相关实验视频

Updated: Jun 3, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

染色质中的相过渡:介光学和中场方法

R Tiani¹, M Jardat¹, V Dahirel¹

¹CNRS, Laboratoire PHENIX (Physicochimie des Electrolytes et Nanosystèmes Interfaciaux), Sorbonne Université, 4 Place Jussieu, 75005 Paris, France.

The Journal of chemical physics

|January 9, 2025

概括

染色体组织涉及两个阶段过渡. 我们的模型表明,根据凝结蛋白度,染色质域可以凝结或扩展,影响遗传调节.

科学领域:

生物物理学的生物物理.
分子生物学分子生物学
遗传学是一个遗传学.

背景情况:

染色体组织对于基因调节至关重要.
两个关键过程影响着色氨酸结构:液体-液体相分离形成生物凝聚物和色氨酸纤维的线圈-球体过渡.
了解它们的相互作用对于理解细胞功能至关重要.

研究的目的:

为了研究生物凝聚物形成和染色体纤维卷积对染色体组织的联合影响.
探索不同度的凝聚物形成分子如何影响染色质结构和动态.
阐明对遗传调节的影响.

主要方法:

开发一个最小物理模型,模拟相隔二元流体内的染色质域.
整合一个和潜力来模仿孤立的聚合物链行为 (线圈和球体状态).
分析聚合物的旋转半径,以应对液滴材料的体积分数.

主要成果:

染色质聚合物的旋转半径表现出与滴状物质 (B) 的体积分数相比的非单调行为,类似于共同非溶性.
低度的滴状物质B可以导致染色质崩,而高度会导致膨胀.
有限大小的效应影响了线圈-球体过渡,导致染色体域的大小依赖的反应.

结论:

染色体域大小和凝结蛋白的度是决定染色体对染色体结合蛋白变化的反应 (凝结或扩张) 的关键因素.
这为细胞如何通过染色体组织动态调节基因表达提供了机械的洞察力.
这些发现表明,基因调节的调节机制基于相分离和聚合物物理学.

更多相关视频

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

Published on: April 11, 2014

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

Published on: January 5, 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...

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...

Position-effect Variegation

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.

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...

Euchromatin

Euchromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...

Heterochromatin

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...