МЕТОД

Нокдаун генов с использованием малых интерферирующих РНК

Информация об авторах

1 Лаборатория функциональной геномики,
Медико-генетический научный центр, Москва

2 Лаборатория медицинских генетических технологий, отдел фундаментальных исследований НИМСИ,
Московский государственный медико-стоматологический университет имени А. И. Евдокимова, Москва

3 Лаборатория функционального анализа генома,
Московский физико-технический институт (государственный университет), Долгопрудный

Для корреспонденции: Скоблов Михаил Юрьевич
ул. Москворечье, д. 1, Москва, 115478; moc.liamg@volboksm

Информация о статье

Вклад авторов в работу: Ю. В. Вяхирева — анализ литературы, планирование исследования, сбор, анализ и интерпретация данных, подготовка черновика рукописи; А. Ю. Филатова — анализ литературы, сбор, анализ и интерпретация данных, подготовка черновика рукописи; И. А. Кривошеева — анализ литературы, сбор, анализ и интерпретация данных, подготовка черновика рукописи; М. Ю. Скоблов — подготовка черновика рукописи. Все авторы принимали участие во внесении исправлений в текст рукописи.

Статья получена: 25.06.2017 Статья принята к печати: 28.06.2017 Опубликовано online: 19.07.2017
|
  1. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski E et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep; 22 (9): 1760–74. DOI: 10.1101/gr.135350.111.
  2. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 2014 Feb; 21 (2): 198–206. DOI: 10.1038/nsmb.2764.
  3. Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B et al. MEG3 long noncoding RNA regulates the TGF-beta pathway genes through formation of RNA-DNA triplex structures. Nat Commun. 2015 Jul 24; 6: 7743. DOI: 10.1038/ncomms8743.
  4. Tufarelli C, Stanley JA, Garrick D, Sharpe JA, Ayyub H, Wood WG et al. Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet. 2003 Jun; 34 (2): 157–65. DOI: 10.1038/ng1157.
  5. Yap KL, Li S, Munoz-Cabello AM, Raguz S, Zeng L, Mujtaba S et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell. 2010 Jun 11; 38 (5): 662–74. DOI: 10.1016/j.molcel.2010.03.021.
  6. Prelich G. Gene overexpression: uses, mechanisms, and interpretation. Genetics. 2012 Mar; 190 (3): 841–54. DOI: 10.1534/genetics.111.136911.
  7. Skoblov MYu. Prospects of technologies of antisense therapy. Mol Biol (Mosk). 2009; 43 (6): 917–29.
  8. Zamecnik PC, Stephenson ML. Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proc Natl Acad Sci U S A. 1978 Jan; 75 (1): 280–4.
  9. Марахонов А. В., Баранова А. В., Скоблов М. Ю. РНК-интерференция: фундаментальные и прикладные аспекты. Медицинская генетика. 2008; 7 (10): 44–56.
  10. Glebova K, Reznik ON, Reznik AO, Mehta R, Galkin A, Baranova A et al. Technology in Kidney Transplantation: Current Status and Future Potential. BioDrugs. 2014 Aug; 28 (4): 345–61. DOI: 10.107/s40259-014-0087-0.
  11. Glebova KV, Marakhonov AV, Baranova AV, Skoblov MIu. Therapeutic siRNAs and nonviral systems for their delivery. Mol Biol (Mosk). 2012 May–Jun; 46 (3): 371–86.
  12. Филатова А. Ю., Скоблов М. Ю. Использование siРНК в терапии кардиоваскулярных заболеваний. Клиническая и экспериментальная хирургия. 2014; (4): 12–9.
  13. Вяхирева Ю. В., Зернов Н. В., Марахонов А. В., Гуськова А. А., Скоблов М. Ю. Современные подходы к лечению миодистрофий. Медицинская генетика. 2016; 15 (10): 3–16.
  14. Ramachandran PV, Ignacimuthu S. RNA interference--a silent but an efficient therapeutic tool. Appl Biochem Biotechnol. 2013 Mar; 169 (6): 774–89. DOI: 10.1007/s12010-013-0098-1.
  15. O’Keefe EP. siRNAs and shRNAs: Tools for Protein Nockdown by Gene Silencing. Mater Methods. 2013; 3: 197. DOI: 10.13070/mm.en.3.197.
  16. Chaudhary A, Srivastava S, Garg S. Development of a software tool and criteria evaluation for efficient design of small interfering RNA. Biochem Biophys Res Commun. 2011 Jan 7; 404 (1): 313–20. DOI: 10.1016/j,bbrc.2010.11.114.
