vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ18.345vavilov-1439Research ArticleКЛЕТОЧНАЯ И МОЛЕКУЛЯРНАЯ БИОЛОГИЯCELL AND MOLECULAR BIOLOGYПоиск микроРНК, потенциально задействованных в поддержании самообновления плюрипотентных клеток лабораторной крысыThe search for microRNAs potentially involved in the selfrenewal maintaining of laboratory rat pluripotent stem cellsШерстюкВ. В.SherstyukV. V.

Новосибирск

Novosibirsk

svv@bionet.nsc.ruМедведевС. П.MedvedevS. P.

Новосибирск

Novosibirsk

РиМ. Т.RiM. T.

Новосибирск;

Вобурн, США

Novosibirsk;

Woburn, USA

ВяткинЮ. В.VyatkinY. V.

Новосибирск;

Вобурн, США

Novosibirsk;

Woburn, USA

СайкО. В.SaikO. V.

Новосибирск

Novosibirsk

ШтокалоД. Н.ShtokaloD. N.

Новосибирск;

Вобурн, США

Novosibirsk;

Woburn, USA

ЗакиянС. М.ZakianS. M.

Новосибирск

Novosibirsk

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Национальный медицинский исследовательский центр имени академика Е.Н. Мешалкина Министерства здравоохранения Российской Федерации; Институт химической биологии и фундаментальной медицины Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics SB RAS; E.N. Meshalkin National Medical Research Center, Ministry of Health of Russian Federation; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk State UniversityRussian FederationООО «АкадемДжин»; Институт Сен-ЛоранаРоссияAcademGene LLC; St. Laurent InstituteRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университет; ООО «АкадемДжин» Институт Сен-ЛоранаРоссияInstitute of Cytology and Genetics SB RAS; Novosibirsk State University; AcademGene LLC; St. Laurent InstituteRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics SB RASRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; ООО «АкадемДжин»; Институт Сен-Лорана; Институт систем информатики им. А.П. Ершова Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics SB RAS; AcademGene LLC; St. Laurent Institute; A.P. Ershov Institute of Informatics Systems SB RASRussian Federation201806042018222179186Copyright © Шерстюк В.В., Медведев С.П., Ри М.Т., Вяткин Ю.В., Сайк О.В., Штокало Д.Н., Закиян С.М., 20182018Шерстюк В.В., Медведев С.П., Ри М.Т., Вяткин Ю.В., Сайк О.В., Штокало Д.Н., Закиян С.М.Sherstyuk V.V., Medvedev S.P., Ri M.T., Vyatkin Y.V., Saik O.V., Shtokalo D.N., Zakian S.M.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/1439

Самообновление культивируемых плюрипотентных клеток – сложный процесс, объединяющий множество функциональных и регуляторных уровней. В поддержании самообновления клеток принимают участие сеть транскрипционных факторов, широкий спектр их генов-мишеней, включая ферменты, регулирующие структуру хроматина, сигнальные каскады, а также контур, содержащий систему регуляторных некодирующих РНК. Изучение молекулярно-генетических основ поддержания самообновления и реализации свойства плюрипотентности культивируемых клеток млекопитающих является крайне важной задачей для понимания процессов, происходящих в доимплантационном эмбриогенезе, а также для построения эффективных методик получения линий плюрипотентных стволовых клеток в интересах экспериментальной биологии и медицины. МикроРНК (миРНК) играют важную роль в процессах поддержания плюрипотентного состояния и репрограммирования клеток. Однако участие данного класса некодирующих РНК в представленных процессах и функции отдельных миРНК изучены недостаточно. Целью настоящего исследования был поиск миРНК, потенциально участвующих в процессах поддержания плюрипотентного состояния и репрограммирования клеток крысы Rattus norvegicus. С использованием методов биоинформатики и данных, полученных в результате секвенирования нового поколения, нами проанализирована экспрессия миРНК в эмбриональных стволовых клетках, индуцированных плюрипотентных стволовых клетках и эмбриональных фибробластах крысы. Проведенный анализ дифференциальной экспрессии между группами плюрипотентных клеток и фибробластов, а также анализ проверенных экспериментально генов-мишеней дифференциально экспрессирующихся известных миРНК крысы позволили выявить новых потенциальных участников процессов поддержания плюрипотентного состояния и репрограммирования. Кроме того, новые потенциальные участники этих процессов обнаружены среди ранее не аннотированных миРНК крысы. Использование биоинформатических подходов и методов системной биологии – первый необходимый шаг при выборе кандидатов для дальнейшего экспериментального изучения. Полученные результаты существенно дополняют представления о системе регуляции самообновления у такого модельного организма, как лабораторная крыса, и расширяют знания о данной системе у млекопитающих в целом.

