SSBD:database

394-Fukute-DNAunderwind

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

2026-02-06

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

Anatomical information

UBERON

Anatomical entities

Gene ontology

GO: Biological processes

GO: Cellular components

nucleus (GO:0005634)

GO: Molecular functions

Molecular biological information

Gene names

Protein names

Nucleophosmin (Q61937)
DNA topoisomerase 1 (Q04750)
rRNA 2'-O-methyltransferase fibrillarin (P35550)
DNA-directed RNA polymerase II subunit RPB1 (P08775)

Genetic methods

antibody (FBbi_00000401)
DNA Binding (NCIT_C18597)

Protein tags

Probes

Alexa Fluor 568 (FBbi:00000442)
DAPI (FBbi:00000056)

Oligo Primer

Genotype

Reagent or Compound

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 information

Dimensions

2048x2048x20x3x1, 2560x2560x33x3x1, 2560x2560x24x3x1, 2560x2560x1x3x1, 2048x2048x40x3x1, 512x512x40x3x1, 2560x2560x17x3x1, 2560x2560x1x4x1, 520x520x25x3x1, 2048x2048x26x3x1, 2048x2048x34x3x1, 2048x2048x35x3x1, 2048x2048x36x3x1,

X scales

0.05 micrometer, 0.03 micrometer,

Y scales

0.05 micrometer, 0.03 micrometer,

Z scales

0.25 micrometer, 0.20 micrometer, 0.32 micrometer, 0.40 micrometer, 0.44 micrometer, NA,

T scales

NA,

Channels

3 channel, 4 channel,

Biological Imaging Methods Ontology

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

Download zip

Fig2b_DNAunderwind

Mus musculus (NCBI:txid10090)

NA / DNA-directed RNA polymerase II subunit RPB1 (P08775)

2048x2048x35x3x1

840MB

Gallery Index

Download zip

Fig2c_DNAunderwind

Mus musculus (NCBI:txid10090)

NA / DNA topoisomerase 1 (Q04750)

512x512x40x3x1

60MB

Gallery Index

Download zip

Fig3a_DNAunderwind

Mus musculus (NCBI:txid10090)

NA / rRNA 2'-O-methyltransferase fibrillarin (P35550)

2560x2560x1x4x1

50MB

Gallery Index

Download zip

Fig3c_DNAunderwind_FBL

Mus musculus (NCBI:txid10090)

NA / rRNA 2'-O-methyltransferase fibrillarin (P35550)

520x520x25x3x1

39MB

Gallery Index

Download zip

Fig3c_DNAunderwind_NPM

Mus musculus (NCBI:txid10090)

NA / Nucleophosmin (Q61937)

2048x2048x36x3x1

864MB

Gallery Index

Download zip

Fig3c_DNAunderwind_RNAPI

Mus musculus (NCBI:txid10090)

2048x2048x40x3x1

960MB

Gallery Index

Download zip

Fig4a_DNAunderwind_ctrl

Mus musculus (NCBI:txid10090)

NA / Nucleophosmin (Q61937)

2560x2560x33x3x1

1.2GB

Gallery Index

Download zip

Fig4a_DNAunderwind_CX

Mus musculus (NCBI:txid10090)

NA / Nucleophosmin (Q61937)

2048x2048x26x3x1

624MB

Gallery Index

Download zip

Fig4a_DNAunderwind_ActD

Mus musculus (NCBI:txid10090)

NA / Nucleophosmin (Q61937)

2560x2560x24x3x1

900MB

Gallery Index

Download zip

Fig5b_DNAunderwind_ctrl

Mus musculus (NCBI:txid10090)

NA / Nucleophosmin (Q61937)

2048x2048x34x3x1

816MB

Gallery Index

Download zip

Fig5b_DNAunderwind_TMPyP4

Mus musculus (NCBI:txid10090)

NA / Nucleophosmin (Q61937)

2048x2048x20x3x1

480MB

Gallery Index

Download zip

Fig5e_DNAunderwind_ctrl

Mus musculus (NCBI:txid10090)

NA / rRNA 2'-O-methyltransferase fibrillarin (P35550)

2560x2560x1x3x1

38MB

Gallery Index

Download zip

Fig5e_DNAunderwind_TMPyP4

Mus musculus (NCBI:txid10090)

NA / rRNA 2'-O-methyltransferase fibrillarin (P35550)

2560x2560x17x3x1

638MB

Gallery Index

Download zip