T, Donath A, Meusemann K, Podsiadlowski L, Petersen M, Peters RS, Mayer C, Liu S, Zhou X, et al. Phylogenetic origin and diversification of RNAi pathway genes in insects. Genome Biology and Evolution. 2017;8(12):3784–3793. doi:10.1093/gbe/evw281..
  • Rao DD, Vorhies JS, Senzer N, Nemunaitis J. siRNA vs. shRNA: Similarities and differences. Adv Drug Delivery Rev. 2009;61:746–59. doi:10.1016/j.addr.2009.04.004.
  • van Rij RP, Andino R. The silent treatment: RNAi as a defense against virus infection in mammals. Trends Biotechnol. 2006;24:186–93. doi:10.1016/j.tibtech.2006.02.006.
  • Aflalo ED, Dandu RVSN, Verghese JT, Rao N, Samraj TYC, Ovadia O, Sagi A. Neo-females production and all-male progeny of a cross between two Indian strains of prawn (Macrobrachium rosenbergii): Population structure and growth performance under different harvest strategies. Aquaculture 2014;428:7–15. doi:10.1016/j.aquaculture.2014.02.021
  • Alkalay AS, Rosen O, Sokolow SH, Faye YPW, Faye DS, Aflalo ED, Jouanard N, Zilberg D, Huttinger E, Sagi A. The prawn Macrobrachium vollenhovenii in the senegal river basin: Towards sustainable restocking of all-male populations for biological control of schistosomiasis. PLoS Negl Trop Dis. 2014;8:e3060. doi:10.1371/journal.pntd.0003060.
  • Lezer Y, Aflalo ED, Manor R, Sharabi O, Abilevich LK, Sagi A. On the safety of RNAi usage in aquaculture: The case of all-male prawn stocks generated through manipulation of the insulin-like androgenic gland hormone. Aquaculture. 2015;435:157–66. doi:10.1016/j.aquaculture.2014.09.040
  • Meister G, Tuschl T. Mechanisms of gene silencing by double-stranded RNA. Nature. 2004;431:343–9. doi:10.1038/nature02873.
  • Myers JW, Ferrell JE. Silencing gene expression with Dicer-generated siRNA pools. RNA Silencing: Methods and Protocols. 2005:93–196. doi:10.1385/1-59259-935-4:093.
  • Xie JF, Lu L, Deng M, Weng SP, Zhu JY, Wu Y, Gan L, Chan SM, He J. Inhibition of reporter gene and Iridovirus-tiger frog virus in fish cell by RNA interference. Virology. 2005;338:43–52. doi:10.1016/j.virol.2005.04.040.
  • Dang LT, Kondo H, Hirono I, Aoki T. Inhibition of red seabream iridovirus (RSIV) replication by small interfering RNA (siRNA) in a cell culture system. Antivir Res. 2008;77:142–9. doi:10.1016/j.antiviral.2007.10.007.
  • Dechklar M, Udomkit A, Panyim S. Characterization of Argonaute cDNA from Penaeus monodon and implication of its role in RNA interference. Biochem Biophys Res Commun. 2008;367:768–74. doi:10.1016/j.bbrc.2008.01.031.
  • Wang S, Chen AJ, Shi LJ, Zhao XF, Wang JX. TRBP and eIF6 homologue in Marsupenaeus japonicus play crucial roles in antiviral response. PLoS ONE. 2012;7:e30057. doi:10.1371/journal.pone.0030057.
  • Sharabi O, Manor R, Weil S, Aflalo ED, Lezer Y, Levy T, Aizen J, Ventura T, Mather PB, Khalaila I, et al. Identification and characterization of an insulin-like receptor involved in crustacean reproduction. Endocrinology. 2016;157:928–41. doi:10.1210/en.2015-1391.
  • Shih JD, Fitzgerald MC, Sutherlin M, Hunter CP. The SID-1 double-stranded RNA transporter is not selective for dsRNA length. RNA. 2009;15:384–90. doi:10.1261/rna.1286409.
  • Shpak N, Manor R, Aflalo ED, Sagi A. Three generations of cultured prawn without W chromosome. Aquaculture. 2017;467:41–48. doi:10.1016/j.aquaculture.2016.06.008.
  • Kuris AM, Raanan Z, Sagi A, Cohen D. Morphotypic differentiation of male malaysian giant prawns, Macrobrachium rosenbergii. J Crustac Biol. 1987;7:219–37. doi:10.2307/1548603
  • Ventura T, Manor R, Aflalo ED, Weil S, Khalaila I, Rosen O, Sagi A. Expression of an androgenic gland-specific insulin-like peptide during the course of prawn sexual and morphotypic differentiation. ISRN endocrinology. 2011;2011:476283. doi:10.5402/2011/476283.
  • Ventura T, Manor R, Aflalo ED, Chalifa-Caspi V, Weil S, Sharabi O, Sagi A. Post-embryonic transcriptomes of the prawn Macrobrachium rosenbergii: Multigenic succession through metamorphosis. PLoS ONE. 2013;8:e55322. doi:10.1371/journal.pone.0055322.
  • Schultz J, Milpetz F, Bork P, Ponting CP. SMART, a simple modular architecture research tool: Identification of signaling domains. Proc Natl Acad Sci U S A. 1998;95:5857–64. doi:10.1073/pnas.95.11.5857.
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9. doi:10.1093/molbev/mst197.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.