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相关概念视频

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

12.0K
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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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Cooperative Binding of Transcription Regulators02:13

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Operon Model01:23

Operon Model

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The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
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Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

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Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
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相关实验视频

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

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使用语言模型设计 prokaryotic cis-regulatory 元素.

Yan Xia1,2, Jinyuan Sun3, Xiaowen Du1

  • 1Department of Gastroenterology, Aerospace Center Hospital, College of Life Science, Beijing Institute of Technology, Beijing 100081, China.

Nucleic acids research
|February 16, 2026
PubMed
概括
此摘要是机器生成的。

研究人员开发了PromoGen2,一种语言模型,用于在没有先前数据的情况下设计 prokaryotic cis-regulatory elements (CREs). 这种工具可以为数千种 prokaryotes 提供功能性促进器设计,从而推进合成生物学和微生物学.

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Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster
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Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster
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科学领域:

  • 计算生物学 计算生物学
  • 基因组学就是基因组学.
  • 合成生物学 合成生物学

背景情况:

  • 对 prokaryotes 进行 cis 调节元件 (CREs) 的设计对于合成生物学和微生物学来说至关重要.
  • 现有的CRE设计的深度学习模型在各种 prokaryotic 物种的范围和适用性上是有限的.
  • 需要一个广泛适用的平台来产生成千上万个核细胞的功能促进剂.

研究的目的:

  • 在没有先前的实验数据的情况下,引入PromoGen2,一种用于设计 prokaryotic CREs 的新语言模型.
  • 开发一个框架 (Promoter-Factory) 来设计使用PromoGen2.2从未注释的基因组中设计促销者.
  • 为了创建一个分类学意识的模型 (PromoGen2-proka) 基于 prokaryotic 基因的 CRE 设计.

主要方法:

  • 预训练PromoGen2对来自1.7万个 prokaryotic 基因组的 CREs.
  • 评估PromoGen2对跨物种促进体强度的零射击预测准确度.
  • 在多种细菌物种中设计和实验验证人造CREs.
  • 在未注释的基因组中开发和应用促进器-工厂框架,用于促进器设计.
  • 引入和验证PromoGen2-proka用于属特定的CRE设计.

主要成果:

  • 促销Gen2实现了促销器强度的最高零射击预测相关性 (0.50斯皮尔曼相关性),显著超过了基线.
  • 设计的人工CREs在四种不同的细菌物种中显示出100%的成功率.
  • 促销商-工厂成功设计了一个新分离的性细菌的活性促销剂,导致了烯的过度生产.
  • 在实验验验证中,PromoGen2-proka在基因特异性CRE设计方面表现出可靠的成功率.

结论:

  • 在没有先前的实验数据的情况下,PromoGen2提供了一个广泛适用的平台来设计功能性 prokaryotic CREs.
  • 促销商-工厂框架允许从未注释的基因组进行促销商设计,支持合成生物学应用.
  • 通过考虑 prokaryotic 分类学,PromoGen2-proka 增强了 CRE 设计的特异性.
  • 这些结合的工具解决了 prokaryotic 合成生物学和微生物学研究中的关键需求.