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相关概念视频

Epigenetic Regulation01:46

Epigenetic Regulation

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Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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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...
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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...
8.1K
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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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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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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Chromatin Packaging01:32

Chromatin Packaging

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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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相关实验视频

Updated: May 13, 2025

Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis
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以虚拟表观基因组揭示染色质动力学

Ming-Yu Lin1, Yu-Cheng Lo1, Jui-Hung Hung2,3

  • 1Department of Computer Science, National Yang Ming Chiao Tung University, HsinChu, Taiwan, ROC.

Nature communications
|April 12, 2025
PubMed
概括

EpiVerse使用深度学习从表观遗传数据中预测色素相互作用,提高了细胞类型和组织的准确性. 这种计算工具使得新的in silico实验能够研究基因组架构.

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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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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
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科学领域:

  • 基因组学和表观遗传学
  • 计算生物学 计算生物学
  • 系统生物学 系统生物学

背景情况:

  • 染色体的3D组织对于基因调节和细胞功能至关重要,表观基因组发挥着中心作用.
  • 高C技术揭示了染色质相互作用,但成本昂贵和复杂,限制了广泛的应用.
  • 目前对色素相互作用的预测模型通常使用有限的ChIP-seq数据,影响准确性和概括性.

研究的目的:

  • 开发一种计算方法,EpiVerse,用于准确预测使用假定表观遗传信号的染色质相互作用.
  • 通过将染色体状态预测集成到多任务学习框架中来提高模型的可解释性.
  • 为了提供对39个人体组织的染色质结构的全面了解,并使干扰实验成为可能.

主要方法:

  • 借助假定表观遗传信号和先进的深度学习技术.
  • 采用了多任务学习框架,包括染色体状态预测.
  • 应用该模型来预测39个人体组织的Hi-C接触地图.

主要成果:

  • 与现有的方法相比,EpiVerse显著提高了跨细胞类型Hi-C预测的准确性.
  • 该模型通过与Hi-C接触一起预测染色质状态来增强可解释性.
  • 为39个人体组织生成了全面的Hi-C接触图,揭示了复杂的染色质结构-基因调节关系.

结论:

  • EpiVerse提供了一种强大而准确的计算工具,用于预测色素相互作用和理解3D基因组组织.
  • 这种方法促进了新的in silico实验,在特定条件下探索色素结构.
  • EpiVerse推进了表观遗传学研究及其在各种人体组织中基因调节中的作用.