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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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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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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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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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Exploring functionally annotated transcriptional consensus regulatory elements with CONREL.

Davide Dalfovo1, Samuel Valentini1, Alessandro Romanel

  • 1Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy.

Database : the Journal of Biological Databases and Curation
|November 13, 2020
PubMed
Summary
This summary is machine-generated.

CONREL is a new web application for exploring human genome regulatory elements and transcription factor interactions. It offers a comprehensive resource for understanding gene regulatory networks across various cell types and tissues.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Understanding gene regulatory networks is crucial for deciphering cellular functions.
  • Human genome regulatory elements and transcription factors play key roles in gene expression.
  • Existing resources may lack comprehensive data or user-friendly exploration tools.

Purpose of the Study:

  • To develop CONREL, a web application for exploring functionally annotated transcriptional 'consensus' regulatory elements.
  • To provide an extensive collection of regulatory elements across diverse cell lines and tissue types.
  • To integrate genomic data and transcription factor binding affinities for functional annotation.

Main Methods:

  • Developed a web application (CONREL) for exploring regulatory elements.
  • Compiled consensus promoters, enhancers, and active enhancers for 198 cell lines and 38 tissue types.
  • Integrated 1000 Genomes Project genotype data and transcription factor binding motif affinities.

Main Results:

  • CONREL offers a comprehensive collection of regulatory elements with functional annotations.
  • The application integrates genotype and binding affinity data for detailed characterization.
  • CONREL facilitates exploration of genomic loci, genes, and regions across cell lines and tissues.

Conclusions:

  • CONREL provides a valuable and unique resource for studying gene regulatory networks.
  • The integration of diverse datasets enhances the functional annotation of regulatory elements.
  • CONREL offers advantages over existing resources for exploring genomic regulatory information.