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Transcription Factors

Transcription Factors

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...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

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...

General Transcription Factors

General Transcription Factors

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...

RNA Polymerase II Accessory Proteins

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...

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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...

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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...

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Updated: Sep 9, 2025

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

Múltiples sitios de unión superpuestos determinan la ocupación del factor de transcripción

Shubham Khetan¹, Brent S Carroll¹, Martha L Bulyk^2,3

¹Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.

|September 3, 2025

Resumen

Este resumen es generado por máquina.

Desarrollamos PADIT-seq para descubrir nuevos sitios de unión de ADN de baja afinidad para los factores de transcripción (TF). Esto revela cómo los sitios de unión superpuestos controlan colectivamente la expresión génica e influyen en los rasgos humanos y las enfermedades.

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Área de la Ciencia:

La genómica
Biología molecular
La bioinformática

Sus antecedentes:

Los factores de transcripción (TF) regulan la expresión génica a través de interacciones de ADN específicas de la secuencia.
Los métodos de alto rendimiento existentes luchan por identificar sitios de unión de TF de baja afinidad, cruciales para la regulación génica.
Los sitios de baja afinidad son cada vez más reconocidos por su papel en el control preciso de la expresión génica espacio-temporal.

Objetivo del estudio:

Desarrollar un nuevo método para el análisis exhaustivo de las preferencias de unión al ADN de TF.
Identificar los sitios de enlace TF de baja afinidad no detectados anteriormente.
Proponer un nuevo modelo para la unión de TF y su papel en la regulación genética y la enfermedad.

Principales métodos:

Desarrollo de la afinidad proteica con el ADN por transcripción in vitro y secuenciación de ARN (PADIT-seq).
Análisis exhaustivo de las preferencias de unión para seis TF en todas las secuencias de ADN de diez pares de bases.
Análisis de la superposición del sitio de unión de TF y su impacto en la ocupación genómica.

Principales resultados:

PADIT-seq detectó con éxito cientos de nuevos sitios de unión al ADN de menor afinidad para los TF.
Los nucleótidos que flanquean los sitios de alta afinidad crean sitios superpuestos de menor afinidad que modulan la unión de TF in vivo.
Se propuso un modelo de enlace TF basado en la suma de múltiples sitios superpuestos.

Conclusiones:

La unión de TF está determinada por el efecto colectivo de múltiples sitios de unión superpuestos, no solo por sitios individuales de alta afinidad.
El modelo de vinculación superpuesta explica la competencia de TF y el uso diferencial del sitio de vinculación por parte de TFs parálogos.
Este modelo redefine el impacto de las variantes no codificantes, mostrando cómo alteran múltiples sitios para influir en la expresión génica, los rasgos humanos y las enfermedades.