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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...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

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

Published on: February 11, 2019

TFinDit: transcription factor-DNA interaction data depository.

Daniel Turner1, RyangGuk Kim, Jun-tao Guo

  • 1Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.

BMC Bioinformatics
|September 5, 2012
PubMed
Summary
This summary is machine-generated.

TFinDit is a new database and web tool for studying transcription factor-DNA interactions. It provides annotated structural data to advance research in gene regulation and protein-DNA recognition mechanisms.

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Investigating Interactions Between Histone Modifying Enzymes and Transcription Factors in vivo by Fluorescence Resonance Energy Transfer
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Area of Science:

  • Structural bioinformatics
  • Molecular biology
  • Genomics

Background:

  • Transcription factor-DNA binding is crucial for gene expression regulation.
  • Understanding binding affinity and specificity at a structural level is key to deciphering gene regulation mechanisms.
  • A specialized database is needed for transcription factor-DNA interactions to support structural bioinformatics studies.

Purpose of the Study:

  • To introduce TFinDit, a comprehensive relational database and web service.
  • To facilitate structural bioinformatics studies of transcription factor-DNA interactions.
  • To support the development of interaction potentials, docking algorithms, and the study of recognition mechanisms.

Main Methods:

  • Developed TFinDit as a relational database and web search tool.
  • Included annotated transcription factor-DNA complex structures and related data (unbound structures, thermodynamic data, binding sequences).
  • Provided a user-friendly interface for querying entries and generating datasets.

Main Results:

  • TFinDit is a specialized structural database containing annotated transcription factor-DNA complex structures.
  • The database includes preprocessed data relevant to protein-DNA interactions.
  • A user-friendly interface allows for flexible data retrieval and dataset generation.

Conclusions:

  • TFinDit serves as a valuable resource for the scientific community.
  • The database and web service can accelerate the development and testing of computational tools for TF-DNA interactions.
  • It aids in understanding the fundamental mechanisms of protein-DNA recognition.