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Related Concept Videos

Transcription Factors02:16

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...
Transcription Factors02:16

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...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...
General Transcription Factors01:30

General 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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Updated: May 16, 2026

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
11:25

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

Published on: February 11, 2019

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.

Jie Wang1, Jiali Zhuang, Sowmya Iyer

  • 1Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

Nucleic Acids Research
|December 4, 2012
PubMed
Summary
This summary is machine-generated.

The Encyclopedia of DNA Elements (ENCODE) project identifies functional human genome elements. Factorbook.org is a new wiki repository for ENCODE transcription factor ChIP-seq data and analyses.

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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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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • The human genome contains functional elements like transcripts and regulatory regions.
  • Understanding chromatin states and DNA methylation is crucial for genome function.
  • The Encyclopedia of DNA Elements (ENCODE) project aims to map these elements.

Purpose of the Study:

  • To develop a centralized, accessible repository for ENCODE transcription factor (TF) ChIP-seq data.
  • To provide a TF-centric view of TF-binding regions and associated genomic data.
  • To facilitate the analysis and discovery of functional genomic elements.

Main Methods:

  • Utilizing chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) to identify TF-binding regions.
  • Developing a web-accessible, wiki-formatted repository (Factorbook.org).
  • Analyzing ChIP-seq data to determine histone modification profiles, nucleosome positioning, and enriched sequence motifs.

Main Results:

  • Factorbook.org hosts 457 ChIP-seq datasets for 119 TFs across multiple human cell lines.
  • The repository includes average profiles of histone modifications and nucleosome positioning around TF-binding sites.
  • Enriched sequence motifs and their positional preferences within TF-binding regions are cataloged.

Conclusions:

  • Factorbook.org serves as a valuable resource for exploring TF-binding and regulatory elements in the human genome.
  • The integrated data enables deeper insights into genome regulation.
  • This TF-centric approach enhances the discoverability of functional genomic information.