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相关概念视频

The Eukaryotic Promoter Region02:40

The Eukaryotic Promoter Region

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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
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Bacterial Transcription01:53

Bacterial Transcription

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RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
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Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
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Transcription Initiation01:47

Transcription Initiation

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Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
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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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lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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相关实验视频

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基于自然语言技术的任务导向字典挖掘和预测模型.

Ruolei Zeng1, Zihan Li2, Jialu Li3

  • 1Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.

Scientific reports
|January 3, 2025
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概括

本研究引入了一种新的DNA序列细分方法,用于使用BERT-Inception架构改进促进体识别. 这种方法增强了基因表达分析和生物信息学中的深度学习可解释性.

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科学领域:

  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学
  • 基因组学就是基因组学.

背景情况:

  • 促进体是调节基因表达的关键DNA序列,对于理解基因调节网络至关重要.
  • 准确的促进体鉴定对于破译基因表达模式至关重要.
  • 目前用于促进器预测的深度学习方法,包括BERT,由于在预训练期间的任意DNA序列分割而面临限制.

研究的目的:

  • 开发一种新的DNA序列细分方法,以提高促进者预测的准确性.
  • 为DNA序列分割和BERT预训练引入一个精细的字典.
  • 提高DNA序列分析中的深度学习模型的可解释性.

主要方法:

  • 开发了一种新的DNA序列细分方法,并使用了精细的字典.
  • 在BERT预训练中使用了精细的字典.
  • 采用BERT-Inception架构,将BERT与Inception神经网络集成在一起,以捕获多个细分信息.

主要成果:

  • 伯特-Inception模型在与主办方识别相关的几个下游任务上表现得更好.
  • 新的细分方法和架构增强了在DNA序列中跨多个颗粒度捕获信息的能力.
  • 这项研究引入了深度学习的解释性,为DNA序列信息提供了新的见解.

结论:

  • 拟议的BERT-Inception架构与新的DNA序列分割显著提升了促进者预测.
  • 这种方法提供了一种更精细的方法,用于预训练BERT模型进行基因组序列分析.
  • 增强的解释性为理解DNA序列信息和基因调节提供了有价值的视角.