Curriculum Vitae Ekaterina E. Savitskaya, PhD

Senior research scientist at the Skolkovo Institute of Science and Technology, Moscow, Russia Senior researcher at Institute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia [email protected] tel.+79164939857

Date and place of birth 06.08.1976 Moscow, Russia

Education 2001 PhD in Molecular Genetics, Institute of Gene Biology Russian Academy of Sciences 1998 Diploma with honours in Biochemistry, Moscow State University Courses 2012 CSHL course “Genomic data analysis” 2014 CSHL course “Computational and comparative genomics” 2016 Visual science course “Information design in scientific communication” 2016/2017 Moscow State University/Skoltech course “Academical writing”

Work experience

May 2013-present Senior research scientist, Skolkovo Institute of Science and Technology. Study of CRISPR-Cas prokaryotic immune system. June 2016-August 2016 Visiting scientist, Laboratory of prof. prof. D. Bikard, Pasteur Institute, Paris, France April 2014-June 2014 Visiting scientist, Laboratory of prof. F. Mojica, Alicante University, Spain October 2011-May 2013 Senior research scientist, Institute of Molecular Genetics, RAS. Study of CRISPR-Cas prokaryotic immune system. February 2010-October 2011 Scientific consultant, the Foundation “Science for life extension”, Moscow, Russia. February 2005-January 2010 Research scientist, Center “Bioengineering” RAS, Moscow, Russia. Study of methylated DNA-binding protein Kaiso and its homologs, high density sequencing of Kaiso genomic DNA binding sites. January 2002, February 2004 –April 2004 Visiting scientist, Laboratory of prof. Peter Becker, Ludwig- Maximilian Universität München, Adolf Butenandt Institute, Munchen, Germany. Nov. 2001-October 2004 Research scientist, Institute of Gene Biology RAS, Moscow, Russia. Study of regulatory elements in Drosophila melanogaster genome: insulators, enhancers, and silencers. November 2001 PhD thesis “New properties of the Su(Hw) insulator of Drosophila melanogaster”. Sept. 1998- November 2001 PhD student of the laboratory of gene processes regulation, Institute of Gene Biology RAS, Moscow, Russia.

Area of expertise and skills CRISPR-Cas biology, genome maintenance mechanisms, phage-host interactions, high-throughput approaches in molecular genetics. Wide range of basic and advanced methods in experimental molecular biology, Illumina high throughput sequencing, bioinformatics analysis and visualisation of next generation sequencing data. Major grants and fellowships 2016 Metchnikoff fellowship from France Embassy for short term research project RFFI 16-04-00767 Cross-talk between CRISPR-Cas system and mechanisms ensuring genome stability in Escherichia coli. 2016-2018. Grant holder. RFFI 14-04-00916 The mechanisms of CRISPR/Cas interference regulation in Escherichia coli. 2013-2014. Grant holder. RNF 14-14-00988 Molecular mechanisms of CRISPR/Cas adaptation in bacteria. 2014-2016. Participant. RNF 14-14-00988 (prolongation) Molecular mechanisms of CRISPR/Cas adaptation in bacteria. 2017-2018. Participant. The Russian Government Megagrant. Creation of molecular, ecological, and industrial microbiology laboratory in the St. Petersburg State Polytechnical University. 2013- 2015. Participant. RFFI 11-04-01373-a CRISPR/Cas interference system of small RNA in E. coli: mechanism, regulation of activity, evolution, role in phage defence. 2011-2013. Participant. МК-4554.2008.4 Grant of President of Russian Federation for young post-graduated scientists. Role of tne methyl-DNA binding protein Kaiso in regulatation of gene expression. 2008. Grant holder.

