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Related Concept Videos

What is Gene Expression?01:42

What is Gene Expression?

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Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
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Regulation of Expression at Multiple Steps01:23

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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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Regulation of Expression Occurs at Multiple Steps02:24

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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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General Transcription Factors01:30

General Transcription Factors

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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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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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Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
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Decoding transcriptional regulation via a human gene expression predictor.

Yuzhou Wang1, Yu Zhang2, Ning Yu3

  • 1The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, Anhui 230027, China.

Journal of Genetics and Genomics = Yi Chuan Xue Bao
|January 24, 2023
PubMed
Summary

Researchers developed EXPLICIT-Human, a predictive model that accurately reconstructs human transcriptomes using transcription factors (TFs). This tool decodes gene expression regulation and identifies key TFs controlling cellular activities and development.

Keywords:
Gene expression predictorGene moduleGene regulatory networkGraphical Gaussian modelHumanMouse

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Area of Science:

  • Genomics
  • Systems Biology
  • Transcriptional Regulation

Background:

  • Transcription factors (TFs) are crucial regulators of cellular activities by controlling gene expression.
  • A quantitative predictive model for TF-mediated human transcriptome modulation is currently lacking.

Purpose of the Study:

  • To develop a universal human gene expression predictor, EXPLICIT-Human, to decode transcriptional regulation.
  • To identify significant TF-target gene interactions and infer TF regulators for various biological pathways.

Main Methods:

  • Construction of EXPLICIT-Human, a predictive model utilizing the expression of 1613 TFs.
  • Reconstitution of human transcriptomes across diverse tissues and conditions using the predictor.
  • Extraction of significant TF-target gene pairs and downstream inference of TF regulators.

Main Results:

  • EXPLICIT-Human accurately reconstitutes human transcriptomes, demonstrating broad applicability across tissues and conditions.
  • The model recapitulates quantitative TF-target gene relationships.
  • Identification of key TFs regulating development, immunity, metabolism, and stress response, including an atlas for hematopoiesis.
  • EXPLICIT-Human outperforms existing tools in recovering correct TF regulators.

Conclusions:

  • EXPLICIT-Human provides a powerful tool for decoding transcriptional regulation and understanding TF-mediated gene expression.
  • The method successfully delineates TFs responsible for cell fate determination, with conserved examples found between humans and mice.