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相关概念视频

DNA as a Genetic Template02:05

DNA as a Genetic Template

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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...
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
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Epistasis Analysis01:09

Epistasis Analysis

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Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
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相关实验视频

Updated: Jan 15, 2026

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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对基因组语言模型的核酸依赖性分析检测功能元素.

Pedro Tomaz da Silva1,2, Alexander Karollus1,2, Johannes Hingerl1,2

  • 1School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.

Nature genetics
|October 10, 2025
PubMed
概括

我们引入核酸依赖性来解释基因组语言模型 (gLMs). 这种方法有效地识别了功能性基因组元素,并预测了变体的有害性,改善了我们对基因组调节的理解.

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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
  • 生物信息学是一种生物信息学.

背景情况:

  • 基因组语言模型 (gLMs) 从DNA序列中学习,但缺乏用于发现功能元素的解释性.
  • 识别基因组中编码的监管指令和分子机器仍然是一个重大挑战.

研究的目的:

  • 开发一种可解释的方法来从gLMs中解读功能基因组元素.
  • 引入和验证核酸依赖性作为基因组分析的工具.

主要方法:

  • 开发了核酸依赖性分析,以量化核酸替代对基因组序列概率的影响.
  • 将核酸依赖性与基于对齐的保护和gLM重建进行比较,用于变体有害性预测.
  • 应用依赖性分析以确定调节动机和RNA结构元素.

主要成果:

  • 核酸依赖性在预测遗传变异的有害性方面优于现有的方法.
  • 该方法精确检测调节动机,并揭示新的RNA结构,包括伪结和三级接触.
  • 依赖性分析发现了当前gLM架构和培训策略的局限性.

结论:

  • 核酸依赖性分析为发现和研究功能性基因组元素及其相互作用提供了一种新的,可解释的方法.
  • 这种方法增强了gLMs对于理解基因组功能和疾病的实用性.
  • 这些发现为RNA结构预测和分析开辟了新的途径.