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Cis-regulatory Sequences02:02

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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...
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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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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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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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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Data integration for inferring context-specific gene regulatory networks.

Brittany Baur1, Junha Shin1, Shilu Zhang1

  • 1Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.

Current Opinion in Systems Biology
|November 23, 2020
PubMed
Summary
This summary is machine-generated.

This review explores computational methods for integrating genomic data to understand gene regulatory networks. These approaches reveal how these networks change in specific contexts like disease or development.

Keywords:
DataEnhancerGene regulatory networksGene regulationPromoterSingle cell

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Area of Science:

  • Genomics
  • Systems Biology
  • Computational Biology

Background:

  • Transcriptional regulatory networks govern context-specific gene expression crucial for biological processes and diseases.
  • Genomic technologies enable measurement of regulatory components at single-cell and population levels.
  • Integrating diverse regulatory genomic data is essential for a comprehensive understanding of gene networks.

Purpose of the Study:

  • To review recent computational methods for integrating regulatory genomic data.
  • To highlight approaches for inferring context specificity and dynamics in gene regulatory networks.

Main Methods:

  • Focus on computational strategies for data integration.
  • Analysis of methods inferring network context and dynamics.

Main Results:

  • Identification of key computational approaches for integrating multi-omics regulatory data.
  • Demonstration of how integration reveals context-dependent network behavior.

Conclusions:

  • Computational integration of regulatory genomic data is vital for dissecting complex biological systems.
  • These methods advance our understanding of gene regulation in various disease, environmental, and developmental settings.