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Related Concept Videos

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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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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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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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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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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Quantifying the tissue-specific regulatory information within enhancer DNA sequences.

Philipp Benner1, Martin Vingron1

  • 1Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany.

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|November 3, 2021
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Summary
This summary is machine-generated.

Researchers explored DNA sequences in enhancers to predict cell type-specific gene regulation. Computational models identified sequence patterns, revealing insights into epigenetic signals and transcription factor footprints for gene expression control.

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Area of Science:

  • Genomics
  • Epigenetics
  • Computational Biology

Background:

  • Epigenetic marks provide insights into cell type-specific gene regulation.
  • Understanding the DNA sequence correlates of these epigenetic signals is crucial.

Purpose of the Study:

  • To investigate if DNA sequences within enhancers correlate with epigenetic signals.
  • To computationally predict cell type-specific regulatory activity using sequence patterns.

Main Methods:

  • Utilized epigenetic data across diverse cell types and tissues.
  • Developed computational classifiers to predict enhancer activity in specific tissues.
  • Identified sequence features predictive of tissue-specific gene regulation.

Main Results:

  • Demonstrated that DNA sequence patterns can predict tissue-specific enhancer activity.
  • Showcased examples of accurate prediction of tissue-specific regulation from sequence alone.
  • Found that informative sequence patterns often contain transcription factor footprints.

Conclusions:

  • DNA sequence in enhancers contains information predictive of cell type-specific gene regulation.
  • Computational analysis of sequence patterns can uncover regulatory mechanisms.
  • Transcription factor binding sites are key sequence features in cell-specific regulation.