Self-renewal of cultured pluripotent stem cells is a complex process, which includes multiple functional and regulatory levels. Transcription factors, their target genes, chromatin modifiers, signaling pathways, and regulatory noncoding RNAs are involved in the maintaining of self-renewal. Studies of molecular and genetic bases of maintaining self-renewal and pluripotency in cultured mammalian cells are important to understand processes in preimplantation embryogenesis and to develop efficient techniques to obtain pluripotent stem cell lines for experimental biology and medicine. MicroRNAs (miRNAs) play an important role in pluripotency maintaining and reprogramming. However, involvement of this class of noncoding RNAs and functions of individual molecules are poorly studied. The goal of this study was the search for the miRNAs potentially involved in the pluripotency maintaining and reprogramming of Rattus norvegicus cells. We analyzed the expression of miRNAs in rat embryonic stem cells, induced pluripotent stem cells and embryonic fibroblasts using bioinformatic methods and data obtained with next generation sequencing. The analysis of differential expression between groups of rat pluripotent cells and fibroblasts, and the analysis of experimentally confirmed target genes of differentially expressed known rat miRNAs revealed novel potential players of pluripotency maintaining and reprogramming processes. In addition, novel members of these processes were revealed among novel rat miRNAs. The use of bioinformatic and systems biology approaches is the first step, which is necessary for choosing candidates for the subsequent experimental studies. The results obtained substantially improve our understanding of the self-renewal regulation system of the laboratory rat, a popular biomedical object, and our knowledge about the system in mammals.

