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Related Concept Videos

The Eukaryotic Promoter Region02:40

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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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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
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Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Related Experiment Video

Updated: Jun 17, 2025

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
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CAPE: a deep learning framework with Chaos-Attention net for Promoter Evolution.

Ruohan Ren1, Hongyu Yu2, Jiahao Teng3

  • 1Zhili College, Tsinghua University, Beijing 100084, China.

Briefings in Bioinformatics
|August 9, 2024
PubMed
Summary

Predicting promoter strength in synthetic biology is improved by CAPE, a new model that uses evolutionary information. This approach enhances accuracy and enables in silico directed evolution, reducing experimental costs.

Keywords:
chaos game representationdeep learningdirected evolutionpromoter design

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Area of Science:

  • Synthetic Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Promoter strength prediction and directed evolution are vital for synthetic biology, reducing experimental costs.
  • Previous machine learning and deep learning models had limitations due to neglecting evolutionary information.

Purpose of the Study:

  • To introduce the Chaos-Attention net for Promoter Evolution (CAPE) model.
  • To address limitations in existing methods for promoter strength prediction and directed evolution.

Main Methods:

  • Utilizing merged chaos game representation to extract evolutionary information from promoters.
  • Processing information with modified DenseNet and Transformer structures.
  • Applying transfer learning to enhance model adaptability.

Main Results:

  • Achieved state-of-the-art results on prokaryotic promoter strength prediction tasks.
  • Demonstrated enhanced accuracy through the incorporation of evolutionary information.
  • Validated CAPE's efficacy in simulating in silico directed evolution of promoters.

Conclusions:

  • CAPE represents a significant advancement in predictive modeling for prokaryotic promoter strength.
  • The model's effectiveness in in silico directed evolution is confirmed experimentally.
  • A user-friendly website and open-source code are provided for practical implementation.