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Transcription Factors02:16

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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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 Control02:33

Combinatorial Gene Control

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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.
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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Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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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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Video Experimental Relacionado

Updated: Jan 13, 2026

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
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Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

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STAN, un marco computacional para inferir la actividad de factores de transcripción informada espacialmente

Linan Zhang1, April Sagan2, Bin Qin3

  • 1Department of Applied Mathematics, School of Mathematics and Statistics, Ningbo University, Ningbo, Zhejiang 315211, China.

Nucleic acids research
|January 12, 2026
PubMed
Resumen

Desarrollamos STAN, un método computacional para mapear la actividad de los factores de transcripción (FT) dentro de los tejidos utilizando transcriptómica espacial. Esto revela cómo las redes de FT influyen en la identidad celular y la organización espacial en diversas enfermedades y contextos biológicos.

Palabras clave:
transcriptómica espacialfactores de transcripciónactividad génicaredes reguladoras de genesbiología computacionalorganización tisularidentidad celularanálisis de datosmodelado lineal de efectos mixtosdescubrimiento biológico

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Área de la Ciencia:

  • Biología Computacional; Genómica; Biología de Sistemas

Sus antecedentes:

  • Los factores de transcripción (FT) regulan las respuestas celulares y están influenciados por los microambientes.
  • La transcriptómica espacial (ST) ofrece información sobre los microambientes tisulares, pero no se ha aprovechado al máximo para inferir la actividad de FT.
  • Comprender los roles de los FT en la identidad celular y la organización espacial es crucial.

Objetivo del estudio:

  • Desarrollar un enfoque computacional para inferir la actividad de FT resuelta espacialmente a partir de datos de ST.
  • Investigar la relación entre la actividad de FT, la identidad celular y la arquitectura tisular.
  • Mejorar las capacidades analíticas de los datos de ST para el descubrimiento biológico.

Principales métodos:

  • Introdujo STAN (Spatially informed Transcription factor Activity Network), un modelo lineal de efectos mixtos.
  • Integró datos previos de genes diana de FT, expresión de ARNm, coordenadas espaciales y características histológicas.
  • Aplicó STAN a diversos conjuntos de datos de ST (ganglio linfático, cerebro, cáncer de mama, glioblastoma).

Principales resultados:

  • STAN predijo con éxito las actividades de FT específicas de los puntos.
  • Identificó FT asociados con distintos tipos celulares, regiones espaciales y zonas patológicas.
  • Reveló la participación de FT en interacciones ligando-receptor dentro de los microambientes tisulares.

Conclusiones:

  • STAN infiere eficazmente la actividad de FT a partir de datos de ST, proporcionando contexto espacial.
  • El enfoque mejora la utilidad de ST para comprender los roles de los FT en la función celular y la organización tisular.
  • Destaca la intrincada interacción entre las redes de FT y la biología espacial en diversos sistemas biológicos.