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相关概念视频

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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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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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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Euchromatin01:01

Euchromatin

6.8K
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...
6.8K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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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...
23.2K
Heterochromatin02:38

Heterochromatin

9.9K
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...
9.9K
Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

1.6K
Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
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相关实验视频

Updated: May 28, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

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IGN:基于基因组的不变规范化,用于分析染色体可访问性资料数据分析.

Shengen Shawn Hu1,2, Hai-Hui Xue3, Chongzhi Zang1,2

  • 1Department of Genome Sciences, University of Virginia, Charlottesville, VA 22908, USA.

Computational and structural biotechnology journal
|February 11, 2025
PubMed
概括
此摘要是机器生成的。

我们为ATAC-seq和DNase-seq数据开发了不变基因规范化 (IGN). 即使在全球信号变化时,IGN也能准确地使染色质可访问性正常化,超过了现有的差异分析方法.

关键词:
ATAC-seqq 的使用情况.染色体的可访问性 染色体的可访问性在DNase-seqq中使用DNase.不同分析差异分析.规范化 规范化 规范化

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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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相关实验视频

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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies
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科学领域:

  • 基因组学就是基因组学.
  • 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
  • 计算生物学 计算生物学

背景情况:

  • 像ATAC-seq和DNase-seq这样的染色体可访问性测试可以提供对基因调节的见解.
  • 准确的规范化对于染色质动态的差异分析至关重要.
  • 当前的方法可能会失败,当全球色素可访问性水平在样本之间显著不同时.

研究的目的:

  • 引入不变基因规范化 (IGN),一种用于规范化ATAC-seq和DNase-seq数据的新方法.
  • 解决现有规范化技术的局限性,这些技术假定基因组信号分布均.
  • 为差异色素可访问性分析提供一个强大的工具,特别是在存在全球信号变化的情况下.

主要方法:

  • 通过使用具有稳定表达基因 (来自RNA-seq) 的基因,IGN使促进体染色质可访问性信号正常化.
  • 该方法推断出这些稳定信号,以规范全基因组染色质可访问性配置文件.
  • 使用中央记忆 CD8+ T 细胞激活数据证明了有效性.

主要成果:

  • IGN有效地规范化了染色质可访问性数据,考虑了样本之间的全球差异.
  • 该方法在微分分析中优于现有的规范化技术.
  • 在T细胞激活过程中,IGN在分析复杂的染色质和基因表达变化方面被证明是有效的.

结论:

  • IGN是第一个对染色质可访问性的规范化方法,它解释了全球信号差异.
  • 这种方法提高了差异性ATAC-seq和DNase-seq分析的准确性.
  • IGN为研究染色体动态和基因调节提供了广泛适用的解决方案.