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Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
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SYSNO ASEP 0566546 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes Author(s) Randall, R. S. (CH)
Jourdain, C. (DE)
Nowicka, Anna (UEB-Q) ORCID
Kaduchová, Kateřina (UEB-Q) ORCID
Kubová, M. (CZ)
Ayoub, M. A. (DE)
Schubert, V. (DE)
Tatout, C. (FR)
Colas, I. (FR)
Kalyanikrishna, A. (DE)
Desset, S. (FR)
Mermet, S. (FR)
Boulaflous-Stevens, A. (FR)
Kubalová, I. (CZ)
Mandáková, T. (CZ)
Heckmann, S. (DE)
Lysák, M. A. (CZ)
Panatta, M. (CH)
Santoro, R. (DE)
Schubert, D. (DE)
Pečinka, Aleš (UEB-Q) ORCID, RID
Routh, D. (CH)
Baroux, C. (CH)Number of authors 23 Source Title Nucleus. - : Taylor & Francis - ISSN 1949-1034
Roč. 13, č. 1 (2022), s. 277-299Number of pages 23 s. Language eng - English Country US - United States Keywords 3D organization ; chromatin ; chromosome ; crossovers ; image analysis ; meiosis ; metaphase ; mitosis ; nuclear bodies ; nuclear speckles ; Nucleus ; oligo FISH ; pachytene ; quantification ; RNA Pol II ; segmentation ; sim ; spatial distribution ; STED imaging ; transcription factories OECD category Cell biology R&D Projects EF16_019/0000827 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) LM2018129 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) GA21-02929S GA ČR - Czech Science Foundation (CSF) Method of publishing Open access Institutional support UEB-Q - RVO:61389030 UT WOS 000898422400001 EID SCOPUS 85143064143 DOI 10.1080/19491034.2022.2144013 Annotation Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images. Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization, 3D: three-dimensional, ASY1: ASYNAPTIC 1, CC: chromocenters, CO: Crossover, DAPI: 4',6-diamidino-2-phenylindole, DMC1: DNA MEIOTIC RECOMBINASE 1, DSB: Double-Strand Break, FISH: fluorescence in situ hybridization, GFP: GREEN FLUORESCENT PROTEIN, HEI10: HUMAN ENHANCER OF INVASION 10, NCO: Non-Crossover, NE: Nuclear Envelope, Oligo-FISH: oligonucleotide fluorescence in situ hybridization, RNPII: RNA Polymerase II, SC: Synaptonemal Complex, SIM: structured illumination microscopy, ZMM (ZIP: MSH4: MSH5 and MER3 proteins), ZYP1: ZIPPER-LIKE PROTEIN 1. Workplace Institute of Experimental Botany Contact David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Year of Publishing 2023 Electronic address https://doi.org/10.1080/19491034.2022.2144013
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