相关实验视频
Updated: Jun 11, 2025

14:49
Associated Chromosome Trap for Identifying Long-range DNA Interactions
Published on: April 23, 2011
14.4K
从使用TwinC的DNA序列预测和功能解释染色体间基因组结构
Anupama Jha1, Borislav Hristov1, Xiao Wang1,2
1Department of Genome Sciences, University of Washington, Seattle, WA, USA.
bioRxiv : the preprint server for biology
|September 30, 2024
概括
双胞胎C准确地预测了使用新型神经网络的染色体间 (跨) DNA 接触. 该模型揭示了影响跨基因组架构和基因调节的关键基因组特征.
科学领域:
- 基因组学就是基因组学.
- 计算生物学 计算生物学
- 分子生物学分子生物学
背景情况:
- 三维核DNA架构涉及染色体内 (cis) 折叠和较少理解的染色体间 (trans) 相互作用.
- 现有的3D基因组折叠的预测模型主要集中在cis接触上,忽略了trans接触.
- 对于能够预测和解释跨基因组组织的模型有很大的需求.
研究的目的:
- 为预测染色体间 (跨) DNA 接触而开发出一个强大且可解释的模型.
- 了解跨基因组组织的原则和功能相关性.
- 确定有助于形成跨人接触的基因组特征.
主要方法:
- 开发TwinC,一个可解释的卷积神经网络模型.
- 使用来自复制全基因组染色体构造捕获 (Hi-C) 实验的配对序列设计.
- 训练模型学习DNA跨越跨基因相互作用中的单个基对相关性.
主要成果:
- TwinC在从心脏组织 Hi-C 数据中采集的染色体交叉测试中实现了跨人接触的高预测准确性 (AUROC=0.80).
- 该模型确定了基因组组件,染色质可访问性,集群转录因子结合和G-四重复合体在形成跨接触中的重要性.
- 双胞胎C提供了对跨基因组架构的可解释的观点.
结论:
- TwinC有效地模拟和解释了染色体间 (跨) 基因组架构.
- 这些发现揭示了对跨基因组组织的不太了解的机制.
- 这项工作通过3D基因组结构的透视来推进我们对基因调节的理解.
相关概念视频
Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Polytene Chromosomes
10.0K
Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also...
10.0K
DNA as a Genetic Template
21.8K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
21.8K
Duplication of Chromatin Structure
5.4K
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...
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...
5.4K
Chromatin Position Affects Gene Expression
23.3K
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...
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
23.3K
Karyotyping
59.1K
Overview
59.1K