плюрипотентностьмикроРНКсистемная биологияpluripotencymicroRNAsystem biologyReferencesAgarwal V., Bell G.W., Nam J.W., Bartel D.P. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4. DOI 10.7554/eLife.05005.Agarwal V., Bell G.W., Nam J.W., Bartel D.P. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4. DOI 10.7554/eLife.05005.An J., Zheng Y., Dann C.T. Mesenchymal to epithelial transition mediated by CDH1 promotes spontaneous reprogramming of male germline stem cells to pluripotency. Stem Cell Reports. 2017;8(2):446459. DOI 10.1016/j.stemcr.2016.12.006.An J., Zheng Y., Dann C.T. Mesenchymal to epithelial transition mediated by CDH1 promotes spontaneous reprogramming of male germline stem cells to pluripotency. Stem Cell Reports. 2017;8(2):446459. DOI 10.1016/j.stemcr.2016.12.006.Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136(2):215-233. DOI 10.1016/j.cell.2009.01.002.Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136(2):215-233. DOI 10.1016/j.cell.2009.01.002.Betel D., Wilson M., Gabow A., Marks D.S., Sander C. The microRNA. org resource: targets and expression. Nucleic Acids Res. 2008;36: D149-D153. DOI 10.1093/nar/gkm995.Betel D., Wilson M., Gabow A., Marks D.S., Sander C. The microRNA. org resource: targets and expression. Nucleic Acids Res. 2008;36: D149-D153. DOI 10.1093/nar/gkm995.Buehr M., Meek S., Blair K., Yang J., Ure J., Silva J., McLay R., Hall J., Ying Q.L., Smith A. Capture of authentic embryonic stem cells from rat blastocysts. Cell. 2008;135(7):1287-1298. DOI 10.1016/j.cell. 2008.12.007.Buehr M., Meek S., Blair K., Yang J., Ure J., Silva J., McLay R., Hall J., Ying Q.L., Smith A. Capture of authentic embryonic stem cells from rat blastocysts. Cell. 2008;135(7):1287-1298. DOI 10.1016/j.cell. 2008.12.007.Calabrese J.M., Seila A.C., Yeo G.W., Sharp P.A. RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA. 2007;104(46):18097-18102. DOI 10.1073/pnas. 0709193104.Calabrese J.M., Seila A.C., Yeo G.W., Sharp P.A. RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA. 2007;104(46):18097-18102. DOI 10.1073/pnas. 0709193104.Cao Y., Guo W.T., Tian S., He X., Wang X.W., Liu X., Gu K.L., Ma X., Huang D., Hu L., Cai Y., Zhang H., Wang Y., Gao P. miR-290/371-Mbd2-Myc circuit regulates glycolytic metabolism to promote pluripotency. EMBO J. 2015;34(5):609-623. DOI 10.15252/embj.201490441.Cao Y., Guo W.T., Tian S., He X., Wang X.W., Liu X., Gu K.L., Ma X., Huang D., Hu L., Cai Y., Zhang H., Wang Y., Gao P. miR-290/371-Mbd2-Myc circuit regulates glycolytic metabolism to promote pluripotency. EMBO J. 2015;34(5):609-623. DOI 10.15252/embj.201490441.Chang H., Yi B., Ma R., Zhang X., Zhao H., Xi Y. CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo. Sci. Rep. 2016;6:22312. DOI 10.1038/srep22312.Chang H., Yi B., Ma R., Zhang X., Zhao H., Xi Y. CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo. Sci. Rep. 2016;6:22312. DOI 10.1038/srep22312.Chen J., Wang G., Lu C., Guo X., Hong W., Kang J., Wang J. Synergetic cooperation of microRNAs with transcription factors in iPS cell generation. PLoS One. 2012;7(7):e40849. DOI 10.1371/journal. pone.0040849.Chen J., Wang G., Lu C., Guo X., Hong W., Kang J., Wang J. Synergetic cooperation of microRNAs with transcription factors in iPS cell generation. PLoS One. 2012;7(7):e40849. DOI 10.1371/journal. pone.0040849.Essletzbichler P., Konopka T., Santoro F., Chen D., Gapp B.V., Kralovics R., Brummelkamp T.R., Nijman S.M., Burckstummer T. Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. Genome Res. 2014;24(12):2059-2065. DOI 10.1101/gr.177220.114.Essletzbichler P., Konopka T., Santoro F., Chen D., Gapp B.V., Kralovics R., Brummelkamp T.R., Nijman S.M., Burckstummer T. Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. Genome Res. 2014;24(12):2059-2065. DOI 10.1101/gr.177220.114.Eulalio A., Huntzinger E., Izaurralde E. Getting to the root of miRNAmediated gene silencing. Cell. 2008;132(1):9-14. DOI 10.1016/j. cell.2007.12.024.Eulalio A., Huntzinger E., Izaurralde E. Getting to the root of miRNAmediated gene silencing. Cell. 2008;132(1):9-14. DOI 10.1016/j. cell.2007.12.024.Evans M.J., Kaufman M.H. Establishment in culture of pluripotential cells from mouse embryos. Nature. 1981;292(5819):154-156.Evans M.J., Kaufman M.H. Establishment in culture of pluripotential cells from mouse embryos. Nature. 1981;292(5819):154-156.Filipowicz W., Bhattacharyya S.N., Sonenberg N. Mechanisms of posttranscriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet. 2008;9(2):102-114. DOI 10.1038/nrg2290.Filipowicz W., Bhattacharyya S.N., Sonenberg N. Mechanisms of posttranscriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet. 2008;9(2):102-114. DOI 10.1038/nrg2290.Friedlander M.R., Mackowiak S.D., Li N., Chen W., Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012; 40(1):37-52. DOI 10.1093/nar/gkr688.Friedlander M.R., Mackowiak S.D., Li N., Chen W., Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012; 40(1):37-52. DOI 10.1093/nar/gkr688.Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., DeRamo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M., Hawes A., Gill R., Celera, Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., BosdetI., FjellC., Jones S., Krzywinski M., MathewsonC., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.Z., Li B., Liu Y., Qin X., Cawley S., Worley K.C., CooneyA.J., D’Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Alba M.M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Hubner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Venter J.C., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F., Rat Genome Sequencing Project C. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004;428(6982):493-521. DOI 10.1038/nature 02426.Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., DeRamo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M., Hawes A., Gill R., Celera, Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., BosdetI., FjellC., Jones S., Krzywinski M., MathewsonC., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.Z., Li B., Liu Y., Qin X., Cawley S., Worley K.C., CooneyA.J., D’Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Alba M.M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Hubner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Venter J.C., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F., Rat Genome Sequencing Project C. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004;428(6982):493-521. DOI 10.1038/nature 02426.Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A., Enright A.J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006;34(Database issue):D140-D144. DOI 10.1093/nar/gkj112.Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A., Enright A.J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006;34(Database issue):D140-D144. DOI 10.1093/nar/gkj112.Hackenberg M., Rodriguez-Ezpeleta N., Aransay A.M. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res. 2011;39:W132W138. DOI 10.1093/nar/gkr247.Hackenberg M., Rodriguez-Ezpeleta N., Aransay A.M. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res. 2011;39:W132W138. DOI 10.1093/nar/gkr247.Hackett J.A., Surani M.A. Regulatory principles of pluripotency: from the ground state up. Cell Stem Cell. 2014;15(4):416-430. DOI 10.1016/j.stem.2014.09.015.Hackett J.A., Surani M.A. Regulatory principles of pluripotency: from the ground state up. Cell Stem Cell. 2014;15(4):416-430. DOI 10.1016/j.stem.2014.09.015.Ho T.T., Zhou N., Huang J., Koirala P., Xu M., Fung R., Wu F., Mo Y.Y. Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines. Nucleic Acids Res. 2015;43(3):e17. DOI 10.1093/ nar/gku1198.Ho T.T., Zhou N., Huang J., Koirala P., Xu M., Fung R., Wu F., Mo Y.Y. Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines. Nucleic Acids Res. 2015;43(3):e17. DOI 10.1093/ nar/gku1198.Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31(13):3429-3431.Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31(13):3429-3431.Hsu S.D., Lin F.M., Wu W.Y., Liang C., Huang W.C., Chan W.L., Tsai W.T., Chen G.Z., Lee C.J., Chiu C.M., Chien C.H., Wu M.C., Huang C.Y., Tsou A.P., Huang H.D. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 2011;39:D163-D169. DOI 10.1093/nar/gkq1107.Hsu S.D., Lin F.M., Wu W.Y., Liang C., Huang W.C., Chan W.L., Tsai W.T., Chen G.Z., Lee C.J., Chiu C.M., Chien C.H., Wu M.C., Huang C.Y., Tsou A.P., Huang H.D. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 2011;39:D163-D169. DOI 10.1093/nar/gkq1107.Huang G., Ye S., Zhou X., Liu D., Ying Q.L. Molecular basis of embryonic stem cell self-renewal: from signaling pathways to pluripotency network. Cell Mol. Life Sci. 2015;72(9):1741-1757. DOI 10.1007/ s00018-015-1833-2.Huang G., Ye S., Zhou X., Liu D., Ying Q.L. Molecular basis of embryonic stem cell self-renewal: from signaling pathways to pluripotency network. Cell Mol. Life Sci. 2015;72(9):1741-1757. DOI 10.1007/ s00018-015-1833-2.Huang H.N., Chen S.Y., Hwang S.M., Yu C.C., Su M.W., Mai W., Wang H.W., Cheng W.C., Schuyler S.C., Ma N., Lu F.L., Lu J. miR-200c and GATA binding protein 4 regulate human embryonic stem cell renewal and differentiation. Stem Cell Res. 2014;12(2):338353. DOI 10.1016/j.scr.2013.11.009.Huang H.N., Chen S.Y., Hwang S.M., Yu C.C., Su M.W., Mai W., Wang H.W., Cheng W.C., Schuyler S.C., Ma N., Lu F.L., Lu J. miR-200c and GATA binding protein 4 regulate human embryonic stem cell renewal and differentiation. Stem Cell Res. 2014;12(2):338353. DOI 10.1016/j.scr.2013.11.009.Ivanisenko V.A., Saik O.V., Ivanisenko N.V., Tiys E.S., Ivanisenko T.V., Demenkov P.S., Kolchanov N.A. ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. BMC Syst. Biol. 2015;9(2):S2. DOI 10.1186/1752-05099-S2-S2.Ivanisenko V.A., Saik O.V., Ivanisenko N.V., Tiys E.S., Ivanisenko T.V., Demenkov P.S., Kolchanov N.A. ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. BMC Syst. Biol. 2015;9(2):S2. DOI 10.1186/1752-05099-S2-S2.Jouneau A., Ciaudo C., Sismeiro O., Brochard V., Jouneau L., Vandormael-Pournin S., Coppee J.Y., Zhou Q., Heard E., Antoniewski C., Cohen-Tannoudji M. Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles. RNA. 2012;18(2):253264. DOI 10.1261/rna.028878.111.Jouneau A., Ciaudo C., Sismeiro O., Brochard V., Jouneau L., Vandormael-Pournin S., Coppee J.Y., Zhou Q., Heard E., Antoniewski C., Cohen-Tannoudji M. Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles. RNA. 2012;18(2):253264. DOI 10.1261/rna.028878.111.Lee C.G., McCarthy S., Gruidl M., Timme C., Yeatman T.J. MicroRNA-147 induces a mesenchymal-to-epithelial transition (MET) and reverses EGFR inhibitor resistance. PLoS One. 2014;9(1):e84597. DOI 10.1371/journal.pone.0084597.Lee C.G., McCarthy S., Gruidl M., Timme C., Yeatman T.J. MicroRNA-147 induces a mesenchymal-to-epithelial transition (MET) and reverses EGFR inhibitor resistance. PLoS One. 2014;9(1):e84597. DOI 10.1371/journal.pone.0084597.Leonardo T.R., Schultheisz H.L., Loring J.F., Laurent L.C. The functions of microRNAs in pluripotency and reprogramming. Nat. Cell Biol. 2012;14(11):1114-1121. DOI 10.1038/ncb2613.Leonardo T.R., Schultheisz H.L., Loring J.F., Laurent L.C. The functions of microRNAs in pluripotency and reprogramming. Nat. Cell Biol. 2012;14(11):1114-1121. DOI 10.1038/ncb2613.Li P., Tong C., Mehrian-Shai R., Jia L., Wu N., Yan Y., Maxson R.E., Schulze E.N., Song H., Hsieh C.L., Pera M.F., Ying Q.L. Germline competent embryonic stem cells derived from rat blastocysts. Cell. 2008;135(7):1299-1310. DOI 10.1016/j.cell.2008.12.006.Li P., Tong C., Mehrian-Shai R., Jia L., Wu N., Yan Y., Maxson R.E., Schulze E.N., Song H., Hsieh C.L., Pera M.F., Ying Q.L. Germline competent embryonic stem cells derived from rat blastocysts. Cell. 