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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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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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Next-generation Sequencing03:00

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
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Cis-regulatory Sequences02:02

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相关实验视频

Updated: Jul 14, 2025

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression
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使用DeepSEED进行深度侧翼序列工程,以实现高效的促销器设计.

Pengcheng Zhang1, Haochen Wang1, Hanwen Xu1

  • 1Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, China.

Nature communications
|October 9, 2023
PubMed
概括
此摘要是机器生成的。

一个人工智能框架DeepSEED通过整合专家知识和深度学习来设计合成促进器. 它通过揭示隐含的序列特征来改善促进子特性,推进合成生物学应用.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
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相关实验视频

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科学领域:

  • 合成生物学 合成生物学
  • 计算生物学是一种计算生物学.
  • 基因组学就是基因组学.

背景情况:

  • 促进器设计对于合成生物学至关重要,传统上依赖于已知的转录因子结合位 (TFBS).
  • 经常被忽视的cis-regulatory元素的侧面序列,但影响促进器功能.
  • 深度学习擅长识别大型生物数据集中的复杂模式.

研究的目的:

  • 引入DeepSEED,这是一个人工智能辅助的框架,用于高效的合成促进器设计.
  • 利用深度学习来揭示侧面序列在促进器属性的作用.
  • 改进各种生物系统中现有的促进器设计.

主要方法:

  • 开发了DeepSEED,这是一个结合专家知识和深度学习的AI框架.
  • 应用DeepSEED来设计大肠杆菌和哺乳动物细胞的合成促进剂.
  • 在侧边区域分析隐性序列特征,包括k-mer频率和DNA形状.

主要成果:

  • DeepSEED成功地改善了构成性,IPTG诱导性和Dox诱导性促进体的特性.
  • 该框架证明了侧边序列在确定促销者特征中的重要性.
  • 鉴定了DeepSEED捕获的隐性序列特征,例如k-mer频率和DNA形状.

结论:

  • 通过整合人工智能和生物专业知识,DeepSEED提供了一种高效的合成促进器设计方法.
  • 这项研究强调了侧翼序列的重要性,这些序列在推广器工程中以前被低估了.
  • 隐性序列特征的AI驱动分析可以显著提高功能合成促进体的设计.