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Critical Reviews™ in Eukaryotic Gene Expression
Fator do impacto: 1.841 FI de cinco anos: 1.927 SJR: 0.649 SNIP: 0.516 CiteScore™: 1.96

ISSN Imprimir: 1045-4403
ISSN On-line: 2162-6502

Critical Reviews™ in Eukaryotic Gene Expression

DOI: 10.1615/CritRevEukaryotGeneExpr.v24.i3.40
pages 225-247

Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part B− Structuromics

Martin Falk
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Michael Hausmann
Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
Emilie Lukasova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Abin Biswas
Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Radiation Oncology, University Medical Center Mannheim, University of Heidelberg, Heidelberg, Germany
Georg Hildenbrand
Department of Radiation Oncology, University Medical Center Mannheim, Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
Marie Davidkova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic
Evgeny Krasavin
Joint Institute for Nuclear Research, Dubna, Moscow, Russia
Zdenek Kleibl
Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
Iva Falkova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Lucie Jezkova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Joint Institute for Nuclear Research, Dubna, Moscow, Russia; Institute of Chemical Technology Prague, Prague, Czech Republic
Lenka Stefancikova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Jan Sevcik
Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
Michal Hofer
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Alena Bacikova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Pavel Matula
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
Alla Boreyko
Joint Institute for Nuclear Research, Dubna, Moscow, Russia
Jana Vachelova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic
Anna Michaelidesova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic; Proton Therapy Center, Prague, Czech Republic
Stanislav Kozubek
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic

RESUMO

Recent groundbreaking developments in Omics and bioinformatics have generated new hope for overcoming the complexity and variability of (radio)biological systems while simultaneously shedding more light on fundamental radiobiological questions that have remained unanswered for decades. In the era of Omics, our knowledge of how genes and dozens of proteins interact in the frame of complex signaling and repair pathways (or, rather, networks) to preserve the integrity of the genome has been rapidly expanding. Nevertheless, these functional networks must be observed with strong correspondence to the cell nucleus, which is the main target of ionizing radiation. Information regarding these intricate processes cannot be achieved using high-throughput Omics approaches alone; it requires sophisticated structural probing and imaging. In the first part of this review, the article "Giving Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part A−Radiomics," we showed the development of different Omics solutions and how they are contributing to a better understanding of cellular radiation response. In this Part B we show how high-resolution confocal microscopy as well as novel approaches of molecular localization nanoscopy fill the gaps to successfully place Omics data in the context of space and time. The dynamics of double-strand breaks during repair processes and chromosomal rearrangements at the microscale correlated to aberration induction are explained. For the first time we visualize pan-nuclear nucleosomal rearrangements and clustering at the nanoscale during repair processes. Finally, we introduce a novel method of specific chromatin nanotargeting based on a computer database search of uniquely binding oligonucleotide combinations (COMBO-FISH). With these challenging techniques on hand, we speculate future perspectives that may combine specific COMBO-FISH nanoprobing and structural nanoscopy to observe structure-function correlations in living cells in real-time. Thus, the Omics networks obtained from function analyses may be enriched by real-time visualization of Structuromics.


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