Related Experiment Video
Updated: Jan 21, 2026
10:15
Capturing Chromosome Conformation Across Length Scales
Published on: January 20, 2023
4.1K
Cut-C: cleavage under tethered nuclease for conformational capture
Takashi Shimbo1, Machika Kawamura2,3, Edward Wijaya2,3
1Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 5650871, Japan. shimbot@sts.med.osaka-u.ac.jp.
BMC Genomics
|July 31, 2019
Summary
We developed Cut-C, a new method to map protein-mediated 3D genome structures and protein locations. This technique simplifies chromatin conformation analysis, especially for precious samples like clinical ones.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Understanding genome 3D structure is key to gene regulation.
- Chromosome conformation capture (3C) and Hi-C reveal chromatin structure.
- Protein-centric chromatin conformation requires coupling Hi-C with ChIP, which is time-consuming.
Purpose of the Study:
- To develop a method for simultaneously identifying protein-centric chromatin conformation and target protein localization.
- To simplify and improve the efficiency of chromatin conformation analysis.
Main Methods:
- Developed Cut-C, combining antibody-mediated cleavage with chromosome conformation capture.
- Utilized tethered nuclease for protein-specific cleavage.
- Applied Cut-C to identify H3K4me3 and CTCF-mediated chromatin interactions.
Main Results:
- Successfully identified H3K4me3-mediated chromatin loops and genome-wide H3K4me3 distribution.
- Demonstrated Cut-C's general applicability by identifying CTCF-mediated chromatin loops.
- Validated the method's ability to pinpoint protein-centric chromatin conformation.
Conclusions:
- Cut-C efficiently identifies protein-centric chromatin conformations and target protein distributions.
- The simplified protocol enhances chromatin conformation analysis, particularly for precious samples.
- Cut-C offers a streamlined approach for studying genome architecture and protein function.
Related Concept Videos
01:20Conformity
47.9K
Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.
47.9K
01:33Cleavage and Blastulation
49.9K
After a large-single-celled zygote is produced via fertilization, the process of cleavage occurs while zygotes travel through the uterine tube. Cleavage is a mitotic cell division that does not result in growth. With each round of successive cell division, daughter cells get increasingly smaller.
49.9K
02:20Conformations of Butane
17.7K
Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
17.7K
02:29Conformations of Cycloalkanes
14.1K
Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3 hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
14.1K
02:11Conformations of Cyclohexane
15.3K
Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
15.3K
01:17Cut-off Frequency of BJT
1.4K
Cut-off frequencies in Bipolar Junction Transistors (BJTs) mark the transition between the signal's pass band and stop band, influencing their performance in amplifying or attenuating frequencies. These frequencies are crucial for designing BJTs to meet specific operational requirements in electronic circuits.
Alpha Cut-Off Frequency: Pertinent to the common-base configuration, the alpha cut-off frequency defines the upper-frequency limit at which the current gain, alpha, remains stable. As...
Alpha Cut-Off Frequency: Pertinent to the common-base configuration, the alpha cut-off frequency defines the upper-frequency limit at which the current gain, alpha, remains stable. As...
1.4K