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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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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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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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A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers
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Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.

Emma K Farley1, Katrina M Olson2, Wei Zhang3

  • 1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544; ekfarley@princeton.edu msl2@princeton.edu.

Proceedings of the National Academy of Sciences of the United States of America
|May 8, 2016
PubMed
Summary

Researchers uncovered a "regulatory code" for DNA enhancers, revealing that the precise arrangement of transcription factor binding sites is crucial for gene activation. This finding helps explain how enhancers with weak binding sites can still drive strong gene expression.

Keywords:
enhancerenhancer grammargene regulationregulatory principlestranscription

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Area of Science:

  • Molecular Biology
  • Developmental Biology
  • Genomics

Background:

  • Transcriptional enhancers regulate gene expression but the relationship between DNA sequence and enhancer activity is not fully understood.
  • The role of "syntax"—the order, orientation, and spacing of transcription factor binding sites—in enhancer function remains unclear.

Purpose of the Study:

  • To elucidate the
  • regulatory code
  • governing notochord-specific gene expression in Ciona embryos.
  • To investigate the interplay between binding site affinity and syntax in determining enhancer activity.

Main Methods:

  • High-throughput screening to identify synthetic notochord enhancers.
  • Experimental manipulation of enhancer sequences and syntax.
  • In silico discovery of enhancers using the derived regulatory code.

Main Results:

  • A regulatory code integrating sequence and syntax features for notochord expression was elucidated.
  • This code enabled the discovery of novel notochord enhancers, including those with low-affinity binding sites.
  • A new Ci-Bra "shadow enhancer" with weak binding sites but optimal syntax was identified, driving strong notochord expression.

Conclusions:

  • Optimal regulatory syntax can compensate for low-affinity transcription factor binding sites.
  • The balance between binding affinity and syntax has historically obscured the importance of regulatory syntax.
  • Enhancers with low binding affinities but optimal syntax represent an underappreciated component of the regulatory genome.