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相关概念视频

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

12.1K
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...
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Transcription Factors02:16

Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Combinatorial Gene Control02:33

Combinatorial Gene Control

9.5K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
9.5K

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相关实验视频

Updated: Jan 15, 2026

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells
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IceQream:使用物理TF模型进行定量染色体可访问性分析.

Akhiad Bercovich1,2, Aviezer Lifshitz1,2, Michal Eldar1,2

  • 1Weizmann Institute of Science, Department of Computer Science and Applied Mathematics, Rehovot, Israel.

Nature communications
|October 9, 2025
PubMed
概括
此摘要是机器生成的。

我们开发了IceQream (IQ),这是一种使用转录因子结合的物理模型来预测DNA序列的基因调节的新方法. 智商为深度学习提供了一种机械和可解释的替代方案,实现了可比性能.

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

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科学领域:

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

背景情况:

  • 单细胞测序揭示了染色体可访问性模式,改善了从DNA序列的表观遗传学预测.
  • 目前的定量模型缺乏可解释的组成部分来解释表观基因组.
  • 从序列来预测表观基因组活动的建模是一个活跃的研究领域.

研究的目的:

  • 开发一种新的建模策略和推理算法,用于从序列回归可访问性,使用转录因子 (TF) 结合的物理模型.
  • 创建一个机械和可解释的基线,以了解基因和基因组从序列调节.
  • 推断TF有效度及其相互作用.

主要方法:

  • IceQream (IQ) 采用了跨TF-DNA亲属性和相对于目标位置的定位的序列的空间集成.
  • IQ将TF有效度推断为潜在变量,模拟调节元件的非线性激活/抑制.
  • 结合了协同和对抗的双对TF相互作用.

主要成果:

  • 在人类和小鼠数据上,智商表现出与最先进的深度神经网络模型相当或优于其性能.
  • 该模型成功地推断了TF的有效度及其相互作用.
  • 智商为表观基因组建模提供可解释的组件.

结论:

  • 智商提供了一种机械和可解释的方法,用于从序列中建模表观基因组活动.
  • 这种方法可以作为基因调节未来研究的有价值的基线.
  • 智商提升了对DNA序列如何决定调节元件功能的理解.