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Related Concept Videos

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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Cooperative Binding of Transcription Regulators02:13

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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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Combinatorial Gene Control02:33

Combinatorial Gene Control

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Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Master Transcription Regulators02:23

Master Transcription Regulators

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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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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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Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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Related Experiment Video

Updated: May 21, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
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CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.

Xuejian Cui1, Qijin Yin1, Zijing Gao1

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

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Summary
This summary is machine-generated.

CREATE, a new deep learning framework, identifies and characterizes cis-regulatory elements (CREs) by integrating multiple genomic data types. This advances understanding of gene regulation in health and disease.

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Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Cis-regulatory elements (CREs) are crucial for gene regulation but current identification methods are limited.
  • Existing approaches often focus on individual CRE types and lack cell-type specificity.

Purpose of the Study:

  • To develop a comprehensive framework for CRE identification and characterization.
  • To enable cell-type-specific analysis of CREs and their regulatory functions.

Main Methods:

  • Introduced CREATE, a multimodal deep learning framework utilizing Vector Quantized Variational AutoEncoder.
  • Integrated genomic sequences, chromatin accessibility, and chromatin interaction data.
  • Generated discrete CRE embeddings for multi-class classification and characterization.

Main Results:

  • CREATE accurately identifies cell-type-specific CREs.
  • The framework provides quantitative and interpretable insights into CRE features and regulatory codes.
  • Facilitated large-scale prediction of CREs in specific cell types.

Conclusions:

  • CREATE enhances the understanding of gene regulatory landscapes.
  • The framework aids in recognizing disease- or phenotype-associated CRE variabilities.
  • Advances the study of gene regulation in both health and disease contexts.