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Related Concept Videos

Transcription01:10

Transcription

158.7K
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...
158.7K
Transcription01:17

Transcription

35.3K
Transcription is the synthesis of 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 correctly synthesizing messenger RNA (mRNA). Transcriptional regulation is responsible for the differentiation of different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
35.3K
Global Regulatory Systems01:28

Global Regulatory Systems

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Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
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Master Transcription Regulators02:23

Master Transcription Regulators

8.0K
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...
8.0K
Master Transcription Regulators02:23

Master Transcription Regulators

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2.9K
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Related Experiment Video

Updated: Mar 27, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

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Deciphering transcriptional regulations coordinating the response to environmental changes.

Vicente Acuña1,2, Andrés Aravena3, Carito Guziolowski4

  • 1Center for Mathematical Modeling (UMI-CNRS 2807), Universidad de Chile, Santiago, Chile. viacuna@dim.uchile.cl.

BMC Bioinformatics
|January 17, 2016
PubMed
Summary

LOMBARDE, a new bioinformatics method, refines transcriptional regulatory networks (TRNs) by identifying key transcription factors (TFs) and binding sites (BSs) involved in gene co-expression, reducing spurious predictions.

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Related Experiment Videos

Last Updated: Mar 27, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
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Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • Transcriptional regulatory networks (TRNs) coordinate gene expression in response to environmental changes.
  • Predicting TRNs from transcription factor (TF) and binding site (BS) affinities often results in over-estimation and spurious relations.

Purpose of the Study:

  • To develop a bioinformatics method, LOMBARDE, for extracting accurate subnetworks from predicted TRNs.
  • To identify the most relevant TFs and BSs involved in observed gene co-expressions.

Main Methods:

  • LOMBARDE employs an optimization approach to select confident regulatory paths within a TRN.
  • It identifies subnetworks connecting common regulators to co-expressed genes via regulatory cascades.

Main Results:

  • Applied to Escherichia coli data, LOMBARDE explained nearly all co-expressions using only 19% of predicted TF/BS affinities.
  • The method incorporated 66% of validated regulations and demonstrated increased precision with integrated validated data.
  • The resulting subnetworks exhibited topological characteristics similar to known TRNs.

Conclusions:

  • LOMBARDE offers a robust modeling framework for understanding gene regulation mechanisms.
  • It serves as a valuable tool for genome-scale transcriptional regulation studies and environmental response research.