Personal profile
Biography
From 1997-2003 Nikolay Shirokikh studied Biochemistry and Molecular Biology at the M.V. Lomonosov Moscow State University (Moscow, Russia). In 2004, he worked on the mechanisms defining start codon selection fidelity during his postgraduate internship in the laboratory of Profs Pestova and Hellen (State University of New York, Brooklyn, NY, USA). In 2011, he completed his PhD in the laboratory of Prof Spirin (Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia), where he investigated unusual properties of viral mRNA leaders that define their ability to ‘hijack’ ribosomes and overtake the host protein synthesis.
In 2012, he was awarded Go8 European Fellowship (The Group of Eight Universities, Australia) to collaborate with the RNA Biology Laboratory headed by Prof Preiss for an innovative project on the mechanisms of eukaryotic translation initiation. From 2015, he worked in the Preiss group where he primarily used high-throughput sequencing methods to explore functions of eukaryotic RNA in live cells. Together with Prof Preiss and Dr Archer, he has created an approach allowing to dissect all translation control in vivo (translation complex profile sequencing, TCP-seq).
In 2019, Nikolay Shirokikh was awarded an NHMRC Emerging Leadership Investigator Grant to expand the research of rapid translational control in the areas of cell stress response and cancer biology.
Qualifications
Ph.D. in Biology, Higher Attestation Commission, Moscow, Russia (2011)
Research Interests
Dr Nikolay Shirokikh is a biochemist and molecular biologist interested in mechanisms underlying the decoding of genetic information. Instructions on how, when and where to make proteins to fulfil the ever-changing requirements of the living cells are encoded in the ribonucleic acid messages (messenger(m)RNA). Translation of mRNA into protein is central to all life. Mechanisms regulating translation are important for cell survival and wellbeing.
In eukaryotic cells, where production of each type or variant of protein can be individually regulated, translational control is especially complex. Control of protein synthesis is directly involved in the processes critical for multicellular eukaryotes, such as cell differentiation, synaptic plasticity, adaptation and pro- and counter-survival decision making of the somatic and germline cells. Malignant cells utilise alternative translation pathways to survive and escape treatment through drug resistance.
The primary interest of Dr Shirokikh is to obtain deep knowledge of eukaryotic translation that will allow to decipher, and eventually manipulate, the mRNA regulatory elements responsible for mRNA-wise regulation of protein synthesis. Dr Shirokikh has a particular interest and expertise in mammalian translation, but also works with yeast when accessibility of genetics is necessary. He uses a variety of molecular biology, biophysics, biochemistry and genetics approaches applied to synthetic systems that model in vivo molecular interactions, and also works directly with live cells. He is currently using high-throughput RNA sequencing methods to obtain the new knowledge of how different eukaryotic mRNAs can control their translation.
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Collaborations and top research areas from the last five years
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Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing with RISER
Sneddon, A., Ravindran, A., Shanmuganandam, S., Kanchi, M., Hein, N., Jiang, S., Shirokikh, N. & Eyras, E., 24 May 2024, In: Nature Communications. 15, 17 p., 4422.Research output: Contribution to journal › Article › peer-review
3 Citations (Scopus) -
Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress
Horvath, A., Janapala, Y., Woodward, K., Mahmud, S., Cleynen, A., Gardiner, E. E., Hannan, R. D., Eyras, E., Preiss, T. & Shirokikh, N. E., 22 Jul 2024, In: Nucleic Acids Research. 52, 13, p. 7925–7946 22 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Citations (Scopus) -
Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications
Mateos, P. A., Sethi, A. J., Ravindran, A., Srivastava, A., Woodward, K., Mahmud, S., Kanchi, M., Guarnacci, M., Xu, J., Yuen, Z. W. S., Zhou, Y., Sneddon, A., Hamilton, W., Gao, J., Starrs, L. M., Hayashi, R., Wickramasinghe, V., Zarnack, K., Preiss, T. & Burgio, G. & 3 others, , 9 May 2024, In: Nature Communications. 15, 17 p., 3899.Research output: Contribution to journal › Article › peer-review
64 Citations (Scopus) -
An Improved Method for Purification of the Residual Bodies from the Seminiferous Tubules of Mice
Apu, M. N. H., Shirokikh, N. E., Khochbin, S. & Soboleva, T. A., 7 Nov 2023, In: Current Protocols. 3, 11, 15 p., e920.Research output: Contribution to journal › Article › peer-review
Open Access -
Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation
Smith, A. B., Ganguly, D. R., Moore, M., Bowerman, A. F., Janapala, Y., Shirokikh, N. E., Pogson, B. J. & Crisp, P. A., 10 Nov 2023, In: Plant Journal. 117, 3, p. 818-839 22 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Citations (Scopus)
Projects
- 7 Finished
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Nonlinear spectroscopy at the nanoscale from extreme ultraviolet to infrared
Kruk, S. (PI), Kivshar, Y. (CoI), Lee, S. (CoI) & Shirokikh, N. (CoI)
3/03/23 → 31/12/23
Project: Research
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NHMRC Small Equipment Grant 2022 - Luna FX7 Automated Cell Counter - Link to ARIES 41237
Shirokikh, N. (PI), Bruestle, A. (CoI), Burgio, G. (CoI), Enders, A. (CoI), Eyras, E. (CoI), Fischer, T. (CoI), Hayashi, R. (CoI), McMorran, B. (CoI), Preiss, T. (CoI) & Schulte, K.-M. (CoI)
22/07/22 → 31/12/23
Project: Research
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NHMRC Equipment Grant 2021: ACDT Equipment - Linked to ARIES ID 39296
Hannan, R. (PI), Burgio, G. (CoI), Dehorter, N. (CoI), Fischer, T. (CoI), Gardiner, E. (CoI), George, A. (CoI), McMorran, B. (CoI), Palmer, S. (CoI), Schulte, K.-M. (CoI), Shirokikh, N. (CoI) & Soboleva, T. (CoI)
6/10/21 → 31/12/21
Project: Research
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