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相关概念视频

Lampbrush Chromosomes01:51

Lampbrush Chromosomes

7.9K
In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps.
LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops...
7.9K
Chromatin Packaging02:21

Chromatin Packaging

15.3K
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
15.3K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

8.3K
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...
8.3K
Nucleosome Remodeling02:54

Nucleosome Remodeling

9.1K
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...
9.1K
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

5.5K
The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
5.5K
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

11.1K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
11.1K

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相关实验视频

Updated: Jun 25, 2025

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

15.4K

CD-Loop:一种基于扩散模型的染色素循环检测方法.

Jiquan Shen1, Yang Wang1, Junwei Luo1

  • 1School of Software, Henan Polytechnic University, Jiaozuo, China.

Frontiers in genetics
|May 21, 2024
PubMed
概括
此摘要是机器生成的。

CD-Loop是一种新的深度学习框架,可以从Hi-C接触图中准确预测染色质循环. 这种方法即使在较低的测序深度上也是卓越的,性能优于现有的工具,并揭示了细胞类型特定的基因组结构.

关键词:
这是一个Hi-C联系地图.染色体循环的染色体循环是什么深度学习是一种深度学习.扩散模型的扩散模型.这是一个三维结构结构.

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CRISPR-Mediated Reorganization of Chromatin Loop Structure
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CRISPR-Mediated Reorganization of Chromatin Loop Structure

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Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
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Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

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相关实验视频

Last Updated: Jun 25, 2025

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

15.4K
CRISPR-Mediated Reorganization of Chromatin Loop Structure
09:20

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Published on: September 14, 2018

12.5K
Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
14:43

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Published on: August 27, 2014

11.6K

科学领域:

  • 基因组学就是基因组学.
  • 计算生物学 计算生物学
  • 分子生物学分子生物学

背景情况:

  • 像Hi-C这样的染色体构造捕获技术对于理解染色体3D结构至关重要.
  • 从Hi-C数据中说明拓结构至关重要,但由于染色质循环的动态性而具有挑战性.
  • 现有的循环预测方法在特征提取和准确性方面扎,特别是在低测序深度.

研究的目的:

  • 开发一个深度学习框架,从Hi-C接触地图中准确预测染色质循环.
  • 为了解决当前处理各种染色体结构和低序列数据的方法的局限性.
  • 为了改善三维基因组结构的注释.

主要方法:

  • 开发了一个深度学习框架,CD-Loop,利用一个扩散模型.
  • 输入的Hi-C数据进行了预训练,以获得分类的先前概率.
  • 一个与预先训练的概率相结合的denoising过程预测了候选循环,然后是基于密度的聚类来进行最终的循环注释.

主要成果:

  • 与Peakachu,Chromosight和Mustache相比,CD-Loop在色素循环注释方面表现出更好的表现.
  • 该框架在不同细胞类型,物种和测序深度方面实现了高精度.
  • CD-Loop成功预测了染色体循环,并确定了特定细胞类型的基因组结构.

结论:

  • CD-Loop提供了一种准确而强大的方法,用于从Hi-C数据中预测色素循环.
  • 基于扩散模型的方法增强了特征提取和预测准确性,特别是在低序列化场景中.
  • CD-Loop有助于更好地了解基因组拓和细胞类型特定组织.