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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Co-activators and Co-repressors

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...

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Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
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Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Published on: June 15, 2016

Nonlinear dynamic trans/cis regulatory circuit for gene transcription via microarray data.

Yu-Hsiang Chang1, Yu-Chao Wang, Bor-Sen Chen

  • 1Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan.

Gene Regulation and Systems Biology
|November 26, 2009
PubMed
Summary

This study models nonlinear gene transcription regulatory circuits in yeast using gene expression data and transcription factor binding sites. The developed method quantifies regulatory abilities and aids in designing gene circuits.

Keywords:
cell cyclenonlinear dynamic modeltrans/cis regulatory circuittranscription factor

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Area of Science:

  • Systems Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • Gene transcription relies on complex trans-regulatory and cis-regulatory circuits.
  • Understanding these circuits is crucial for deciphering gene expression regulation.

Purpose of the Study:

  • To construct nonlinear trans/cis regulatory circuits for gene transcription in yeast.
  • To develop a nonlinear dynamic modeling and parameter estimation method for circuit construction.
  • To quantify regulatory abilities and identify cis-element interactions in yeast cell cycle genes.

Main Methods:

  • Utilized yeast microarray data, translation time delay, and transcription factor binding site information.
  • Developed a nonlinear dynamic modeling approach.
  • Implemented a parameter estimation method for circuit construction.

Main Results:

  • Successfully constructed trans/cis regulatory circuits for yeast cell cycle-related genes.
  • Quantified the regulatory abilities of these circuits.
  • Identified potential cis-element interactions and their roles in gene expression.

Conclusions:

  • The developed method provides a powerful tool for understanding gene transcription.
  • The approach is applicable to data from various species, not just yeast.
  • Offers a quantitative basis for gene circuit system analysis and potential for gene regulatory circuit design.