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相关概念视频

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

11.2K
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...
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Heterochromatin02:38

Heterochromatin

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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...
13.7K
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
Lampbrush Chromosomes01:51

Lampbrush Chromosomes

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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

8.3K
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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...
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相关实验视频

Updated: Jul 14, 2025

Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease
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Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease

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一个轻量级的框架,用于在单细胞水平上检测染色体循环.

Fuzhou Wang1, Hamid Alinejad-Rokny2, Jiecong Lin3,4

  • 1Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
|October 10, 2023
PubMed
概括
此摘要是机器生成的。

scGSLoop是一个用于分析单细胞Hi-C数据的新框架. 它通过利用稀疏的数据,提高准确性和保持单细胞分辨率,有效地识别了染色体组织中的调节循环.

关键词:
染色质环节是染色质的环节.功能循环的功能循环.多重连接的枢纽.一个单细胞的Hi-C.

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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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Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation
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Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation

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相关实验视频

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Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease
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CRISPR-Mediated Reorganization of Chromatin Loop Structure
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Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation
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科学领域:

  • 基因组学和生物信息学
  • 分子和细胞生物学分子和细胞生物学

背景情况:

  • 单细胞Hi-C (scHi-C) 能够在单个细胞水平上进行染色质组织分析.
  • scHi-C数据稀少,对现有的循环调用方法构成挑战,这些方法需要密集的接触图.
  • 目前的方法带来了高的计算成本,并且由于数据归算而失去单细胞分辨率.

研究的目的:

  • 为循环调用稀疏 scHi-C 数据开发一个计算效率高,准确的框架.
  • 克服现有方法在处理数据稀疏性和保存单细胞信息方面的局限性.
  • 为了使染色质循环变异性和单细胞水平的调节作用的调查.

主要方法:

  • 介绍了scGSLoop,这是一个使用基于图形的深度学习的轻量级框架.
  • 适应的培训和推断策略,以利用基因组序列特征和1D位置信息.
  • 设计模型以利用数据稀疏性作为计算效率的优势.

主要成果:

  • scGSLoop通过有效处理稀疏的scHi-C数据,实现了前所未有的计算效率.
  • 与现有方法相比,该框架在循环预测中显示出更高的准确性.
  • scGSLoop识别了更多的潜在监管循环,并为每个单元格保留了不同的循环信息.

结论:

  • scGSLoop为scHi-C循环调用设定了一个新范式,解决了稀疏性和计算挑战.
  • 该方法增强了对单细胞中的染色质循环变异性和调节机制的理解.
  • scGSLoop的功能可以扩展到研究复杂的多连接基因组枢纽.