Related Experiment Video
Updated: Jul 17, 2026
11:36
An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
Published on: April 21, 2023
Tissue-specific regulatory elements in mammalian promoters.
Andrew D Smith1, Pavel Sumazin, Michael Q Zhang
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Molecular Systems Biology
|January 17, 2007
Summary
Researchers identified gene regulatory elements in mammalian promoters that control tissue-specific gene expression. This catalog aids in understanding tissue-specific regulatory networks and gene regulation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Transcription factor-binding sites and cis-regulatory modules are key to gene expression.
- Previous work demonstrated the predictive power of promoter motifs for mammalian tissue-specific transcription.
Purpose of the Study:
- To systematically analyze promoters for tissue-specific gene expression in human and mouse across multiple tissues.
- To create a catalog of predicted tissue-specific motifs, modules, and cis-regulatory elements.
- To provide a foundation for understanding tissue-specific regulatory networks.
Main Methods:
- Integrated multiple gene expression datasets to identify tissue-specific transcripts.
- Analyzed corresponding promoters to predict regulatory motifs and elements.
- Applied statistical evidence to support predicted regulatory interactions.
Main Results:
- Compiled sets of transcripts with strong evidence for tissue-specific regulation.
- Generated a catalog of predicted tissue-specific motifs, modules, and cis-regulatory elements.
- Identified statistically supported predicted regulatory interactions.
Conclusions:
- The catalog provides a resource for understanding tissue-specific gene regulation.
- The methods offer a model for analyzing genomic regions regulating differentially expressed genes.
- This work advances the study of tissue-specific regulatory networks.
Related Concept Videos
02:40The Eukaryotic Promoter Region
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...
02:40The Eukaryotic Promoter Region
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...
02:16Transcription Factors
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...
01:30General Transcription Factors
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...
02:23Master Transcription Regulators
Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
02:36RNA Polymerase II Accessory Proteins
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...