SSBD:database v3

394-Fukute-DNAunderwind

OMERO gallery,
OMERO index

Project

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.
License
CC BY
Released at
Oct. 20, 2025, midnight
Updated at
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.).
# of image datasets
14

Papers

Papers
Paper information: Fukute J, Maki K, Adachi T. The nucleolar shell provides anchoring sites for DNA untwisting. Commun Biol. 2024 Jan 23;7(1):83.,
Pubmed ID: 38263258,
PMCID: PMC10805735,
DOI: https://doi.org/10.1038/s42003-023-05750-w,
URL: https://pubmed.ncbi.nlm.nih.gov/38263258/

Contacts

Contacts
Koichiro Maki (Imaging Contributor) , Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies , Kyoto University
Jumpei Fukute (Imaging Contributor) , Kyoto University
Taiji Adachi (Imaging Contributor) , Kyoto University

Biosamples

Organisms
Mus musculus (NCBI:txid10090)
Strains

Cells

Cell lines
MC3T3-E1 cell

Ontologies

UBERON
Anatomical entities
GO: Biological processes
GO: Cellular components
nucleus (GO:0005634)
GO: Molecular functions

Genetics

Gene names
Protein names
rRNA 2'-O-methyltransferase fibrillarin (P35550)
DNA topoisomerase 1 (Q04750)
DNA-directed RNA polymerase II subunit RPB1 (P08775)
Nucleophosmin (Q61937)
Genetic methods
DNA Binding (NCIT_C18597)
antibody (FBbi_00000401)
Protein tags
Probes
DAPI (FBbi:00000056)
Alexa Fluor 568 (FBbi:00000442)
Oligo Primer
Genotype

Treatments

Reagent or Compound
Concentration
Fold Dilution
CX-5461 (CHEBI:156287)
3 micromolar (UO_0000064)
actinomycin D (CHEBI:27666)
50 nanomolar (UO_0000065)
meso-tetrakis(N-methyl-4-pyridyl)porphine(4+) (CHEBI:37447)
100 micromolar (UO_0000064)
meso-tetrakis(N-methyl-4-pyridyl)porphine(4+) (CHEBI:37447)
100 micromolar (UO_0000064)

Imaging Methods

Dimensions
2048x2048x34x3x1, 520x520x25x3x1, 2048x2048x26x3x1, 2560x2560x1x3x1, 512x512x40x3x1, 2048x2048x36x3x1, 2048x2048x40x3x1, 2048x2048x35x3x1, 2560x2560x24x3x1, 2560x2560x1x4x1, 2560x2560x17x3x1, 2560x2560x33x3x1, 2048x2048x20x3x1,
X scales
0.03 micrometer, 0.05 micrometer,
Y scales
0.03 micrometer, 0.05 micrometer,
Z scales
0.25 micrometer, NA, 0.44 micrometer, 0.32 micrometer, 0.20 micrometer, 0.40 micrometer,
T scales
NA,
Channels
4 channel, 3 channel,
Microscopy types
Detection methods
Visualization methods
Illumination methods
Sources of contrast
Contrast enhancing methods
Resolution enhancing methods
Imaged parameters
Sample preparation methods

Instruments

Body
Elyra7 super-resolution microscope (Zeiss)
Model
Light source
Detector
Objective
Plan-Apochromat 40×/1.4 oil objective lens
Filter set
Dichroic

Datasets

Dataset name
Organism
Gene / Protein
Dimensions
File size
SSBD:OMERO
Download
Fig2a_DNAunderwind
Mus musculus (NCBI:txid10090)
NA / Nucleophosmin (Q61937)
2048x2048x36x3x1
864MB
Gallery, Index
zip
Fig2b_DNAunderwind
Mus musculus (NCBI:txid10090)
NA / DNA-directed RNA polymerase II subunit RPB1 (P08775)
2048x2048x35x3x1
840MB
Gallery, Index
zip
Fig2c_DNAunderwind
Mus musculus (NCBI:txid10090)
NA / DNA topoisomerase 1 (Q04750)
512x512x40x3x1
60MB
Gallery, Index
zip
Fig3a_DNAunderwind
Mus musculus (NCBI:txid10090)
NA / rRNA 2'-O-methyltransferase fibrillarin (P35550)
2560x2560x1x4x1
50MB
Gallery, Index
zip
Fig3c_DNAunderwind_FBL
Mus musculus (NCBI:txid10090)
NA / rRNA 2'-O-methyltransferase fibrillarin (P35550)
520x520x25x3x1
39MB
Gallery, Index
zip
Fig3c_DNAunderwind_NPM
Mus musculus (NCBI:txid10090)
NA / Nucleophosmin (Q61937)
2048x2048x36x3x1
864MB
Gallery, Index
zip
Fig3c_DNAunderwind_RNAPI
Mus musculus (NCBI:txid10090)
2048x2048x40x3x1
960MB
Gallery, Index
zip
Fig4a_DNAunderwind_ctrl
Mus musculus (NCBI:txid10090)
NA / Nucleophosmin (Q61937)
2560x2560x33x3x1
1.2GB
Gallery, Index
zip
Fig4a_DNAunderwind_CX
Mus musculus (NCBI:txid10090)
NA / Nucleophosmin (Q61937)
2048x2048x26x3x1
624MB
Gallery, Index
zip
Fig4a_DNAunderwind_ActD
Mus musculus (NCBI:txid10090)
NA / Nucleophosmin (Q61937)
2560x2560x24x3x1
900MB
Gallery, Index
zip
Fig5b_DNAunderwind_ctrl
Mus musculus (NCBI:txid10090)
NA / Nucleophosmin (Q61937)
2048x2048x34x3x1
816MB
Gallery, Index
zip
Fig5b_DNAunderwind_TMPyP4
Mus musculus (NCBI:txid10090)
NA / Nucleophosmin (Q61937)
2048x2048x20x3x1
480MB
Gallery, Index
zip
Fig5e_DNAunderwind_ctrl
Mus musculus (NCBI:txid10090)
NA / rRNA 2'-O-methyltransferase fibrillarin (P35550)
2560x2560x1x3x1
38MB
Gallery, Index
zip
Fig5e_DNAunderwind_TMPyP4
Mus musculus (NCBI:txid10090)
NA / rRNA 2'-O-methyltransferase fibrillarin (P35550)
2560x2560x17x3x1
638MB
Gallery, Index
zip