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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...
23.4K
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

6.3K
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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Position-effect Variegation02:32

Position-effect Variegation

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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
6.4K
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

7.0K
In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
7.0K
Chromatin Structure and RNA Splicing02:41

Chromatin Structure and RNA Splicing

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2.7K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

8.3K
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...
8.3K

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相关实验视频

Updated: Jul 17, 2025

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
04:41

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

Published on: January 9, 2020

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使用基因组序列和染色质结构来学习非编码变异效应的多模式学习.

Wuwei Tan1, Yang Shen1,2,3

  • 1Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, United States.

Bioinformatics (Oxford, England)
|September 5, 2023
PubMed
概括

计算模型现在可以通过整合1D基因组序列和3D染色体结构数据来预测非编码遗传变异对人类特征和疾病的影响,从而改进了仅序列的方法.

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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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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Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
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Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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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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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:

  • 非编码的遗传变异,包括单核酸多态变异,越来越多地与复杂的人类特征和疾病有关.
  • 解释这些变异的功能影响是具有挑战性的,因为当前的计算模型往往忽视了3D染色质结构的作用.

研究的目的:

  • 开发一个计算模型,预测非编码变异对表观遗传特征的影响.
  • 将1D基因组序列和3D染色体结构数据结合起来,以提高预测准确度.

主要方法:

  • 开发了一种多式深度学习框架,集成卷积和循环神经网络用于序列嵌入和图形神经网络用于结构嵌入.
  • 利用最近的DNA语言模型来弥合序列和结构数据之间的分辨率差距.
  • 采用了无监督 (零射击) 和监督 (少数射击) 的学习方法.

主要成果:

  • 在预测表观遗传特征方面,多式模式显著优于仅序列模型.
  • 该模型有效地捕捉了远程相互作用,补充了仅用于监管动机识别的序列方法.
  • 对非编码变异对基因表达和致病性产生影响的强有力的预测性能.

结论:

  • 将3D染色体结构与1D序列数据集成,可以更全面地了解非编码变异效应.
  • 开发的深度学习方案为预测遗传变异的功能影响提供了一个强大的工具.
  • 这些发现推动了人类疾病中非编码变异的机械解释.