Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation

Zoltan Simandi; Attila Horvath; Peter Nagy; Laszlo Nagy

doi:10.3791/53978

Prédiction et validation des éléments de réglementation gène activé Pendant l'acide rétinoïqu...

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Developmental Biology

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JoVE Journal Developmental Biology

Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation

Prédiction et validation des éléments de réglementation gène activé Pendant l'acide rétinoïque induit la différenciation des cellules souches embryonnaires

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09:07 min

June 21, 2016

DOI: 10.3791/53978-v

Zoltan Simandi*¹, Attila Horvath*², Peter Nagy¹, Laszlo Nagy^1,2,3

¹Sanford-Burnham-Prebys Medical Discovery Institute at Lake Nona, ²Department of Biochemistry and Molecular Biology,Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, ³MTA-DE “Lendulet” Immunogenomics Research Group,University of Debrecen

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Overview

This video presents an integrated set of methods for identifying and validating genomic regulatory elements known as enhancers. It highlights the workflow's adaptability for various cellular model systems.

Key Study Components

Area of Science

Genomic regulatory elements
Enhancer identification
Cellular model systems

Background

Enhancers play a crucial role in gene regulation.
Understanding enhancer selection is vital for studying transcription.
Cell differentiation and responses to stimuli can be influenced by enhancers.
ChIP-seq analysis aids in identifying candidate enhancers.

Purpose of Study

To provide a workflow for enhancer identification and validation.
To facilitate research on transcription and gene regulation.
To demonstrate the adaptability of the protocol across different cellular models.

Methods Used

Selection of candidate enhancers based on ChIP-seq data.
Utilization of genome browsers to analyze binding sites.
Experimental validation of enhancer activity.
Adaptation of methods for various cellular systems.

Main Results

Identification of active enhancers in different contexts.
Validation of enhancer functionality through experimental approaches.
Demonstration of the workflow's versatility.
Insights into enhancer usage during cell differentiation.

Conclusions

The presented workflow is effective for enhancer research.
It can be adapted for various experimental setups.
Enhancer identification is crucial for understanding gene regulation.

Frequently Asked Questions

What are enhancers?

Enhancers are regulatory DNA sequences that increase the likelihood of transcription of particular genes.

How can enhancers be identified?

Enhancers can be identified using techniques such as ChIP-seq to analyze protein-DNA interactions.

What is the significance of enhancer validation?

Validating enhancers is essential to confirm their role in gene regulation and their functional impact on biological processes.

Can the methods be used in different cell types?

Yes, the workflow is designed to be adaptable for various cellular model systems.

What role do enhancers play in cell differentiation?

Enhancers influence gene expression patterns that are crucial for cell differentiation and response to stimuli.

Dans ce travail, nous fournissons un flux de travail expérimental sur la façon dont les amplificateurs actifs peuvent être identifiés et validés expérimentalement.

L’objectif général de cette vidéo est de fournir un ensemble intégré de méthodes pour identifier et valider expérimentalement les éléments régulateurs généomiques appelés amplificateurs. Cette méthode peut aider à répondre à des questions clés dans la transcription et la régulation d’événements biologiques, y compris la sélection et l’utilisation d’amplificateurs, en utilisant la différenciation cellulaire ou en réponse à des stimuli externes. Le principal avantage du flux de travail présenté est qu’un protocole peut être facilement adapté et utilisé dans n’importe quel système de modèle cellulaire.

Je vais vous montrer les étapes de la procédure. Pour commencer, choisissez un amplificateur candidat en fonction de l’analyse de séquençage de puce préexistante. Utilisez un navigateur génomique pour afficher les résultats de l’expérience de séquençage de puce souhaitée et identifier les sites de liaison à proximité du gène d’intérêt.

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