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Related Concept Videos

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...
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...
Transcription Elongation Factors02:35

Transcription Elongation Factors

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 into a...
Transcription Elongation Factors02:35

Transcription Elongation Factors

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 into a...
Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These domains are...

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Related Experiment Video

Updated: Jul 9, 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

DBD--taxonomically broad transcription factor predictions: new content and functionality.

Derek Wilson1, Varodom Charoensawan, Sarah K Kummerfeld

  • 1MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK. dbd@mrc-lmb.cam.ac.uk

Nucleic Acids Research
|December 13, 2007
PubMed
Summary
This summary is machine-generated.

The DNA-binding domain (DBD) database now includes over 700 proteomes, identifying sequence-specific DNA-binding transcription factors (TFs). This expansion reveals distinct TF evolutionary trends between eukaryotes and prokaryotes.

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Last Updated: Jul 9, 2026

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Published on: February 11, 2019

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09:58

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Published on: April 16, 2018

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • The DNA-binding domain (DBD) database catalogs predicted sequence-specific DNA-binding transcription factors (TFs).
  • The database has expanded significantly from 150 to over 700 proteomes.
  • Predictions are based on Hidden Markov Model (HMM) matches to DNA-binding domain families.

Purpose of the Study:

  • To present an updated version of the DBD database with expanded proteome coverage.
  • To introduce new search functionalities on the http://transcriptionfactor.org website.
  • To analyze evolutionary trends in DBD family occurrence across the tree of life.

Main Methods:

  • Utilized Hidden Markov Models (HMMs) to identify sequence-specific DNA-binding domains.
  • Integrated predictions for over 700 publicly available proteomes.
  • Developed new web-based search options for gene names, DBD families, and organisms.

Main Results:

  • The DBD database now encompasses over 700 proteomes, significantly increasing TF predictions.
  • New search features allow for detailed exploration of TF data by gene, family, and organism.
  • Analysis revealed a clear divergence in DBD expansions between eukaryotic and prokaryotic lineages.
  • Eukaryotic TF increase rates are slower than prokaryotic, potentially due to splice variants or combinatorial control.

Conclusions:

  • The expanded DBD database provides a comprehensive resource for studying transcription factors.
  • Comparative analysis highlights distinct evolutionary trajectories of DBDs in different life domains.
  • Further research may elucidate the mechanisms driving TF evolution, such as alternative splicing and gene regulation complexity.