Related Experiment Video
Updated: May 19, 2026
11:36
An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
Published on: April 21, 2023
Gene isoform specificity through enhancer-associated antisense transcription.
Courtney S Onodera1, Jason G Underwood, Sol Katzman
1Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.
Plos One
|September 1, 2012
Summary
Enhancers can regulate gene expression by producing antisense RNAs, controlling specific gene versions. This newly discovered mechanism highlights lineage-specific transcriptional regulation via enhancer-associated non-coding RNAs (ncRNAs).
Area of Science:
- Molecular Biology
- Genetics
- Developmental Biology
Background:
- Enhancers and antisense RNAs are crucial for transcriptional regulation.
- The functional role of enhancer-associated non-coding RNAs (ncRNAs) remains largely unclear.
- Understanding these interactions is key to deciphering gene expression control.
Purpose of the Study:
- To investigate the functional role of enhancer-associated antisense transcripts.
- To identify novel ncRNAs involved in gene regulation.
- To explore the mechanisms of isoform-specific gene expression control.
Main Methods:
- RNA-Sequencing of mouse embryonic stem cells (mESCs) and neural precursor cells (NPs).
- Analysis of enhancer activity and antisense RNA expression.
- Overexpression and knockdown experiments to assess functional impact.
Main Results:
- Identified two novel enhancer-associated antisense transcripts in mESCs, absent in NPs.
- Antisense RNA expression correlated with shorter isoforms of overlapping protein-coding genes (Zmynd8, Brd1).
- Demonstrated cis-acting regulatory mechanisms of antisense transcripts on sense gene isoform expression.
Conclusions:
- Enhancers can regulate isoform-specific gene expression through ncRNA intermediates.
- This mode of transcriptional regulation appears to be lineage-specific and evolved independently.
- Findings suggest a broader role for enhancer-ncRNA interactions in gene regulation across species.
Related Concept Videos
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...
01:58Cell Specific Gene Expression
Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
01:58Cell Specific Gene Expression
Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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...
01:52Eukaryotic Transcription Inhibitors
Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a DNA...
Eukaryotic transcription inhibitors usually contain two distinct domains, a DNA...
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...