相关实验视频

Updated: Sep 16, 2025

In-Nucleus Hi-C in Drosophila Cells

In-Nucleus Hi-C in Drosophila Cells

Published on: September 15, 2021

动态屏障调节凝聚力定位和基因组折叠在固定占用时

Hadi Rahmaninejad¹, Yao Xiao², Maxime M C Tortora²

¹Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA rahmanin@usc.edu fudenber@usc.edu.

Genome research

|July 8, 2025

概括

基因组折叠依赖于CTCF屏障和凝聚力挤出器. 这项研究表明,即使是短暂的CTCF障碍,当动态时,也可以解释基因组折叠特征,这表明CTCF和凝聚蛋白结合时间相似.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
生物物理学的生物物理.

背景情况:

哺乳动物基因组折叠在相间细胞中涉及由定向CTCF结合约束的凝聚性循环挤出.
拓关联域 (TADs) 是由这个过程形成和维护的,在CTCF站点的凝聚丰富.
在短CTCF居住时间和更长的凝聚生命周期之间存在差异,这就提出了关于屏障动态的问题.

研究的目的:

调查短暂的CTCF障碍是否可以解释观察到的基因组折叠模式.
开发一个包含CTCF绑定和解绑的动态屏障模型.
评估屏障动态对基因组和成像数据的影响.

主要方法:

开发了一个动态屏障模型,其中CTCF站点在受约束和不受约束状态之间切换.
使用动态屏障模型模拟了ChIP-seq,Hi-C和显微镜数据.
整合了多个实验数据源来验证模型.

主要成果:

发现CTCF和凝聚素结合时间表显著影响基因组折叠特征.
证明了障碍的时间,而不仅仅是占用,对基因组结构至关重要.
表明边界与挤出机寿命影响的比率模拟了ChIP-seq和Hi-C数据.
观察到,动态障碍是解释染色体形态学实验变化的必要条件.

结论:

对于理解基因组折叠来说,CTCF屏障动力学是必不可少的,即使有暂时的屏障.
该模型表明,CTCF屏障约束时间与凝聚力挤出机寿命相当.
蛋白质动态的生物物理知情模型增强了我们对基因组折叠机制的理解.

更多相关视频

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

Author Spotlight: Efficient Nucleosome Reconstitution for Single-Molecule Techniques

Author Spotlight: Efficient Nucleosome Reconstitution for Single-Molecule Techniques

Published on: September 6, 2024

相关概念视频

Spreading of Chromatin Modifications

Spreading of Chromatin Modifications

The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...

Nucleosome Remodeling

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...

Cohesins

Cohesins

Cohesin protein complexes are a molecular glue that holds two sister chromatids together. They play an important role both in mitosis and meiosis. In mitosis, all cohesin complexes present on the chromosomes are removed before the start of the anaphase stage.
Cohesin complexes in Meiotic Division
Meiosis involves two distinct rounds of chromosomal segregation and cell divisions— Meiosis I followed by Meiosis II – producing four daughter cells. Meiosis I includes the separation of...

Forces Acting on Chromosomes

Forces Acting on Chromosomes

During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis.
Microtubules and motor proteins exert two types of forces on...

Chromatin Position Affects Gene Expression

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area.
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...

Condensins

Condensins

Condensins are large protein complexes that use ATP to fuel the assembly of chromosomes during mitosis. They transform the tangled, shapeless mass of post-interphase DNA into individualized chromosomes by compacting, organizing, and segregating chromosomal DNA.
The plant and animal cells contain two types of condensin complexes—condensin I and condensin II. Both complexes have five subunits: two SMC (Structural Maintenance of Chromosomes) subunits, a kleisin subunit, and two HEAT-repeat...