In bioimaginggroup/nucim: Nucleome Imaging Toolbox

knitr::opts_chunk$set(echo = TRUE)

Description and instructions

Volker J. Schmid, Marion Cremer, Thomas Cremer: Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy. Methods 123 (2017) 33-46. [DOI]

Some publications using nucim

Arroyo M, Hastert FD, Zhadan A, Schelter F, Zimbelmann S, Rausch C, Ludwig AK, Carell T, Cardoso MC: Isoform-specific and ubiquitination depen- dent recruitment of Tet1 to replicating het- erochromatin modulates methylcytosine oxidation. nature communications (2022) [DOI]
Fischl H, McManus D, Oldenkamp R, Schermelleh L, Mellor J, Jagannath A, Furger A: Cold‐induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm. The EMBO Journal 39:e105604 (2020) [DOI]
Cremer, M, Brandstetter, K, Maiser, A, Rao, SSP, Schmid, VJ, Guirao-Ortiz, M, Mitra, N, Mamberti, S, Klein, KN, Gilbert, DM, Leonhardt, H, Cardoso, MC, Lieberman Aiden, E, Harz, H and Cremer, T: Cohesin depleted cells rebuild functional nuclear compartments after endomitosis. Nature Communications 11:6146 (2020). [DOI]
Miron, E, Oldenkamp, R, Brown, JMS, Pinto, DMS, Shan Xu, C, Faria, AR, Shaban, HA, Rhodes, JDP, Innocent, C, de Ornellas, S, Hess, HF, Buckle, V and Schermelleh, L.: Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin. Science Advances 6:39, eaba8811 (2020). [DOI]
Cremer, M., Schmid, V.J., Kraus, F., Markaki, Y., Hellmann, I., Maiser, A., Leonhardt, H., John, S., Stamatoyannopoulos, J. and Cremer, T.: Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters. Epigenetics & Chromatin 10:39 (2017). [DOI]
Popken J., Schmid V.J., Strauss, A., Guengoer, T., Wolf, E., Zakhartchenko, T.: Stage-dependent remodeling of the nuclear envelope and lamina during rabbit early embryonic development. Journal of Reproduction and Development 62:2 (2016) 127–135. [DOI]
Popken J., Graf A., Krebs S., Blum H., Schmid V.J., Strauss, A., Guengoer, T., Zakhartchenko, T., Wolf, E., Cremer, T.: Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications. PLoS One 10:5 (2015) e0124619. [DOI]
Popken, J., Brero, A., Koehler, D., Schmid, V.J., Strauss, A., Wuensch, A., Guengoer, T., Graf, A., Krebs, S., Blum, H., Zakhartchenko, V., Wolf, E., Cremer, T.: Reprogramming of ﬁbroblast nuclei in cloned bovine embryos is paralleled by major structural remodeling with both striking similarities and differences to nuclear phenotypes of embryos fertilized in vitro. Nucleus 5:6 (2014) 555–589. [DOI]
Smeets, D., Markaki, Y., Schmid, V.J., Kraus, F., Tattermusch, A., Cerase, A., Sterr, M., Fiedler, S., Demmerle, J., Popken, J., Leonhardt, H., Brockdorff, N., Cremer, T., Schermelleh, L., Cremer, M.: 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 7:8 (2014). [DOI]