Dataset Fig5e_DNAunderwind_TMPyP4
Project
394-Fukute-DNAunderwind
Title
Mechanical regulation of DNA underwinding in the nucleus
Description
This project investigates how DNA is underwound in the mechanical environment of the nucleus, by performing super-resolution imaging of underwound DNA and nuclear proteins in mouse cells.
Funding
This work was supported by JST, CREST, Grant Number JPMJCR2023, Japan (J.F., K.M.), JST, CREST, Grant Number JPMJCR22L5, Japan (T.A.), JST, SPRING, Grant Number JPMJSP2110, Japan (J.F.), MEXT/JSPS, KAKENHI, Grant Number JP23KJ1255, Japan (J.F.), and MEXT/JSPS, KAKENHI, Grant Number JP20K20180 and JP23K17196, Japan (K.M.).
Title
Z-series Lattice-SIM images of bio-psoralen, fibrillarin and ribosome DNA in the presence of TMPyP4
Description
Z-series Lattice-SIM images of ribosome DNA, fibrillarin, and bio-psoralen, which labeled underwound DNA, in the presence of TMPyP4. TMPyP4 is a G4-selective ligand and inhibits the interaction with nucleophosmin. Channel1;ribosome DNA, Chennel2;psoralen, Channel3;fibrillarin (a marker for fibrillar component of the nucleoli)
Description
MC3T3-E1 mouse osteoblast-like cells in which underwound nuclear DNA was fluorescently labeled with psoralen
Extrinsic variables
To inhibit the interaction between nucleolar proteins and G-quadruplex (G4), cells were treated with 100 micromolar TMPyP4, a selective G4 ligand, for 15 min. The biotinylated psoralen was applied to the cell and crosslinked to DNA by UV irradiation. After cell fixation, NeutrAvidin Protein, DyLight^{TM} 488 was applied and other staining was conducted. The ribosome DNA was labeled with Cy3- labeld probes for mouse ribosome DNA (BAC clone RP23- 225M6, Chromosome Science Laboratory).
Gene ontology: Biological processes
Gene ontology: Cellular components
Gene ontology: Molecular functions
Protein names
rRNA 2'-O-methyltransferase fibrillarin (
P35550)
Protein tags
NeutrAvidin Protein (DyLight^{TM} 488)
Dimensions
2560x2560x17x3x1
Microscopy types
(Lattice-pattern structured illumination microscopy)
Detection methods
scientific complementary metal oxide semiconductor (sCMOS)
Visualization methods
Cy3
NeutrAvidin Protein (DyLight^{TM} 488)
Alexa Fluor 568
Illumination methods
scientific complementary metal oxide semiconductor (sCMOS)
Contrast enhancing methods
Resolution enhancing methods
structured illumination microscopy (SIM)
Sample preparation methods
formaldehyde fixed tissue
Body
Elyra7 super-resolution microscope (Zeiss)
Objective
Plan-Apochromat 40×/1.4 oil objective lens