Abstract
The posttranscriptional gene silencing mechanism initially mistaken as co-suppression but later identified as RNA interference mediated and regulated by small interfering RNAs (siRNAs), and microRNAs (miRNAs) has gradually emerged as a landmark discovery of the last decade. siRNA-based therapeutics is currently being investigated as an emerging opportunity for healthcare. The lack of structural data of the RNA-induced silencing complex and its key players has hindered the progress of utilization of this unique mechanism in the betterment of humanity. Crystallographic information regarding the Argonaute (Ago)-DNA-RNA complexes have helped in understanding the chemistry of the complex, but other valuable structural details still remain elusive. It is an immediate requirement to understand the exact mechanisms of interactions that occur between the key players of the microprocessor complex or for that matter the holo-RISC. Unless these interaction maps are obtained, complete effective usage and manipulation of this natural phenomenon shall remain uphill tasks for researchers worldwide. To harness the complete potential of siRNAs as therapeutic agents, various chemical modifications need to be performed to prevent nuclease attack, immune activation, increase the specificity of the interaction, and improve pharmacodynamics of the interacting components. Computational molecular dynamics simulations provide a probabilistic alternative for studying such complex structures. Both flexible and rigid docking processes can be utilized to understand the specificities of interactions as both protein-protein and protein nucleic acid docking algorithms have been implemented in free and licensed softwares, complexes obtained from which can then be subjected to analyses using the various interaction mapping tools to formulate a classical map of the RNAi interactome. In this chapter we attempt to elucidate the interactions of the key members of the holo-RISC complex using molecular docking and simulation. Specific interacting residues having the potential to serve as interacting hotspots were identified.
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References
Amarzguioui M et al (2003) Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res 31:589–595
Chiu YL, Rana TM (2003) siRNA function in RNAi: a chemical modification analysis. RNA 9:1034–1048
Das AK et al (2011) Secondary structural analysis of MicroRNA and their precursors in plants. Int J Agric Sci 3(1):62–64
Denli AM et al (2004) Processing of primary microRNAs by the microprocessor complex. Nature 432(7014):231–235
Elbashir SM, Lendeckel W, Tuschl T (2001a) RNA interference is mediated by 21 and 22 nt RNAs. Genes Dev 15:188–200
Elbashir SM et al (2001b) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411(6836):494–498
Elbashir SM et al (2001c) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20(23):6877–6888
Fire A et al (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811
Ganguli S, Datta A (2014) In silico mutagenesis reveals specific binding residues that regulate KSRP – microRNA precursor interactions in human. Ann Res Rev Biol 4(1):143–153
Ganguli S, De M, Datta A (2011) Analyses of argonaute– microRNA interactions in Zea mays. Int J Comput Biol 2(1):32–34
Hamilton AJ, Baulcombe DC (1999) A species ofsmall antisense RNA in posttranscriptional gene silencing in plants. Science 286:950–952
Hammond SM et al (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404(6775):293–296
Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297:2056–2060
Liu Q et al (2003) R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301:1921–1925
Ma JB et al (2005) Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434(7033):666–670
Newman MA, Scott M (2010) Hammond emerging paradigms of regulated microRNA processing. Genes Dev 24:1086–1092
Martinez J et al (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110:563–574
Nykänen A, Haley B, Zamore PD (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107:309–321
Okamura K et al (2004) Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev 18:1655–1666
Orban TI, Izaurralde E (2005) Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA 11:459–469
Parisien M, Major F (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452:51–55
Parker JS, Roe SM, Barford D (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 23:4727–4737
Parker JS, Roe SM, Barford D (2005) Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434:663–666
Parrish S et al (2000) Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. Mol Cell 6:1077–1087
Pham JW et al (2004) A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117:83–94
Rand TA et al (2004) Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc Natl Acad Sci U S A 101:14385–14389
Schwarz DS et al (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199–208
Song JJ et al (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305:1434–1437
Tomari Y et al (2004a) RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116:831–841
Tomari Y et al (2004b) A protein sensor for siRNA asymmetry. Science 306:1377–1380
Tuschl T et al (1999) Targeted mRNA degradation by doublestranded RNA in vitro. Genes Dev 13:3191–3197
Zamore PD et al (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25–33
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Datta, A., Ganguli, S. (2018). The Interactomics of the RNA-Induced Silencing Complex. In: Wadhwa, G., Shanmughavel, P., Singh, A., Bellare, J. (eds) Current trends in Bioinformatics: An Insight. Springer, Singapore. https://doi.org/10.1007/978-981-10-7483-7_11
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DOI: https://doi.org/10.1007/978-981-10-7483-7_11
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