  17. Jackson AL, Linsley PS. Recognizing and avoiding siRNA off- target effects for target identification and therapeutic application. Nat Rev Drug Discov. 2010 Jan; 9 (1): 57–67. DOI: 10.1038/nrd3010.
  18. Ahlquist P. RNA-dependent RNA polymerases, viruses, and RNA silencing. Science. 2002 May 17; 296 (5571): 1270–3. DOI: 10.1126/science.1069132.
  19. Applied Biosystems Inc. Reduced siRNA Concentrations Lead to Fewer Off-Target Effects. TechNotes. 2008; 15 (2): 13–5.
  20. Zhang J, Wu Q, Wang Z, Zhang Y, Zhang G, Fu J et al. Knockdown of PSF1 expression inhibits cell proliferation in lung cancer cells in vitro. Tumour Biol. 2014 Nov 15; 36 (3): 2163–8. DOI: 10.1007/ s13277-014-2826-8.
  21. Yu D, Makkar G, Dong T, Strickland DK, Sarkar R, Monahan TS MARCKS Signaling Differentially Regulates Vascular Smooth Muscle and Endothelial Cell Proliferation through a KIS-, p27kip1- Dependent Mechanism. PLoS One. 2015; 10 (11): e0141397. DOI: 10.1371/journal.pone.0141397.
  22. Huang XH, Jian WH, Wu ZF, Zhao J, Wang H, Li W et al. Small interfering RNA (siRNA)-mediated knockdown of macrophage migration inhibitory factor (MIF) suppressed cyclin D1 expression and hepatocellular carcinoma cell proliferation. Oncotarget. 2014 Jul; 5 (14): 5570–80. DOI: 10.18632/oncotarget.2141.
  23. Takasaki S. Selecting effective siRNA target sequences by using Bayes' theorem. Comput Biol Chem. 2009 Oct; 33 (5): 368–72. DOI: 10.1016/j.compbiolchem.2009.07.009.
  24. Gorodkin J, Ruzzo WL, editors. RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Vol. 1097. New York: Springer Science+Business Media; 2014. DOI: 10.1007/978-1-62703-709-9_1.
  25. Takasaki S. Methods for selecting effective siRNA target sequences using a variety of statistical and analytical techniques. Methods Mol Biol. 2013; 942: 17–55.
  26. Lagana A, Veneziano D, Russo F, Pulvirenti A, Giugno R, Croce MC et al. Computational design of artificial RNA molecules for gene regulation. Methods Mol Biol. 2015; 1269: 393–412.
  27. Cui W, Ning J, Nail UP, Duncan MK. OptiRNAi, an RNAi design tool. Comput Methods Programs Biomed. 2004 Jul; 75 (1): 67–73. DOI: 10.1016/j.cmpb.2003.09.002.
  28. Naito Y, Yoshimura J, Morisita S, Ui-Tei K. siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics. 2009 Nov 30; 10: 392. DOI: 10.1186/1471-2105-10-392.
  29. Matveeva O, Nechipurenko Y, Rossi L, Moore B, Saetrom P, Ogurtsov AY et al. Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res. 2007 Apr 10; 35 (8): e63. DOI: 10.1093/nar/gkm088.
  30. Katoh T, Suzuki T. Specific residues at every third position of siRNA shape its efficient RNAi activity. Nucleic Acids Res. 2007 Jan 26; 35 (4): e27. DOI: 10.1093/nar/gkl1120.
  31. JiangP,WuH,DaY,SangF,WeiJ,SunXetal.RFRCDB- siRNA: improved design of siRNAs by random forest regression model coupled with database searching. Comput Methods Programs Biomed. 2007 Sep; 87 (3): 230–8. DOI: 10.1016/j.cmpb.2007.06.001.
  32. Lu ZJ, Mathews DH. OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Res. 2008 Jul 1; 36 (Web Server issue): W104–8. DOI: 10.1093/nar/gkn250.
  33. Ding Y, Chan CY, Lawrence CE. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 2004 Jul 1; 32 (Web Server issue): W135–41. DOI: 10.1093/nar/gkh449.
  34. Vert JP, Foveau N, Lajaunie C, Vandenbrouck Y. An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinformatics. 2006 Nov 30; 7: 520. DOI: 10.1186/1471-2105-7-520.
  35. Xu P, Zhang Y, Kang L, Roossinck MJ, Mysore KS. Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiol. 2006 Oct; 142 (2): 429–40. DOI: 10.1104/pp.106.083295.