Supervising PhD and MSc students Olga Musharova, PhD (co-supervising, 2017), Elena Fomenko, diploma MSU (2017), Svetlana Zhikrivetskaya, diploma MSU (2013)

Languages Russian (native), English (fluent)

Publications in journals indexed by Scopus/WoS Altogether there are 30 pear reviewed publications, last authorship is in one paper and first or equally to the first author contribution is in 8 papers, h-index= 12 1. Spacer-length DNA intermediates are associated with Cas1 in cells undergoing primed CRISPR adaptation. Musharova O, Klimuk E, Datsenko KA, Metlitskaya A, Logacheva M, Semenova E, Severinov K, Savitskaya E.Nucleic Acids Res. 2017 Apr 7;45(6):3297-3307. 2. The action of Escherichia coli CRISPR-Cas system on lytic bacteriophages with different lifestyles and development strategies. Strotskaya A, Savitskaya E, Metlitskaya A, Morozova N, Datsenko KA, Semenova E, Severinov K. Nucleic Acids Res. 2017 Feb 28;45(4):1946- 1957. 3. Dynamics of Escherichia coli type I-E CRISPR spacers over 42,000 years. Savitskaya E., Lopatina A., Medvedeva S., Kapustin M., Shmakov S., Tikhonov A., Artamonova I., Logacheva M., Severinov K. Mol. Ecol. 2017 Apr;26(7):2019-2026. 4. Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation. Kuznedelov K, Mekler V, Lemak S, Tokmina-Lukaszewska M, Datsenko KA, Jain I, Savitskaya E, Mallon J, Shmakov S, Bothner B, Bailey S, Yakunin AF, Severinov K, Semenova E. Nucleic Acids Res. 2016 Dec 15;44(22):10849-10861. 5. Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex. Semenova E, Savitskaya E, Musharova O, Strotskaya A, Vorontsova D, Datsenko KA, Logacheva MD, Severinov K. Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7626-31. 6. Diversity of CRISPR-Cas-Mediated Mechanisms of Adaptive Immunity in Prokaryotes and Their Application in Biotechnology. Savitskaya EE, Musharova OS, Severinov KV. Biochemistry (Mosc). 2016 Jul;81(7):653-61. 7. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery.Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E. Nucleic Acids Res. 2015 43(22):10848-60. 8. The Cas6e ribonuclease is not required for interference and adaptation by the E. coli type I- E CRISPR-Cas system. Semenova E, Kuznedelov K, Datsenko KA, Boudry PM, Savitskaya E, Medvedeva S, Beloglazova N, Logacheva M, Yakunin AF, Severinov K. Nucleic Acids Res. 2015 Jul 13;43(12):6049-61. 9. Rapid Multiplex Creation of Escherichia coli Strains Capable of Interfering with Phage Infection Through CRISPR. Strotksaya A, Semenova E, Savitskaya E, Severinov K. Methods Mol Biol. 2015;1311:147-59. 10. The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource. Craig T, Smelick C, Tacutu R, Wuttke D, Wood SH, Stanley H, Janssens G, Savitskaya E, Moskalev A, Arking R, de Magalhães JP. Nucleic Acids Res. 2015;43(Database issue):D873-8. 11. Pervasive Generation of Oppositely-Oriented Spacers during CRISPR Adaptation. Smakov S*, Savitskaya E*, Semenova E, Datsenko K, Severinov K. Nucleic Acids Res. 2014;42(9):5907-16. *-equally contributed 12. High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli. Savitskaya E, Semenova E, Dedkov V, Metlitskaya A, Severinov K. RNA Biol. 2013 Apr 25;10(5). 13. Interaction between a pair of gypsy insulators or between heterologous gypsy and Wari insulators modulates Flp site-specific recombination in Drosophila melanogaster. Krivega M, Savitskaya E, Krivega I, Karakozova M, Parshikov A, Golovnin A, Georgiev P. Chromosoma. 2010 Aug;119(4):425-34. 14. Several copies of insulator from MDG4 can determine the interaction between positively and negatively acting regulatory elements and promoter of the miniwhite gene of Drosophila melanogaster. Kostiuchenko MV, Savitskaia EE, Krivega MN, Georgiev PG. Genetika. 2008 Dec;44(12):1693-7. Russian. 