Quantitative analysis of the nuclear landscape

Workflow for quantitative analysis of the nuclear landscape

Quantitative analysis of the 3D nuclear landscape using super-resolved fluorescence microscopy.

Software

• bioimagetools/ is a set of R tools for working with images in 3D and 4D, mostly for biology/microscopy.
• Nucleome Imaging Toolbox (nucim) is an R package for quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

Related Publications

• Yasunori Horikoshi, Hiroki Shima, Jiying Sun, Wataru Kobayashi, Volker J. Schmid, Hiroshi Ochiai, Lin Shi, Atsuhiko Fukuto, Yasuha Kinugasa, Hitoshi Kurumizaka, Tsuyoshi Ikura, Yolanda Markaki, Shin-ichi Tate, Kazuhiko Igarashi, Thomas Cremer, Satoshi Tashiro. Distinctive nuclear zone for RAD51-mediated homologous recombinational DNA repair. – bioRxiv (2021), 2021
• Zahra Amini Farsani, Volker J. Schmid. Co-localization analysis in fluorescence microscopy via maximum entropy copula – International Journal of Biostatistics, (17) 1, pp. 165–175, 2021
• Marion Cremer, Katharina Brandstetter, Andreas Maiser, , Suhas S P Rao, Volker J. Schmid, Namita Mitra, Stefania Mamberti, Kyle-N Klein, David M Gilbert, Heinrich Leonhardt, Maria Cristina Cardoso, Erez Lieberman Aiden, Hartmann Harz, Thomas Cremer. Cohesin depleted cells pass through mitosis and reconstitute a functional nuclear architecture. – Nature Communications 11, 6146 (2020), 2020
• Marion Cremer, Volker J. Schmid, Felix Kraus, Yolanda Markaki, Ines Hellmann, Andreas Maiser, Heinrich Leonhardt, Sam John, John Stamatoyannopoulos, Thomas Cremer. Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters – Epigenetics and Chromatin, 2017
• Volker J. Schmid, Marion Cremer, Thomas Cremer. Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy – Methods, 2017
• Jens Popken, Volker J. Schmid, Axel Strauss, Tuna Guengoer, Eckhard Wolf, Valeri Zakhartchenko. Stage-dependent remodeling of the nuclear envelope and lamina during rabbit early embryonic development – Journal of Reproduction and Development, 2016
• Jens Popken, Alexander Graf, Stefan Krebs, Helmut Blum, Volker J. Schmid, Axel Strauss, Tuna Guengoer, Valeri Zakhartchenko, Eckhard Wolf, Thomas Cremer. Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications – PLOS ONE, 2015
• Jens Popken, Alessandro Brero, Daniela Koehler, Volker J. Schmid, Axel Strauss, Annegret Wuensch, Tuna Guengoer, Alexander Graf, Stefan Krebs, Helmut Blum, Valeri Zakhartchenko, Eckhard Wolf, Thomas Cremer. Reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos – Nucleus, 2014
• Daniel Smeets, Yolanda Markaki, Volker J. Schmid, Felix Kraus, Anna Tattermusch, Andrea Cerase, Michael Sterr, Susanne Fiedler, Justin Demmerle, Jens Popken, Heinrich Leonhardt, Neil Brockdorff, Thomas Cremer, Lothar Schermelleh, Marion Cremer. Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. – Epigenetics & chromatin, 2014
• Yolanda Markaki, Daniel Smeets, Susanne Fiedler, Volker J. Schmid, Lothar Schermelleh, Thomas Cremer, Marion Cremer. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture – BioEssays : news and reviews in molecular, cellular and developmental biology, 2012
• Doris M Seiler, Jacques Rouquette, Volker J. Schmid, Hilmar Strickfaden, Christian Ottmann, Guido a Drexler, Belinda Mazurek, Christoph Greubel, Volker Hable, Gunther Dollinger, Thomas Cremer, Anna a Friedl. Double-strand break-induced transcriptional silencing is associated with loss of tri-methylation at H3K4. – Chromosome research: an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, pp. 883–899, 2011