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Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory Sequences

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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...

Regulation of Expression at Multiple Steps

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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...

Regulation of Expression Occurs at Multiple Steps

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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.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

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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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Un marco computacional escalable para predecir la expresión génica a partir de elementos cis-reguladores candidatos

Qinhu Zhang^1,2, Siguo Wang¹, Zhipeng Li¹

¹Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo 315201, China.

Genome research

|January 16, 2026

Resumen

Este resumen es generado por máquina.

Desarrollamos ScPGE, un marco computacional para predecir la expresión génica a partir de elementos cis-reguladores. ScPGE mejora la precisión en la identificación de interacciones Enhancer-gen y revela patrones regulatorios, mejorando nuestra comprensión de la regulación génica.

Palabras clave:

expresión génica elementos cis-reguladores interacciones Enhancer-gen modelado computacional genómica biología computacional

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Área de la Ciencia:

Genómica
Biología Computacional
Biología Molecular

Sus antecedentes:

Comprender la función del elemento cis-regulador (CRE) en la expresión génica es crucial pero desafiante debido a los CRE dinámicos.
La predicción de la expresión génica a partir de CRE sigue siendo un problema importante sin resolver en biología molecular.

Objetivo del estudio:

Desarrollar un marco computacional escalable (ScPGE) para predecir la expresión génica a partir de CRE candidatos (cCRE).
Mejorar la precisión en la identificación de interacciones activas Enhancer-gen y comprender los mecanismos regulatorios.

Principales métodos:

ScPGE integra secuencias de ADN, puntuaciones de unión del factor de transcripción (TF) y datos epigenómicos de cCRE en tensores 3D.
Emplea un modelo híbrido que combina redes neuronales convolucionales y transformadores para analizar las relaciones cCRE-gen.
Se utilizan mecanismos de atención para identificar interacciones clave Enhancer-gen.

Principales resultados:

ScPGE supera a los modelos de última generación existentes en la predicción de la expresión génica y la identificación de interacciones Enhancer-gen.
El análisis reveló que el efecto regulador de los cCRE disminuye con la distancia al gen diana.
La incorporación de bucles de cromatina mejoró la capacidad de ScPGE para capturar interacciones cCRE-gen distales.
ScPGE identificó motivos TF cruciales y dilucidó diferentes roles regulatorios de los cCRE.

Conclusiones:

ScPGE proporciona un marco potente y escalable para descifrar las relaciones reguladoras CRE-gen.
Los hallazgos del modelo sobre efectos dependientes de la distancia y la utilidad de los bucles de cromatina ofrecen nuevas perspectivas sobre la regulación génica.
ScPGE ayuda a descubrir elementos reguladores y a comprender sus mecanismos funcionales.