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Related Concept Videos

Transcription Factors02:16

Transcription Factors

76.8K
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...
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Transcription Initiation01:47

Transcription Initiation

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Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
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General Transcription Factors01:30

General Transcription Factors

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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...
5.5K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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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...
6.5K
Transcription Elongation Factors02:35

Transcription Elongation Factors

11.1K
Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
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RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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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...
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Related Experiment Video

Updated: Sep 11, 2025

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
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Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

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Defining transcription factor nucleosome binding with Pioneer-seq.

Maria Tsompana1, Patrick D Wilson1, Vijaya Murugaiyan1

  • 1Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America.

Plos Genetics
|August 14, 2025
PubMed
Summary
This summary is machine-generated.

Pioneer-Seq reveals how transcription factors (TFs) bind to nucleosomes. Nucleosome sequence, not TF type, primarily controls binding, though some TFs can access sites near the nucleosome center.

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Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Gene expression regulation depends on transcription factors (TFs) accessing DNA bound within nucleosomes.
  • Understanding TF-nucleosome interactions is crucial for deciphering gene regulation.

Purpose of the Study:

  • To develop and demonstrate a novel method, Pioneer-Seq, for comprehensively analyzing transcription factor binding to nucleosomes.
  • To investigate the mechanistic requirements for pioneer factor binding to nucleosomes.

Main Methods:

  • Pioneer-Seq involves creating libraries of nucleosomes with TF binding sites in all orientations.
  • The method allows simultaneous examination of nucleosome positioning sequences and in vivo targeted nucleosomes (ITNs).
  • TF binding to OCT4, SOX2, KLF4, and c-MYC was assessed using Pioneer-Seq.

Main Results:

  • All tested TFs bind to nucleosome edges, with nucleosome sequence being the main regulatory factor.
  • KLF4 demonstrated binding to a non-canonical TF binding site (TFBS) near the nucleosome dyad.
  • In vivo targeted nucleosomes showed differential binding, with KLF4 and SOX2 favoring sites near the nucleosome center.

Conclusions:

  • Pioneer-Seq provides a powerful tool to study TF-nucleosome interactions and TF binding mechanisms.
  • Differences in TF recognition of TFBS within nucleosomes were observed, highlighting mechanistic requirements for pioneer factors.
  • Nucleosome sequence and position significantly influence transcription factor accessibility and binding.