15. Kostyuchenko M, Savitskaya E, Koryagina E, Melnikova L, Karakozova M, Georgiev P Zeste can facilitate long-range enhancer-promoter communication and insulator bypass in Drosophila melanogaster. Chromosoma. 2009 Oct;118(5):665-74. 16. Ruzov A*, Savitskaya E*, Hackett JA, Reddington JP, Prokhortchouk A, Madej MJ, Chekanov N, Li M, Dunican DS, Prokhortchouk E, Pennings S, Meehan RR. The non-methylated DNA- binding function of Kaiso is not required in early Xenopus laevis development. Development. 2009 Mar;136(5):729-38. *-equally contributed 17. Kostyuchenko MV, Savitskaya EE, Volkov IA, Golovnin AK, Georgiev PG. Study of functional interaction between three copies of the insulator from the MDG4 transposable element in the model system of the miniwhite gene of the Drosophila melanogaster. Dokl Biochem Biophys. 2008 Jul-Aug;421:239-43. Russian. 18. Chetverina D, Savitskaya E, Maksimenko O, Melnikova L, Zaytseva O, Parshikov A, Galkin AV, Georgiev P. Red flag on the white reporter: a versatile insulator abuts the white gene in Drosophila and is omnipresent in mini-white constructs. Nucleic Acids Res. 2008 Feb;36(3):929-37. 19. Comet I, Savitskaya E, Schuettengruber B, Negre N, Lavrov S, Parshikov A, Juge F, Gracheva E, Georgiev P, Cavalli G. PRE-mediated bypass of two Su(Hw) insulators targets PcG proteins to a downstream promoter. Dev Cell. 2006 Jul;11(1):117-24. 20. Kostyuchenko MV, Savitskaya EE, Karakozova MV, Georgiev PG. Study of the regulatory region of gene white of Drosophila melanogaster. Dokl Biochem Biophys. 2005 Nov- Dec;405:383-7. Russian. 21. Savitskaya E, Melnikova L, Kostuchenko M, Kravchenko E, Pomerantseva E, Boikova T, Chetverina D, Parshikov A, Zobacheva P, Gracheva E, A, Georgiev P. Study of long-distance functional interactions between Su(Hw) insulators that can regulate enhancer-promoter communication in Drosophila melanogaster. Mol Cell Biol. 2006 Feb;26(3):754-61. 22. Pomerantseva E, Biryukova I, Silicheva R, Savitskaya E, Golovnin A, Georgiev P. Transposition of Regulatory Elements by P-Element-Mediated Rearrangements in Drosophila melanogaster.Genetics. 2006 Apr;172(4):2283-91. Epub 2005 Dec 30. 23. Kravchenko E, Savitskaya E, Kravchuk O, Parshikov A, Georgiev P, Savitsky M. Pairing between gypsy insulators facilitates the enhancer action in trans throughout the Drosophila genome. Mol Cell Biol. 2005 Nov;25(21):9283-91. 24. Kostyuchenko MV, Georgiev PG, Savitskaya EE. The promoter region of the yellow gene of Drosophila melanogaster contains excess regulatory elements.Dokl Biochem Biophys. 2004 Nov-Dec;399:374-5. Russian. 25. Karakozova M, Savitskaya E, Melnikova L, Parshikov A, Georgiev P. The Mod(mdg4) component of the Su(Hw) insulator inserted in the P transposon can repress its mobility in Drosophila melanogaster.Genetics. 2004 Jul;167(3):1275-80. 26. Karakozova MV, Savitskaya EE, Parshikov AF, Georgiev PG. Cis-modifiers of the yellow gene repression induced by the Su(Hw) insulator in the absence of the Mod(mdg4) protein in Drosophila melanogaster. Dokl Biochem Biophys. 2003 Mar-Apr;389:110-3. Russian. 27. Golovnin A, Birukova I, Romanova O, Silicheva M, Parshikov A, Savitskaya E, Pirrotta V, Georgiev P. An endogenous Su(Hw) insulator separates the yellow gene from the Achaete- scute gene complex in Drosophila. Development. 2003 Jul;130(14):3249-58. 28. Muravyova E**, Golovnin A, Gracheva E, Parshikov A, Belenkaya T, Pirrotta V, Georgiev P. Loss of insulator activity by paired Su(Hw) chromatin insulators. Science. 2001 Jan 19;291(5503):495-8. 29. Murav'eva EE*, Golovnin AK, Parshikov AF, Georgiev PG. New properties of the Su(Hw) insulator. Dokl Biochem Biophys. 2001 May-Jun;378:181-5. Russian. 30. Georgiev PG, Murav'eva EE*, Golovnin AK, Gracheva EM, Belen'kaia TIu. [Insulators and interaction between long-distance regulatory elements in higher eukaryotes] Genetika. 2000 Dec;36(12):1588-97. Review. Russian.

**Muravyova- maiden name.