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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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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...
24.6K
Histone Modification02:32

Histone Modification

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
15.9K
Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

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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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Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

7.2K
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...
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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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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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GECSI:从基因表达中进行大规模的染色质状态归因.

Jingyuan Fu1,2, Jason Ernst1,2,3,4,5,6

  • 1Computer Science Department, University of California, Los Angeles, Los Angeles, CA 90095, United States.

bioRxiv : the preprint server for biology
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PubMed
概括

基于基因表达的染色体状态推断 (GECSI) 预测使用基因表达数据的染色体状态. 这种方法准确地归咎于缺少的表观遗传标记数据,增强了许多生物样本的表观基因组分析.

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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:

  • 染色质状态注释的汇编是有价值的,但对于许多生物样本通常缺乏数据.
  • 基因表达数据比表观遗传标记数据更广泛可用,这为归算提供了机会.

研究的目的:

  • 开发一种计算方法,仅使用基因表达数据来预测色素状态注释.
  • 扩大对缺乏表观遗传数据的生物样本的染色质状态注释的可用性.

主要方法:

  • 开发了基于基因表达的染色体状态推算 (GECSI),一种多类后勤回归模型.
  • 从国际人类表观基因组联盟 (IHEC) 的EpiAtlas资源中使用大量匹配的基因表达和染色质状态注释汇编训练GECSI.
  • 通过交叉验证验证GECSI性能,并将其与替代方法进行比较.

主要成果:

  • GECSI准确地预测染色体状态赋值,并产生可靠的概率估计.
  • 该方法在预测染色体状态方面优于替代方法和基线方法.
  • GECSI预测的状态反映了生物样本的关系,并显示了与观察到的状态相似的转录因子和基因注释丰富.

结论:

  • GECSI提供了一种准确有效的方法,用于从基因表达数据中赋值染色质状态注释.
  • 449个额外的表观基因组的预测注释为更广泛的表观基因组分析提供了宝贵的资源.
  • GECSI软件可以在具有有限表观遗传数据的样本中进行染色质状态分析.