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Cooperative Binding of Transcription Regulators02:13

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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...
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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.
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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...
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Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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Modeling Plant Transcription Factor Networks Using ConSReg.

Qi Song1, Song Li2

  • 1Computational Biology Department, Carnegie Mellon University, Pittsburgh,, PA, USA. sqsq3178@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|October 20, 2022
PubMed
Summary

This study introduces ConSReg, a computational tool to build plant regulatory networks. It uses sequencing data to predict gene interactions specific to environmental stresses like heat and drought.

Keywords:
Machine learningPlant environment stressRegulatory network

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Area of Science:

  • Plant biology
  • Genomics
  • Bioinformatics

Background:

  • Plants possess intricate regulatory systems to adapt to environmental challenges such as heat, drought, and cold.
  • Understanding these biological processes necessitates the accurate construction of regulatory networks detailing transcription factor-target gene interactions.

Purpose of the Study:

  • To present ConSReg, a novel computational tool designed for predicting regulatory interactions in plants.
  • To enable the reconstruction of stress-specific regulatory networks using various biological data.

Main Methods:

  • Utilizes Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data.
  • Incorporates DNA Affinity Purification sequencing (DAP-seq) data.
  • Integrates gene expression data, particularly under specific environmental stress conditions.

Main Results:

  • ConSReg predicts regulatory interactions between transcription factors and target genes.
  • The tool reconstructs interpretable and weighted regulatory networks.
  • Networks generated are specific to the environmental stress conditions used for expression data.

Conclusions:

  • ConSReg provides a robust method for constructing plant regulatory networks.
  • The tool facilitates a deeper understanding of plant responses to environmental stress.
  • Enables the development of stress-specific gene regulatory models.