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Related Concept Videos

Transcription Factors02:16

Transcription Factors

82.7K
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 Elongation Factors02:35

Transcription Elongation Factors

13.9K
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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Transcription Elongation Factors02:35

Transcription Elongation Factors

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General Transcription Factors01:30

General Transcription Factors

7.0K
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...
7.0K
Transcription01:10

Transcription

156.2K
Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
156.2K
Master Transcription Regulators02:23

Master Transcription Regulators

7.8K
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...
7.8K

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Updated: Jan 31, 2026

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
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Optimized ChIP-seq method facilitates transcription factor profiling in human tumors.

Abhishek A Singh1,2, Karianne Schuurman1, Ekaterina Nevedomskaya1,2

  • 1Divisions of Oncogenomics, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands.

Life Science Alliance
|January 9, 2019
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Summary

This study optimized chromatin immunoprecipitation sequencing (ChIP-seq) for analyzing transcription factors in human tissues. Double-cross-linking significantly improved data quality, enabling high-quality results from limited clinical samples.

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A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies
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A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cancer Research

Background:

  • Transcription factor (TF) ChIP-seq in clinical specimens faces challenges due to limited starting material and technical limitations.
  • These limitations often lead to low enrichment and poor signal-to-noise ratios in TF ChIP-seq data.

Purpose of the Study:

  • To develop and validate an optimized protocol for TF ChIP-seq analysis in human tissues.
  • To improve the success rate and data quality of TF ChIP-seq from limited clinical samples.

Main Methods:

  • The optimized protocol involves double-cross-linking using formaldehyde and disuccinimidyl glutarate.
  • The protocol was tested on human breast, prostate, and endometrial cancer tissues.
  • High-quality ChIP-seq data were generated for AR, FOXA1, and H3K27ac from a single prostate cancer biopsy.

Main Results:

  • The optimized protocol achieved an approximately 100% success rate for TF ChIP-seq across analyzed factors.
  • Inclusion of disuccinimidyl glutarate alongside formaldehyde fixation significantly enhanced data quality.
  • High-resolution ChIP-seq data were obtained even from a single core needle biopsy specimen.

Conclusions:

  • Double-cross-linking is a robust method to improve TF ChIP-seq quality in human tumor samples.
  • This optimized protocol facilitates translational research by enabling high-quality analyses on limited tissue amounts.