  36. Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J et al. The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol. 2008 May; 26 (5): 578–83. DOI: 10.1038/nbt1404.
  37. Ichihara M, Murakumo Y, Masuda A, Matsuura T, Asai N, Jijiwa M et al. Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic Acids Res. 2007; 35 (18): e123. DOI: 10.1093/nar/gkm699.
  38. Eurofins Genomics. siMAX siRNA - The RNA Interfering Molecule, siRNA Controls, Non Specific Control 47% GC [Internet]. [cited 2017 Jun] Available from: https://www.eurofinsgenomics.eu/en/dna-rna-oligonucleotides/custom-rna-oligos/simax-sirna.aspx
  39. Zirzow AC, Skoblov M, Patanarut A, Smith C, Fisher A, Chandhoke V et al. Nanoscale «DNA baskets» for the Delivery of siRNA. In: Herold KE, Vossoughi J, Bentley WE, editors. IFMBE Proceedings: 26th Southern Biomedical Engineering Conference SBEC 2010; 2010 Apr 30–May 2; College Park, Maryland, USA. Berlin. Heidelberg: Springer; 2010. p. 130–3.
  40. Glebova KV, Marakhonov AV, Baranova AV, Skoblov MYu. Nonviral delivery systems for small interfering RNAs. Mol Biol (Mosk). 2012; 46 (3): 349–61.
  41. Марахонов А. В., Сержанова В. А., Скоблов М. Ю., Баранова А. В. Разработка системы тестирования средств доставки миРНК. Медицинская генетика. 2010; 9 (12): 12–5.
  42. Biontex Laboratories. Metafectene Manual [Internet]. [cited 2017 Jun] Available from: http://www.n-genetics.com/file/Manual_ METAFECTENE_en.pdf
  43. Invitrogen. TRIzolTM Reagent User Guide [Internet]. [cited 2017 Jun] Available from: https://tools.thermofisher.com/content/sfs/manuals/trizol_reagent.pdf
  44. Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr; 162 (1): 156–9.
  45. Green MR, Sambrook J, editors. Molecular Cloning. A Laboratory Manual. 4th ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 2012.
  46. Diagenode. Bioruptor User Manual [Internet]. [cited 2017 Jun] Available from: http://ipmb.sinica.edu.tw/microarray/index.files/Bioruptor%20Manual.pdf
  47. Thermo Fischer Scientific Inc. DNAse I RNAse free User Guide [Internet]. [cited 2017 Jun] Available from: https://tools.thermofisher.com/content/sfs/manuals/MAN0012000_DNase_I_ RNasefree_1UuL_UG.pdf
  48. Stahlberg A, Hakansson J, Xian X, Semb H, Kubista M. Properties of the reverse transcription reaction in mRNA quantification. Clin Chem. 2004 Mar; 50 (3): 509–15. DOI: 10.1373/clinchem.2003.026161.
  49. Promega. Improm II Reverse Transcription System Protocol [Internet]. [cited 2017 Jun] Available from: https://worldwide.promega.com//media/files/resources/protocols/technical- manuals/0/improm-ii-reverse-transcription-system-protocol.pdf
  50. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009 Apr; 55 (4): 611–22. DOI: 10.1373/clinchem.2008.112797.
  51. Gurvich OL, Skoblov M. Real-time PCR and multiplex approaches. Methods Mol Biol. 2011; 784: 1–13. DOI: 10.1007/978-1-61779-289-2_1.
  52. LifeTechnologies. Real-time PCR handbook [Internet]. [cited 2017 Jun] Available from: http://www.gene-quantification.de/real-time-pcr-handbook-life-technologies-update-flr.pdf
  53. Riss TL, Moravec RA, Niles AL, Duellman S, Benink HA, Worzella TJ et al. Cell Viability Assays. In: Sittampalam GS, Coussens NP, Brimacombe K et al., editors. Assay Guidance Manual. Bethesda (MD): Eli Lilly & Company and the National Center for Advancing Translational Sciences; 2004.
  54. Promega. Technical Bulletin CellTiter 96® Non-Radioactive Cell Proliferation Assay [Internet]. [cited 2017 Jun] Available from: https://www.promega.com/-/media/files/resources/ protocols/technical-bulletins/0/celltiter-96-non-radioactive-cell- proliferation-assay-protocol.pdf
  55. TangB,QiG,SunX,TangF,YuanS,WangZetal.HOXA7playsa critical role in metastasis of liver cancer associated with activation of Snail. Mol Cancer. 2016 Sep 6; 15 (1): 57. DOI: 10.1186/s12943-016-0540-4.