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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Regulation of Nuclear Protein Sorting01:45

Regulation of Nuclear Protein Sorting

Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...
Transducer Mechanism: Nuclear Receptors01:31

Transducer Mechanism: Nuclear Receptors

Nuclear receptors, or NRs, are unique transcription factors that regulate gene transcription and affect the cellular pathways involved in reproduction, development, or metabolism. Their ability to be stimulated by small lipophilic ligands and control vital cellular processes makes them ideal drug targets. Nearly 10-15% of currently prescribed drugs target these receptors.
About 48 different soluble family members of nuclear receptors are identified that can be divided into two main classes:
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...

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Related Experiment Video

Updated: May 19, 2026

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC
09:15

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

ncDNA and drift drive binding site accumulation.

Troy Ruths1, Luay Nakhleh

  • 1Department of Computer Science, Rice University, TX, Houston, USA. troy.ruths@rice.edu

BMC Evolutionary Biology
|September 1, 2012
PubMed
Summary
This summary is machine-generated.

Neutral evolutionary forces, not selection, explain the accumulation of transcription factor binding sites (TFBS) and regulatory complexity across organisms. Non-coding DNA amount and population size are key factors in this process.

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Last Updated: May 19, 2026

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Systems Biology

Background:

  • The number of transcription factor binding sites (TFBS) correlates with organismal regulatory network complexity.
  • The evolutionary origins and accumulation of TFBS, and their impact on fitness, remain poorly understood.
  • Comparative genomics offers a powerful approach to investigate TFBS evolution.

Purpose of the Study:

  • To investigate the evolutionary forces shaping transcription factor binding sites (TFBS) and genome-wide regulatory complexity.
  • To determine the relationship between non-coding DNA (ncDNA) amount, population size, and regulatory complexity.
  • To test the hypothesis that neutral evolutionary processes can explain observed TFBS patterns.

Main Methods:

  • Analysis of TFBS data from five model organisms (E. coli, S. cerevisiae, C. elegans, D. melanogaster, A. thaliana).
  • Development of a genome-based regulatory pathway model.
  • Population genetic simulations to model evolutionary forces acting on the regulatory network.

Main Results:

  • A positive correlation was observed between the amount of non-coding DNA (ncDNA) and regulatory complexity across species.
  • Population genetic simulations demonstrated that neutral evolutionary forces alone can account for TFBS patterns.
  • Selection acting on regulatory network function did not significantly alter the observed TFBS patterns.

Conclusions:

  • The genome's cis-regulome is shaped by both adaptive and non-adaptive (neutral) evolutionary forces.
  • Non-adaptive forces introduce complexity at both the binding site and pathway levels.
  • These findings have broad implications for microbiology, genetics, and synthetic biology.