2008;135(7):1299-1310. DOI 10.1016/j.cell.2008.12.006.Liu Z., Hui Y., Shi L., Chen Z., Xu X., Chi L., Fan B., Fang Y., Liu Y., Ma L., Wang Y., Xiao L., Zhang Q., Jin G., Liu L., Zhang X. Efficient CRISPR/Cas9-mediated versatile, predictable, and donorfree gene knockout in human pluripotent stem cells. Stem Cell Rep. 2016;7(3):496-507. DOI 10.1016/j.stemcr.2016.07.021.Liu Z., Hui Y., Shi L., Chen Z., Xu X., Chi L., Fan B., Fang Y., Liu Y., Ma L., Wang Y., Xiao L., Zhang Q., Jin G., Liu L., Zhang X. Efficient CRISPR/Cas9-mediated versatile, predictable, and donorfree gene knockout in human pluripotent stem cells. Stem Cell Rep. 2016;7(3):496-507. DOI 10.1016/j.stemcr.2016.07.021.Long J.M., Lahiri D.K. MicroRNA-101 downregulates Alzheimer’s amyloid-beta precursor protein levels in human cell cultures and is differentially expressed. Biochem. Biophys. Res. Commun. 2011; 404(4):889-895. DOI 10.1016/j.bbrc.2010.12.053.Long J.M., Lahiri D.K. MicroRNA-101 downregulates Alzheimer’s amyloid-beta precursor protein levels in human cell cultures and is differentially expressed. Biochem. Biophys. Res. Commun. 2011; 404(4):889-895. DOI 10.1016/j.bbrc.2010.12.053.Martin G.R. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl. Acad. Sci. USA. 1981;78(12):7634-7638.Martin G.R. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl. Acad. Sci. USA. 1981;78(12):7634-7638.Picanço-Castro V., Russo-Carbolante E., Reis L.C., Fraga A.M., de Magalhães D.A., Orellana M.D., Panepucci R.A., Pereira L.V., Covas D.T. Pluripotent reprogramming of fibroblasts by lentiviral mediated insertion of SOX2, C-MYC, and TCL-1A. Stem Cells Dev. 2011;20(1):169-180. DOI 10.1089/scd.2009.0424.Picanço-Castro V., Russo-Carbolante E., Reis L.C., Fraga A.M., de Magalhães D.A., Orellana M.D., Panepucci R.A., Pereira L.V., Covas D.T. Pluripotent reprogramming of fibroblasts by lentiviral mediated insertion of SOX2, C-MYC, and TCL-1A. Stem Cells Dev. 2011;20(1):169-180. DOI 10.1089/scd.2009.0424.Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J., Glockner F.O. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590-D596. DOI 10.1093/nar/gks1219.Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J., Glockner F.O. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590-D596. DOI 10.1093/nar/gks1219.Rahkonen N., Stubb A., Malonzo M., Edelman S., Emani M.R., Närvä E., Lähdesmäki H., Ruohola-Baker H., Lahesmaa R., Lund R. Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells. Stem Cell Res. 2016;17(3):498503. DOI 10.1016/j.scr.2016.09.025.Rahkonen N., Stubb A., Malonzo M., Edelman S., Emani M.R., Närvä E., Lähdesmäki H., Ruohola-Baker H., Lahesmaa R., Lund R. Mature Let-7 miRNAs fine tune expression of LIN28B in pluripotent human embryonic stem cells. Stem Cell Res. 2016;17(3):498503. DOI 10.1016/j.scr.2016.09.025.Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-140. DOI 10.1093/ bioinformatics/btp616.Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-140. DOI 10.1093/ bioinformatics/btp616.Samavarchi-Tehrani P., Golipour A., David L., Sung H.K., Beyer T.A., Datti A., Woltjen K., Nagy A., Wrana J.L. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell. 2010;7(1): 64-77. DOI 10.1016/j.stem.2010.04.015.Samavarchi-Tehrani P., Golipour A., David L., Sung H.K., Beyer T.A., Datti A., Woltjen K., Nagy A., Wrana J.L. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell. 2010;7(1): 64-77. DOI 10.1016/j.stem.2010.04.015.Sturm M., Hackenberg M., Langenberger D., Frishman D. TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics. 2010;11:292. DOI 10.1186/14712105-11-292.Sturm M., Hackenberg M., Langenberger D., Frishman D. TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics. 2010;11:292. DOI 10.1186/14712105-11-292.Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126(4):663-676. DOI 10.1016/j.cell.2006.07.024.Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126(4):663-676. DOI 10.1016/j.cell.2006.07.024.Thomas M., Lieberman J., Lal A. Desperately seeking microRNA targets. Nat. Struct. Mol. Biol. 2010;17(10):1169-1174. DOI 10.1038/ nsmb.1921.Thomas M., Lieberman J., Lal A. Desperately seeking microRNA targets. Nat. Struct. Mol. Biol. 2010;17(10):1169-1174. DOI 10.1038/ nsmb.1921.Thomson J.A., Itskovitz-Eldor J., Shapiro S.S., Waknitz M.A., Swiergiel J.J., Marshall V.S., Jones J.M. Embryonic stem cell lines derived from human blastocysts. Science. 1998;282(5391):1145-1147.Thomson J.A., Itskovitz-Eldor J., Shapiro S.S., Waknitz M.A., Swiergiel J.J., Marshall V.S., Jones J.M. Embryonic stem cell lines derived from human blastocysts. Science. 1998;282(5391):1145-1147.Vaskova E.A., Medvedev S.P., Sorokina A.E., Nemudryy A.A., Elisaphenko E.A., Zakharova I.S., Shevchenko A.I., Kizilova E.A., Zhelezova A.I., Evshin I.S., Sharipov R.N., Minina J.M., Zhdanova N.S., Khegay I.I., Kolpakov F.A., Sukhikh G.T., Pokushalov E.A., Karaskov A.M., Vlasov V.V., Ivanova L.N., Zakian S.M. Transcriptome characteristics and X-chromosome inactivation status in cultured rat pluripotent stem cells. Stem Cells Dev. 2015;24(24):2912-2924. DOI 10.1089/scd.2015.0204.Vaskova E.A., Medvedev S.P., Sorokina A.E., Nemudryy A.A., Elisaphenko E.A., Zakharova I.S., Shevchenko A.I., Kizilova E.A., Zhelezova A.I., Evshin I.S., Sharipov R.N., Minina J.M., Zhdanova N.S., Khegay I.I., Kolpakov F.A., Sukhikh G.T., Pokushalov E.A., Karaskov A.M., Vlasov V.V., Ivanova L.N., Zakian S.M. Transcriptome characteristics and X-chromosome inactivation status in cultured rat pluripotent stem cells. Stem Cells Dev. 2015;24(24):2912-2924. DOI 10.1089/scd.2015.0204.Vaskova E.A., Stekleneva A.E., Medvedev S.P., Zakian S.M. “Epigenetic memory” phenomenon in induced pluripotent stem cells. Acta Naturae. 2013;5(4):15-21.Vaskova E.A., Stekleneva A.E., Medvedev S.P., Zakian S.M. “Epigenetic memory” phenomenon in induced pluripotent stem cells. Acta Naturae. 2013;5(4):15-21.Xu N., Papagiannakopoulos T., Pan G., Thomson J.A., Kosik K.S. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell. 2009;137(4):647-658. DOI 10.1016/j.cell.2009.02.038.Xu N., Papagiannakopoulos T., Pan G., Thomson J.A., Kosik K.S. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell. 2009;137(4):647-658. DOI 10.1016/j.cell.2009.02.038.Yuan K., Ai W.B., Wan L.Y., Tan X., Wu J.F. The miR-290-295 cluster as multi-faceted players in mouse embryonic stem cells. Cell Biosci. 2017;7:38. DOI 10.1186/s13578-017-0166-2.Yuan K., Ai W.B., Wan L.Y., Tan X., Wu J.F. The miR-290-295 cluster as multi-faceted players in mouse embryonic stem cells. Cell Biosci. 2017;7:38. DOI 10.1186/s13578-017-0166-2.Yue D., Liu H., Huang Y. Survey of computational algorithms for microRNA target prediction. Curr. Genomics. 2009;10(7):478-492. DOI 10.2174/138920209789208219.Yue D., Liu H., Huang Y. Survey of computational algorithms for microRNA target prediction. Curr. Genomics. 2009;10(7):478-492. DOI 10.2174/138920209789208219.Zhao B., Yang D., Jiang J., Li J., Fan C., Huang M., Fan Y., Jin Y., Jin Y. Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies. BMC Genomics. 2014;15:488. DOI 10.1186/14712164-15-488.Zhao B., Yang D., Jiang J., Li J., Fan C., Huang M., Fan Y., Jin Y., Jin Y. Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies. BMC Genomics. 2014;15:488. DOI 10.1186/14712164-15-488.Zhu S., Li W., Liu J., Chen C.H., Liao Q., Xu P., Xu H., Xiao T., Cao Z., Peng J., Yuan P., Brown M., Liu X.S., Wei W. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat. Biotechnol. 2016;34(12):12791286. DOI 10.1038/nbt.3715.Zhu S., Li W., Liu J., Chen C.H., Liao Q., Xu P., Xu H., Xiao T., Cao Z., Peng J., Yuan P., Brown M., Liu X.S., Wei W. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat. Biotechnol. 2016;34(12):12791286. DOI 10.1038/nbt.3715.

The authors declare that there are no conflicts of interest present.