Related Experiment Video
Updated: May 16, 2026
03:34
Optimized Quantitative Assessment of Enhancer RNA Stability in Mouse Embryonic Stem Cells
Published on: November 21, 2025
Non-canonical TAF complexes regulate active promoters in human embryonic stem cells
Glenn A Maston1, Lihua Julie Zhu, Lynn Chamberlain
1Programs in Gene Function and Expression and Molecular Medicine , University of Massachusetts Medical School , Worcester , United States ; Howard Hughes Medical Institute , Chevy Chase , United States.
Elife
|November 15, 2012
Summary
Human embryonic stem cells (hESCs) use a unique set of TBP-associated factors (TAFs) for self-renewal. Selective TAF composition in hESCs regulates pluripotency and differentiation, revealing a novel mechanism for stem cell maintenance.
Area of Science:
- Molecular Biology
- Stem Cell Biology
- Gene Regulation
Background:
- The general transcription factor TFIID is crucial for gene expression, composed of TATA-box-binding protein (TBP) and TBP-associated factors (TAFs).
- Human embryonic stem cells (hESCs) possess unique regulatory mechanisms for maintaining pluripotency and self-renewal.
- The precise composition and function of TFIID in undifferentiated hESCs remain incompletely understood.
Purpose of the Study:
- To investigate the composition of TFIID in undifferentiated hESCs.
- To elucidate the role of specific TAFs in hESC self-renewal and differentiation.
- To characterize the promoter occupancy patterns of TFIID components in hESCs.
Main Methods:
- Chromatin immunoprecipitation (ChIP) assays (directed and global) to analyze protein-DNA interactions at gene promoters.
- Analysis of TAF composition in hESCs using biochemical methods.
- Functional studies involving depletion or ectopic expression of specific TAFs in hESCs.
Main Results:
- Undifferentiated hESCs express a subset of six TAFs (TAFs 2, 3, 5, 6, 7, and 11), while differentiation leads to the expression of all TAFs.
- Two distinct TFIID promoter occupancy patterns were observed: TBP with TAFs 3 and 5 for most active genes, and TBP with all six hESC TAFs for other active genes.
- A novel complex of TBP with TAFs 2, 6, 7, and 11 was identified in hESCs.
- Manipulation of TAF composition in hESCs resulted in misregulation of pluripotency genes and induced differentiation.
Conclusions:
- The selective expression and utilization of TAFs by TFIID are essential for maintaining hESC self-renewal.
- TAF composition dynamically changes during hESC differentiation, influencing gene expression programs.
- These findings reveal a previously unrecognized layer of gene regulation critical for stem cell pluripotency.
Related Concept Videos
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...
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...
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...
02:36RNA 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...
02:04Co-activators and Co-repressors
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...