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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...
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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Related Experiment Video

Updated: Jul 14, 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

Identifying pattern-defined regulatory islands in mammalian genomes.

Tom H Cheung1, Kristen K B Barthel, Yin Lam Kwan

  • 1Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.

Proceedings of the National Academy of Sciences of the United States of America
|May 31, 2007
PubMed
Summary

Researchers identified conserved clusters of transcription factor binding sites, termed pattern-defined regulatory islands (PRIs), in mammalian genomes. These PRIs are key to understanding gene regulation and can pinpoint critical regulatory elements for cell-specific gene expression.

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Related Experiment Videos

Last Updated: Jul 14, 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

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Identifying cis-regulatory regions is crucial for understanding transcriptional regulation in mammals.
  • Limited knowledge of regulatory element organization and location hinders functional characterization.
  • Conserved genes may exhibit conserved transcriptional regulation and cis-element organization.

Purpose of the Study:

  • To computationally identify conserved cis-regulatory elements across species.
  • To investigate the organization and function of these conserved elements.
  • To utilize conserved features for identifying novel regulatory regions.

Main Methods:

  • Developed a computational approach to find conserved clusters of transcription factor binding sites.
  • Analyzed human, rat, and mouse genomes for conserved order and spacing of binding sites.
  • Termed these conserved regions pattern-defined regulatory islands (PRIs).

Main Results:

  • Discovered pattern-defined regulatory islands (PRIs) that are conserved in order and spacing across human, rat, and mouse genomes.
  • PRIs are frequently active sites of transcriptional regulation, found in ~1.1% of analyzed noncoding regions.
  • Successfully used PRIs to identify known and novel cis-regulatory regions involved in myogenic differentiation.

Conclusions:

  • PRIs represent a fundamental architectural property of cis-regulatory elements in mammalian genomes.
  • This conserved feature can be exploited to identify critical transcriptional regulatory elements.
  • PRIs offer a powerful tool for pinpointing elements controlling cell type-specific gene expression.