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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
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...

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Related Experiment Video

Updated: Jun 1, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Distinct functional constraints partition sequence conservation in a cis-regulatory element.

Antoine Barrière1, Kacy L Gordon, Ilya Ruvinsky

  • 1Department of Ecology and Evolution and Institute for Genomics and Systems Biology, Chicago, Illinois, USA.

Plos Genetics
|June 10, 2011
PubMed
Summary

Promoter regions in genomes evolve at different rates. In nematodes, a distal promoter domain drives robust gene expression without sequence conservation, suggesting AT-rich composition, not specific sequences, is key.

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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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Area of Science:

  • Evolutionary biology
  • Genomics
  • Molecular biology

Background:

  • Different functional constraints drive varying evolutionary rates across genomes.
  • Understanding sequence evolution within cis-regulatory elements is crucial for deciphering gene regulation.

Purpose of the Study:

  • Investigate the function and evolutionary dynamics of the Caenorhabditis elegans unc-47 gene promoter.
  • Determine factors contributing to differential evolutionary rates within a single cis-regulatory locus.

Main Methods:

  • Comparative sequence analysis across closely related nematode species.
  • Functional analysis of promoter domains using gene expression assays.
  • Nucleotide composition analysis of conserved and divergent promoter regions.

Main Results:

  • The unc-47 promoter comprises two domains: a conserved proximal domain for spatial expression and a divergent distal domain.
  • The distal promoter, despite lacking sequence conservation, confers robust gene expression across species.
  • AT-rich nucleotide composition, associated with nucleosome depletion, characterizes robustness-promoting sequences.

Conclusions:

  • Functional constraints, such as maintaining robust expression via AT-rich composition, can allow sequence divergence.
  • Differential functional requirements within a cis-regulatory element explain disparate evolutionary rates.
  • Sequence composition, rather than specific sequence identity, can be a key determinant of evolutionary dynamics in regulatory regions.